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Protein domain
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Pyruvate kinase, a protein from three domains (PDB 1pkn)
A protein domain is a part of protein sequence and structure that can evolve, function, and exist
independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and
often can be independently stable and folded. Many proteins consist of several structural domains. One
domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks
and these may be recombined in different arrangements to create proteins with different functions. Domains
vary in length from between about 25 amino acids up to 500 amino acids in length. The shortest domains
such as zinc fingers are stabilized by metal ions or disulfide bridges. Domains often form functional units,
such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains
can be "swapped" by genetic engineering between one protein and another to make chimeric proteins.
Contents
[hide]
• 1 Background
• 2 Domains are units of protein structure
• 2.1 Tertiary structure of domains
• 2.2 Domains have limits on size
• 2.3 Domains and quaternary structure
• 3 Domains as evolutionary modules
• 4 Multidomain proteins
• 4.1 Origin
• 4.2 Types of organisation
• 5 Domains are autonomous folding units
• 5.1 Folding
• 5.2 Advantage of domains in protein folding
• 6 Domains and protein flexibility
• 6.1 Hinges by secondary structures
• 6.2 Helical to extended conformation
• 6.3 Shear motions
• 6.4 Domain motion and functional dynamics in
enzymes
• 7 Domain definition from structural co-ordinates
• 7.1 Methods
[edit] Background
The concept of the domain was first proposed in 1973 by Wetlaufer after X-ray crystallographic
studies of hen lysozyme [1] and papain [2] and by limited proteolysis studies of immunoglobulins [3][4].
Wetlaufer defined domains as stable units of protein structure that could fold autonomously. In the past
domains have been described as units of:
• compact structure[5]
• function and evolution[6]
• folding [7].
Each definition is valid and will often overlap, i.e. a compact structural domain that is found amongst
diverse proteins is likely to fold independently within its structural environment. Nature often brings several
domains together to form multidomain and multifunctional proteins with a vast number of possibilities [8]. In a
multidomain protein, each domain may fulfil its own function independently, or in a concerted manner with its
neighbours. Domains can either serve as modules for building up large assemblies such as virus particles or
muscle fibres, or can provide specific catalytic or binding sites as found in enzymes or regulatory proteins.
An appropriate example is pyruvate kinase, a glycolytic enzyme that plays an important role in
regulating the flux from fructose-1,6-biphosphate to pyruvate. It contains an all-β regulatory domain, an α/β-
substrate binding domain and an α/β-nucleotide binding domain, connected by several polypeptide linkers [9]
(see figure, right). Each domain in this protein occurs in diverse sets of protein families.
The central α/β-barrel substrate binding domain is one of the most common enzyme folds. It is seen
in many different enzyme families catalysing completely unrelated reactions[10]. The α/β-barrel is commonly
called the TIM barrel named after triose phosphate isomerase, which was the first such structure to be
solved[11]. It is currently classified into 26 homologous families in the CATH domain database [12]. The TIM
barrel is formed from a sequence of β-α-β motifs closed by the first and last strand hydrogen bonding
together, forming an eight stranded barrel. There is debate about the evolutionary origin of this domain. One
study has suggested that a single ancestral enzyme could have diverged into several families[13], while
another suggests that a stable TIM-barrel structure has evolved through convergent evolution [14].
The TIM-barrel in pyruvate kinase is 'discontinuous', meaning that more than one segment of the
polypeptide is required to form the domain. This is likely to be the result of the insertion of one domain into
another during the protein's evolution. It has been shown from known structures that about a quarter of
structural domains are discontinuous.[15][16] The inserted β-barrel regulatory domain is 'continuous', made
up of a single stretch of polypeptide.
Covalent association of two domains represents a functional and structural advantage since there is
an increase in stability when compared with the same structures non-covalently associated [17]. Other,
advantages are the protection of intermediates within inter-domain enzymatic clefts that may otherwise be
unstable in aqueous environments, and a fixed stoichiometric ratio of the enzymatic activity necessary for a
sequential set of reactions [18].
[edit] Domains are units of protein structure

Main article: Protein structure
The primary structure (string of amino acids) of a protein ultimately encodes its uniquely folded 3D
conformation.[19] The most important factor governing the folding of a protein into 3D structure is the
distribution of polar and non-polar side chains.[20] Folding is driven by the burial of hydrophobic side chains
into the interior of the molecule so to avoid contact with the aqueous environment. Generally proteins have a
core of hydrophobic residues surrounded by a shell of hydrophilic residues. Since the peptide bonds
themselves are polar they are neutralised by hydrogen bonding with each other when in the hydrophobic
environment. This gives rise to regions of the polypeptide that form regular 3D structural patterns called
secondary structure. There are two main types of secondary structure: α-helices and β-sheets.
Some simple combinations of secondary structure elements have been found to frequently occur in
protein structure and are referred to as supersecondary structure or motifs. For example, the β-hairpin motif
consists of two adjacent antiparallel β-strands joined by a small loop. It is present in most antiparallel β
structures both as an isolated ribbon and as part of more complex β-sheets. Another common super-
secondary structure is the β-α-β motif, which is frequently used to connect two parallel β-strands. The central
α-helix connects the C-termini of the first strand to the N-termini of the second strand, packing its side chains
against the β-sheet and therefore shielding the hydrophobic residues of the β-strands from the surface.
Structural alignment is an important tool for determining domains.
[edit] Tertiary structure of domains

Several motifs pack together to form compact, local, semi-independent units called domains.[5] The
overall 3D structure of the polypeptide chain is referred to as the protein's tertiary structure. Domains are the
fundamental units of tertiary structure, each domain containing an individual hydrophobic core built from
secondary structural units connected by loop regions. The packing of the polypeptide is usually much tighter
in the interior than the exterior of the domain producing a solid-like core and a fluid-like surface.[21] In fact,
core residues are often conserved in a protein family, whereas the residues in loops are less conserved,
unless they are involved in the protein's function. Protein tertiary structure can be divided into four main
classes based on the secondary structural content of the domain.[22]
• All-α domains have a domain core built exclusively from α-helices. This class is dominated
by small folds, many of which form a simple bundle with helices running up and down.
• All-β domains have a core comprising of antiparallel β-sheets, usually two sheets packed
against each other. Various patterns can be identified in the arrangement of the strands, often giving
rise to the identification of recurring motifs, for example the Greek key motif.[23]
• α+β domains are a mixture of all-α and all-β motifs. Classification of proteins into this class is
difficult because of overlaps to the other three classes and therefore is not used in the CATH domain
database.[12]
• α/β domains are made from a combination of β-α-β motifs that predominantly form a parallel
β-sheet surrounded by amphipathic α-helices. The secondary structures are arranged in layers or
barrels.
[edit] Domains have limits on size

Domains have limits on size.[24] The size of individual structural domains varies from 36 residues in
E-selectin to 692 residues in lipoxygenase-1,[15] but the majority, 90%, have less than 200 residues[25] with
an average of approximately 100 residues.[26] Very short domains, less than 40 residues, are often
stabilised by metal ions or disulfide bonds. Larger domains, greater than 300 residues, are likely to consist of
multiple hydrophobic cores.[27]
[edit] Domains and quaternary structure

Many proteins have a quaternary structure, which consists of several polypeptide chains that
associate into an oligomeric molecule. Each polypeptide chain in such a protein is called a subunit.
Hemoglobin, for example, consists of two α and two β subunits. Each of the four chains has an all-α globin
fold with a heme pocket.
Domain swapping is a mechanism for forming oligomeric assemblies.[28] In domain swapping, a
secondary or tertiary element of a monomeric protein is replaced by the same element of another protein.
Domain swapping can range from secondary structure elements to whole structural domains. It also
represents a model of evolution for functional adaptation by oligomerisation, e.g. oligomeric enzymes that
have their active site at subunit interfaces.[29]
[edit] Domains as evolutionary modules

Nature is a tinkerer and not an inventor,[30] new sequences are adapted from pre-existing
sequences rather than invented. Domains are the common material used by nature to generate new
sequences, they can be thought of as genetically mobile units, referred to as 'modules'. Often, the C and N
termini of domains are close together in space, allowing them to easily be "slotted into" parent structures
during the process of evolution. Many domain families are found in all three forms of life, Archaea, Bacteria
and Eukarya. Domains that are repeatedly found in diverse proteins are often referred to as modules,
examples can be found among extracellular proteins associated with clotting, fibrinolysis, complement, the
extracellular matrix, cell surface adhesion molecules and cytokine receptors.[31]
Molecular evolution gives rise to families of related proteins with similar sequence and structure.
However, sequence similarities can be extremely low between proteins that share the same structure.
Protein structures may be similar because proteins have diverged from a common ancestor. Alternatively,
some folds may be more favored than others as they represent stable arrangements of secondary structures
and some proteins may converge towards these folds over the course of evolution . There are currently about
45,000 experimentally determined protein 3D structures deposited within the Protein Data Bank (PDB).[32]
However this set contains a lot of identical or very similar structures. All proteins should be classified to
structural families to understand their evolutionary relationships. Structural comparisons are best achieved at
the domain level. For this reason many algorithms have been developed to automatically assign domains in
proteins with known 3D structure, see 'Domain definition from structural co-ordinates'.
The CATH domain database classifies domains into approximately 800 fold families, ten of these
folds are highly populated and are referred to as 'super-folds'. Super-folds are defined as folds for which
there are at least three structures without significant sequence similarity.[33] The most populated is the α/β-
barrel super-fold as described previously.
[edit] Multidomain proteins

The majority of genomic proteins, two-thirds in unicellular organisms and more than 80% in metazoa,
are multidomain proteins created as a result of gene duplication events.[34] Many domains in multidomain
structures could have once existed as independent proteins. More and more domains in eukaryotic
multidomain proteins can be found as independent proteins in prokaryotes.[35] For example, vertebrates
have a multi-enzyme polypeptide containing the GAR synthetase, AIR synthetase and GAR transformylase
modules (GARs-AIRs-GARt; GAR: glycinamide ribonucleotide synthetase/transferase; AIR: aminoimidazole
ribonucleotide synthetase). In insects, the polypeptide appears as GARs-(AIRs)2-GARt, in yeast GARs-AIRs
is encoded separately from GARt, and in bacteria each domain is encoded separately.[36]
[edit] Origin
Multidomain proteins are likely to have emerged from a selective pressure during evolution to create
new functions. Various proteins have diverged from common ancestors by different combinations and
associations of domains. Modular units frequently move about, within and between biological systems
through mechanisms of genetic shuffling:
• transposition of mobile elements including horizontal transfers (between species);[37]
• gross rearrangements such as inversions, translocations, deletions and duplications;
• homologous recombination;
• slippage of DNA polymerase during replication.
[edit] Types of organisation

The simplest multidomain organisation seen in proteins is that of a single domain repeated in
tandem.[38] The domains may interact with each other or remain isolated, like beads on string. The giant
30,000 residue muscle protein titin comprises about 120 fibronectin-III-type and Ig-type domains.[39] In the
serine proteases, a gene duplication event has led to the formation of a two β-barrel domain enzyme.[40] The
repeats have diverged so widely that there is no obvious sequence similarity between them. The active site is
located at a cleft between the two β-barrel domains, in which functionally important residues are contributed
from each domain. Genetically engineered mutants of the chymotrypsin serine protease were shown to have
some proteinase activity even though their active site residues were abolished and it has therefore been
postulated that the duplication event enhanced the enzyme's activity.[40]
Modules frequently display different connectivity relationships, as illustrated by the kinesins and ABC
transporters. The kinesin motor domain can be at either end of a polypeptide chain that includes a coiled-coil
region and a cargo domain.[41] ABC transporters are built with up to four domains consisting of two
unrelated modules, ATP-binding cassette and an integral membrane module, arranged in various
combinations.
Not only do domains recombine, but there are many examples of a domain having been inserted into
another. Sequence or structural similarities to other domains demonstrate that homologues of inserted and
parent domains can exist independently. An example is that of the 'fingers' inserted into the 'palm' domain
within the polymerases of the Pol I family.[42] Since a domain can be inserted into another, there should
always be at least one continuous domain in a multidomain protein. This is the main difference between
definitions of structural domains and evolutionary/functional domains. An evolutionary domain will be limited
to one or two connections between domains, whereas structural domains can have unlimited connections,
within a given criterion of the existence of a common core. Several structural domains could be assigned to
an evolutionary domain.
[edit] Domains are autonomous folding units

[edit] Folding
Further information: Protein folding
Protein folding - the unsolved problem : Since the seminal work of Anfinsen over forty years ago,[19]
the goal to completely understand the mechanism by which a polypeptide rapidly folds into its stable native
conformation remains elusive. Many experimental folding studies have contributed much to our
understanding, but the principles that govern protein folding are still based on those discovered in the very
first studies of folding. Anfinsen showed that the native state of a protein is thermodynamically stable, the
conformation being at a global minimum of its free energy.
Folding is a directed search of conformational space allowing the protein to fold on a biologically
feasible time scale. The Levinthal paradox states that if an averaged sized protein would sample all possible
conformations before finding the one with the lowest energy, the whole process would take billions of years.
[43] Proteins typically fold within 0.1 and 1000 seconds, therefore the protein folding process must be
directed some way through a specific folding pathway. The forces that direct this search are likely to be a
combination of local and global influences whose effects are felt at various stages of the reaction.[44]
Advances in experimental and theoretical studies have shown that folding can be viewed in terms of
energy landscapes,[45][46] where folding kinetics is considered as a progressive organisation of an
ensemble of partially folded structures through which a protein passes on its way to the folded structure. This
has been described in terms of a folding funnel, in which an unfolded protein has a large number of
conformational states available and there are fewer states available to the folded protein. A funnel implies
that for protein folding there is a decrease in energy and loss of entropy with increasing tertiary structure
formation. The local roughness of the funnel reflects kinetic traps, corresponding to the accumulation of
misfolded intermediates. A folding chain progresses toward lower intra-chain free-energies by increasing its
compactness. The chains conformational options become increasingly narrowed ultimately toward one native
structure.
[edit] Advantage of domains in protein folding

The organisation of large proteins by structural domains represents an advantage for protein folding,
with each domain being able to individually fold, accelerating the folding process and reducing a potentially
large combination of residue interactions. Furthermore, given the observed random distribution of
hydrophobic residues in proteins,[47] domain formation appears to be the optimal solution for a large protein
to bury its hydrophobic residues while keeping the hydrophilic residues at the surface.[48][49]
However, the role of inter-domain interactions in protein folding and in energetics of stabilisation of
the native structure, probably differs for each protein. In T4 lysozyme, the influence of one domain on the
other is so strong that the entire molecule is resistant to proteolytic cleavage. In this case, folding is a
sequential process where the C-terminal domain is required to fold independently in an early step, and the
other domain requires the presence of the folded C-terminal domain for folding and stabilisation.[50]
It has been found that the folding of an isolated domain can take place at the same rate or
sometimes faster than that of the integrated domain.[51] Suggesting that unfavourable interactions with the
rest of the protein can occur during folding. Several arguments suggest that the slowest step in the folding of
large proteins is the pairing of the folded domains.[27] This is either because the domains are not folded
entirely correctly or because the small adjustments required for their interaction are energetically
unfavourable,[52] such as the removal of water from the domain interface.
[edit] Domains and protein flexibility

The presence of multiple domains in proteins gives rise to a great deal of flexibility and mobility,
leading to protein domain dynamics. Domain motions can be inferred by comparing different structures of a
protein[citation needed], or they can be directly observed using spectra[53][54] measured by neutron spin
echo spectroscopy. They can also be suggested by sampling in extensive molecular dynamics
trajectories[55]. Domain motions are important for:[56]
• catalysis;
• regulatory activity;
• transport of metabolites;
• formation of protein assemblies; and
• cellular locomotion.
One of the largest observed domain motions is the `swivelling' mechanism in pyruvate phosphate
dikinase. The phosphoinositide domain swivels between two states in order to bring a phosphate group from
the active site of the nucleotide binding domain to that of the phosphoenolpyruvate/pyruvate domain.[57] The
phosphate group is moved over a distance of 45A involving a domain motion of about 100 degrees around a
single residue.In enzymes, the closure of one domain onto another captures a substrate by an induced fit,
allowing the reaction to take place in a controlled way. A detailed analysis by Gerstein led to the classification
of two basic types of domain motion; hinge and shear.[56] Only a relatively small portion of the chain, namely
the inter-domain linker and side chains undergo significant conformational changes upon domain
rearrangement.[58]
[edit] Hinges by secondary structures

A study by Hayward[59] found that the termini of α-helices and β-sheets form hinges in a large
number of cases. Many hinges were found to involve two secondary structure elements acting like hinges of
a door, allowing an opening and closing motion to occur. This can arise when two neighbouring strands
within a β-sheet situated in one domain, diverge apart as they join the other domain. The two resulting termini
then form the bending regions between the two domains. α-helices that preserve their hydrogen bonding
network when bent are found to behave as mechanical hinges, storing èlastic energy' that drives the closure
of domains for rapid capture of a substrate.[59]
[edit] Helical to extended conformation

The interconversion of helical and extended conformations at the site of a domain boundary is not
uncommon. In calmodulin, torsion angles change for five residues in the middle of a domain linking α-helix.
The helix is split into two, almost perpendicular, smaller helices separated by four residues of an extended
strand.[60][61]
[edit] Shear motions

Shear motions involve a small sliding movement of domain interfaces, controlled by the amino acid
side chains within the interface. Proteins displaying shear motions often have a layered architecture: stacking
of secondary structures. The interdomain linker has merely the role of keeping the domains in close
proximity.
[edit] Domain motion and functional dynamics in enzymes

The analysis of the internal dynamics of structurally different, but functionally similar enzymes has
highlighted a common relationship between the positioning of the active site and the two principal protein
sub-domains. In fact, for several members of the hydrolase superfamily, the catalytic site is located close to
the interface separating the two principal quasi-rigid domains[55]. Such positioning appears instrumental for
maintaining the precise geometry of the active site, while allowing for an appreciable functionally-oriented
modulation of the flanking regions resulting from the relative motion of the two sub-domains.
[edit] Domain definition from structural co-ordinates

The importance of domains as structural building blocks and elements of evolution has brought about
many automated methods for their identification and classification in proteins of known structure. Automatic
procedures for reliable domain assignment is essential for the generation of the domain databases,
especially as the number of protein structures is increasing. Although the boundaries of a domain can be
determined by visual inspection, construction of an automated method is not straightforward. Problems occur
when faced with domains that are discontinuous or highly associated.[62] The fact that there is no standard
definition of what a domain really is has meant that domain assignments have varied enormously, with each
researcher using a unique set of criteria.[63]
A structural domain is a compact, globular sub-structure with more interactions within it than with the
rest of the protein.[58] Therefore, a structural domain can be determined by two visual characteristics; its
compactness and its extent of isolation.[64] Measures of local compactness in proteins have been used in
many of the early methods of domain assignment[65][66][67][68] and in several of the more recent methods.
[25][69][70][71][72]
[edit] Methods
One of the first algorithms[65] used a Cα-Cα distance map together with a hierarchical clustering
routine that considered proteins as several small segments, 10 residues in length. The initial segments were
clustered one after another based on inter-segment distances; segments with the shortest distances were
clustered and considered as single segments thereafter. The stepwise clustering finally included the full
protein. Go[68] also exploited the fact that inter-domain distances are normally larger than intra-domain
distances; all possible Cα-Cα distances were represented as diagonal plots in which there were distinct
patterns for helices, extended strands and combinations of secondary structures.
The method by Sowdhamini and Blundell clusters secondary structures in a protein based on their
Cα-Cα distances and identifies domains from the pattern in their dendrograms.[62] As the procedure does
not consider the protein as a continuous chain of amino acids there are no problems in treating discontinuous
domains. Specific nodes in these dendrograms are identified as tertiary structural clusters of the protein,
these include both super-secondary structures and domains. The DOMAK algorithm is used to create the
3Dee domain database.[70] It calculates a 'split value' from the number of each type of contact when the
protein is divided arbitrarily into two parts. This split value is large when the two parts of the structure are
distinct.
The method of Wodak and Janin[73] was based on the calculated interface areas between two chain
segments repeatedly cleaved at various residue positions. Interface areas were calculated by comparing
surface areas of the cleaved segments with that of the native structure. Potential domain boundaries can be
identified at a site where the interface area was at a minimum. Other methods have used measures of
solvent accessibility to calculate compactness.[25][74][75]
The PUU algorithm[16] incorporates a harmonic model used to approximate inter-domain dynamics.
The underlying physical concept is that many rigid interactions will occur within each domain and loose
interactions will occur between domains. This algorithm is used to define domains in the FSSP domain
database.[69]
Swindells (1995) developed a method, DETECTIVE, for identification of domains in protein structures
based on the idea that domains have a hydrophobic interior. Deficiencies were found to occur when
hydrophobic cores from different domains continue through the interface region.
RigidFinder is a novel method for identification of protein rigid blocks (domains and loops) from two
different conformations. Rigid blocks are defined as blocks where all inter residue distances are conserved
across conformations.
A general method to identify dynamical domains, that is protein regions that behave approximately as
rigid units in the course of structural fluctuations, has been introduced by Potestio et al.[55] and, among other
applications was also used to compare the consistency of the dynamics-based domain subdivisions with
standard structure-based ones. The method, termed PiSQRD, is publicly available in the form of a
webserver[76]. The latter allows users to optimally subdivide single-chain or multimeric proteins into quasi-
rigid domains[55][76] based on the collective modes of fluctuation of the system. By default the latter are
calculated through an elastic network model[77]; alternatively pre-calculated essential dynamical spaces can
be uploaded by the user.
This article incorporates text and figures from George, R. A. (2002) "Predicting Structural Domains in
Proteins" Thesis, University College London, which were contributed by its author.
[edit] See also
• Amino acid
• Binding domain
• CATH
• Motif domain
• Eukaryotic Linear Motif
• Protein
• Protein structure
• Protein structure prediction
• Protein structure prediction software
• Protein family
• Structural biology
• Structural Classification of Proteins (SCOP)
[edit] Example domains

• Armadillo repeats : named after the β-catenin-like Armadillo protein of the fruit fly Drosophila.
• Basic Leucine zipper domain (bZIP domain) : is found in many DNA-binding eukaryotic
proteins. One part of the domain contains a region that mediates sequence-specific DNA-binding
properties and the Leucine zipper that is required for the dimerization of two DNA-binding regions.
The DNA-binding region comprises a number of basic aminoacids such as arginine and lysine
• Cadherin repeats : Cadherins function as Ca2+-dependent cell-cell adhesion proteins.
Cadherin domains are extracellular regions which mediate cell-to-cell homophilic binding between
cadherins on the surface of adjacent cells.
• Death effector domain (DED) : allows protein-protein binding by homotypic interactions
(DED-DED). Caspase proteases trigger apoptosis via proteolytic cascades. Pro-Caspase-8 and pro-
caspase-9 bind to specific adaptor molecules via DED domains and this leads to autoactivation of
caspases.
• EF hand : a helix-turn-helix structural motif found in each structural domain of the signaling
protein calmodulin and in the muscle protein troponin-C.
• Immunoglobulin-like domains : are found in proteins of the immunoglobulin superfamily
(IgSF).[78] They contain about 70-110 amino acids and are classified into different categories (IgV,
IgC1, IgC2 and IgI) according to their size and function. They possess a characteristic fold in which
two beta sheets form a "sandwich" that is stabilized by interactions between conserved cysteines and
other charged amino acids. They are important for protein-to-protein interactions in processes of cell
adhesion, cell activation, and molecular recognition. These domains are commonly found in
molecules with roles in the immune system.
• Phosphotyrosine-binding domain (PTB) : PTB domains usually bind to phosphorylated
tyrosine residues. They are often found in signal transduction proteins. PTB-domain binding
specificity is determined by residues to the amino-terminal side of the phosphotyrosine. Examples:
the PTB domains of both SHC and IRS-1 bind to a NPXpY sequence. PTB-containing proteins such
as SHC and IRS-1 are important for insulin responses of human cells.
• Pleckstrin homology domain (PH) : PH domains bind phosphoinositides with high affinity.
Specificity for PtdIns(3)P, PtdIns(4)P, PtdIns(3,4)P2, PtdIns(4,5)P2, and PtdIns(3,4,5)P3 have all
been observed. Given the fact that phosphoinositides are sequestered to various cell membranes
(due to their long lipophilic tail) the PH domains usually causes recruitment of the protein in question
to a membrane where the protein can exert a certain function in cell signalling, cytoskeletal
reorganization or membrane trafficking.
• Src homology 2 domain (SH2) : SH2 domains are often found in signal transduction proteins.
SH2 domains confer binding to phosphorylated tyrosine (pTyr). Named after the phosphotyrosine
binding domain of the src viral oncogene, which is itself a tyrosine kinase. See also: SH3 domain.
• Zinc finger DNA binding domain (ZnF_GATA) : ZnF_GATA domain-containing proteins are
typically transcription factors that usually bind to the DNA sequence [AT]GATA[AG] of promoters.
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[edit] Key papers

This article's further reading may not follow Wikipedia's content policies or
guidelines. Please improve this article by removing excessive, less relevant or many
publications with the same point of view; or by incorporating the relevant publications into
the body of the article through appropriate citations. (August 2010)
• Bastian, H. C. (1872). The beginnings of life: being some account of the nature, modes of
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• Berman HM et al. (2000). "The Protein Data Bank". Nucleic Acids Res 28 (1): 235–42.
doi:10.1093/nar/28.1.235. PMID 10592235. PMC 102472.
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• Chothia C. (1992). "Proteins. One thousand families for the molecular biologist". Nature 357
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• Das S, Smith TF. (2000). "Identifying nature's protein Lego set". Adv Protein Chem 54: 159–
83. doi:10.1016/S0065-3233(00)54006-6. PMID 10829228.
• Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L. (2001). "A fully automatic
evolutionary classification of protein folds: Dali Domain Dictionary version 3". Nucleic Acids Res 29
(1): 55–7. doi:10.1093/nar/29.1.55. PMID 11125048. PMC 29815.
• Dill, Ken A.; Chan, Hue Sun (1997). "From Levinthal to pathways to funnels". Nat Struc Biol 4
(1): 10–9. doi:10.1038/nsb0197-10. PMID 8989315.
• Dyson HJ, Sayre JR, Merutka G, Shin HC, Lerner RA, Wright PE. (1992). "Folding of peptide
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• Fersht AR. (1997). "Nucleation mechanisms in protein folding". Curr Opin Struct Biol 7 (1): 3–
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• George DG, Hunt LT, Barker WC. (1996). "PIR-International Protein Sequence Database".
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• Hadley, C and Jones, D.T. (1999). "A systematic comparison of protein structure
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2126(99)80177-4.
• Hayward S. (1999). "Structural principles governing domain motions in proteins". Proteins 36
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• Honig B. (1999). "Protein folding: from the levinthal paradox to structure prediction". J Mol
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• Kim PS, Baldwin RL. (1990). "Intermediates in the folding reactions of small proteins". Annu
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• Murvai J, Vlahovicek K, Barta E, Cataletto B, Pongor S. (2000). "The SBASE protein domain
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• Murzin AG, Brenner SE, Hubbard T, Chothia C. (1995). "SCOP: a structural classification of
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• Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. (2000). "SMART: a web-based tool for
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• Siddiqui AS, Dengler U, Barton GJ. (2001). "3Dee: a database of protein structural domains".
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alpha-Helices". J Mol Biol 252 (3): 351–65. doi:10.1006/jmbi.1995.0502. PMID 7563056.
• Yang AS, Honig B. (1995). "Free energy determinants of secondary structure formation: II.
Antiparallel beta-sheets". J Mol Biol 252 (3): 366–76. doi:10.1006/jmbi.1995.0503. PMID 7563057. }
[edit] External links

• The Protein Families (Pfam) database clan browser provides easy access to information
about protein structural domains. A clan contains two or more Pfam families that have arisen from a
single evolutionary origin.
[edit] Structural domain databases

• Conserved Domains at the National Center for Biotechnology website
• 3Dee
• CATH
• DALI
• SCOP
• Pawson Lab - Protein interaction domains
• Nash Lab - Protein interaction domains in Signal Transduction
• Definition and assignment of structural domains in proteins .
[edit] Sequence domain databases

• InterPro
• Pfam
• PROSITE
• ProDom
• SMART
• NCBI Conserved Domain Database
• SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily
and family) annotations for all completely sequenced organisms
[hide]v · d · eProtein domains
BAR • BIR • BZIP • CARD • C1 • C2 • DED • ENTH • FYVE • HEAT • Kringle • LIM • LRR • NACHT •
PAS • PDZ • Pyrin • PH • PX • SH2 • SH3 • SUN • TRIO • WD40 • zinc finger
[hide]v · d · eProtein tertiary structure
General Structural domain · Protein folding · Structure determination methods
All-α folds: Helix bundle · Globin fold · Homeodomain fold · Alpha solenoid
All-β folds: Immunoglobulin domain · Beta barrel · Beta-propeller
α/β folds: TIM barrel · Leucine-rich repeat · Flavodoxin fold · Rossmann fold ·
Thioredoxin fold · Trefoil knot fold
α+β folds: DNA clamp · Ferredoxin fold · Ribonuclease A · SH2-like fold
Irregular
folds: Conotoxin
←Secondary structure
Quaternary structure→
[hide]v · d · eProteins
Processes Protein biosynthesis · Posttranslational modification · Protein folding · Protein

targeting · Proteome · Protein methods
Structures Protein structure · Protein structural domains · Proteasome
Types List of types of proteins · List of proteins · Membrane protein · Globular protein
(Globulin, Albumin) · Fibrous protein
biochemical families: prot · nucl · carb (glpr, alco, glys) · lipd (fata/i, phld, strd, gllp, eico) · amac/i ·
ncbs/i · ttpy/i
B proteins: BY STRUCTURE: membrane, globular (en, ca, an), fibrous
[hide]v · d · eBiomolecular structure
Protein structure Primary · Secondary · Tertiary · Quaternary · Determination ·

Prediction · Design · Thermodynamics
Nucleic acid Primary · Secondary · Tertiary · Quaternary · Determination ·

structure Prediction · Design · Thermodynamics
See also Protein · Protein domain · Protein engineering · Nucleic acid · DNA ·
RNA · Nucleic acid double helix
Retrieved from "http://en.wikipedia.org/wiki/Protein_domain"
Categories: Protein structure | Protein domains

W000
Genetic memory (biology)


In biology, memory is present if the state of a biological system depends on its past history in
addition to present conditions. If this memory is recorded in the genetic material and stably inherited through
cell division (mitosis or meiosis), it is genetic.
Contents
[hide]
• 1 Molecular biology
• 2 Somatic memory
• 2.1 Cellular memory
• 2.2 In animals
• 2.3 In plants
• 3 Inherited epigenetic memory
• 4 Microbial memory
• 5 Evolution
• 6 Animal behavior
• 7 References
• 8 Further reading
[edit] Molecular biology

In molecular biology, genetic memory resides in the genetic material of the cell and is expressed via
the genetic code used to translate it into proteins.[1][2] The genetic code enables cells to decode the
information needed to construct the protein molecules that make up living cells and therefore record and
store a one-dimensional blueprint for all the parts that make up an organism. This blueprint or genetic
memory in the form of species-specific collections of genes (genotype or genome) is passed from cell to cell
and from generation to generation in the form of DNA molecules. DNA therefore functions as a template for
protein synthesis.[2] Genetic memory can be modified by epigenetic memory, a process by which changes in
gene expression are passed on through mitosis or meiosis through factors other than DNA sequence.
[edit] Somatic memory

Somatic memory is limited to the organism and not passed on to subsequent generations. However,
its mechanism may involve mitotically stable genetic memory. The term applies for cellular memory, animals'
memory, and plants' memory, as described in the following paragraphs.
[edit] Cellular memory

All cells in multicellular organisms are derived from a pluripotent zygote and contain the same
genetic material (with a few exceptions). However, they are capable of recording a history of their
development within the organism leading to their specialized functions and limitations. Cells often employ
epigenetic processes that affect DNA-protein interactions to record this cellular memory in the form of
mitotically stable changes of the genetic material without a change in the DNA sequence itself. This is
typically achieved via changes of the chromatin structure.[3] Examples are methylation patterns of the DNA
molecule itself and proteins involved in packaging DNA, such as histones (also referred to as "histone code").
[4][5]
[edit] In animals
A case of somatic genetic memory is the immunological memory of the adaptive immune response in
vertebrates. The immune system is capable of learning to recognize pathogens and keeping a memory of
this learning process, which is the basis of the success of vaccinations. Antibody genes in B and T
lymphocytes are assembled from separate gene segments, giving each lymphocyte a unique antibody coding
sequence leading to the vast diversity of antibodies in the immune system. If stimulated by an antigen (e.g.
following vaccination or an infection with a pathogen), these antibodies are further fine-tuned via
hypermutation. Memory B cells capable of producing these antibodies form the basis for acquired
immunological memory.[6] Each individual therefore carries a unique genetic memory of its immune system's
close encounters with pathogens. As a somatic memory, this is not passed on to the next generation.
[edit] In plants
Plants that undergo vernalization (promotion of flowering by a prolonged exposure to cold
temperatures) record a genetic memory of winter to gain the competence to flower. The process involves
epigenetically recording the length of cold exposure through chromatin remodeling which leads to mitotically
stable changes in gene expression (the "winter code").[7] This releases the inhibition of flowering initiation
and allows the plants to bloom with the correct timing at the onset of spring. As a somatic memory, this state
is not passed on to subsequent generations but has to be acquired by each individual plant. The process of
vernalization was falsely assumed to be a stably inherited genetic memory passed on to subsequent
generations by the Russian geneticist Trofim Lysenko. Lysenko's claims of genetic memory and efforts to
obtain or fabricate results in proof of it had disastrous effects for Russian genetics in the early 20th century
(also see: Lysenkoism).[8]
[edit] Inherited epigenetic memory

In genetics, genomic imprinting or other patterns of inheritance that are not determined by DNA
sequence alone can form an epigenetic memory that is passed on to subsequent generations through
meiosis. In contrast, somatic genetic memories are passed on by mitosis and limited to the individual, but are
not passed on to the offspring. Both processes include similar epigenetic mechanisms, e.g. involving
histones and methylation patterns.[9][10]
[edit] Microbial memory

In microbes, genetic memory is present in the form of inversion of specific DNA sequences serving
as a switch between alternative patterns of gene expression.[11]
[edit] Evolution
In population genetics and evolution, genetic memory represents the recorded history of adaptive
changes in a species. Selection of organisms carrying genes coding for the best adapted proteins results in
the evolution of species. An example for such a genetic memory is the innate immune response that
represents a recording of the history of common microbial and viral pathogens encountered throughout the
evolutionary history of the species.[12] In contrast to the somatic memory of the adaptive immune response,
the innate immune response is present at birth and does not require the immune system to learn to recognize
antigens.
In the history of theories of evolution, the proposed genetic memory of an individual's experiences
and environmental influences was a central part of Lamarckism to explain the inheritance of evolutionary
changes.
[edit] Animal behavior

In ethology, genetic memory refers the inheritance of instinct in animals and humans.[citation
needed]
[edit] References
1. ^ Nirenberg M (1968). "Genetic memory". JAMA 206 (9): 1973–7.
doi:10.1001/jama.206.9.1973. PMID 4880506.
2. ^ a b Marshall Nirenberg (1968): "The genetic code". Nobel Lecture
3. ^ Hirose S (2007). "Crucial roles for chromatin dynamics in cellular memory". J. Biochem.
141 (5): 615–9. doi:10.1093/jb/mvm092. PMID 17416595.
4. ^ Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6–
21. doi:10.1101/gad.947102. PMID 11782440.
5. ^ Turner BM (2002). "Cellular memory and the histone code". Cell 111 (3): 285–91.
doi:10.1016/S0092-8674(02)01080-2. PMID 12419240.
6. ^ Crotty S, Ahmed R (2004). "Immunological memory in humans". Semin. Immunol. 16 (3):
197–203. doi:10.1016/j.smim.2004.02.008. PMID 15130504.
7. ^ Sung S, Amasino RM (2006). "Molecular genetic studies of the memory of winter". J. Exp.
Bot. 57 (13): 3369–77. doi:10.1093/jxb/erl105. PMID 16980591.
8. ^ Amasino R (2004). "Vernalization, competence, and the epigenetic memory of winter".
Plant Cell 16 (10): 2553–9. doi:10.1105/tpc.104.161070. PMID 15466409.
9. ^ Ooi SL, Henikoff S (2007). "Germline histone dynamics and epigenetics". Curr. Opin. Cell
Biol. 19 (3): 257–65. doi:10.1016/j.ceb.2007.04.015. PMID 17467256.
10.^ Gehring M, Henikoff S (2007). "DNA methylation dynamics in plant genomes". Biochim.
Biophys. Acta 1769 (5-6): 276–86. doi:10.1016/j.bbaexp.2007.01.009. PMID 17341434.
11.^ Casadesús J, D'Ari R (2002). "Memory in bacteria and phage". Bioessays 24 (6): 512–8.
doi:10.1002/bies.10102. PMID 12111734.
12.^ Dempsey PW, Vaidya SA, Cheng G (2003). "The art of war: Innate and adaptive immune
responses". Cell. Mol. Life Sci. 60 (12): 2604–21. doi:10.1007/s00018-003-3180-y. PMID 14685686.
[edit] Further reading
• Alan Bullock and Oliver Stallybrass (1977). "Genetic memory". The Harper Dictionary of
Modern Thought. Harper & Row. pp. 258.
Retrieved from "http://en.wikipedia.org/wiki/Genetic_memory_(biology)"
Categories: Genetics | Evolutionary biology

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Intelligent design movement

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v·d·e
Main article: Intelligent design
The intelligent design movement is a neo-creationist religious campaign for broad social, academic
and political change to promote and support the idea of "intelligent design," which asserts that "certain
features of the universe and of living things are best explained by an intelligent cause, not a possibly
undirected process such as natural selection."[1][2] Its chief activities are a campaign to promote public
awareness of this concept, the lobbying of policymakers to include its teaching in high school science
classes, and legal action, either to defend such teaching or to remove barriers otherwise preventing it.[3][4]
The movement arose out of the previous Christian fundamentalist and evangelistic creation science
movement in the United States,[5] and is driven by a small group of proponents.[6][7]
The overall goal of the intelligent design movement is to "overthrow materialism" and atheism. Its
proponents believe that society has suffered "devastating cultural consequences" from adopting materialism
and that science is the cause of the decay into materialism because it seeks only natural explanations, and is
therefore atheistic. They believe that the theory of evolution implies that humans have no spiritual nature, no
moral purpose, and no intrinsic meaning. They seek to "defeat [the] materialist world view" represented by
the theory of evolution in favor of "a science consonant with Christian and theistic convictions".[3]
To achieve their goal of defeating a materialistic world view, advocates of intelligent design take a
two-pronged approach. Alongside the promotion of intelligent design, proponents also seek to "Teach the
Controversy"; discredit evolution by emphasizing perceived flaws in the theory of evolution, or disagreements
within the scientific community and encourage teachers and students to explore non-scientific alternatives to
evolution, or to critically analyze evolution and the controversy surrounding the teaching of evolution. But the
world's largest general scientific society, the American Association for the Advancement of Science, has
stated that "There is no significant controversy within the scientific community about the validity of evolution."
and that "Evolution is one of the most robust and widely accepted principles of modern science."[8] The
ruling in the Dover trial, Kitzmiller v. Dover Area School District, where the claims of intelligent design
proponents were considered by a United States federal court, stated that "evolution, including common
descent and natural selection, is 'overwhelmingly accepted' by the scientific community."[9][10]
The Discovery Institute[11] is a conservative Christian think tank that drives the intelligent design
movement.[12] The Institute's Center for Science and Culture (CSC) counts most of the leading intelligent
design advocates among its membership, most notably its program advisor Phillip E. Johnson. Johnson is
the architect of the movement's key strategies, the "wedge strategy" and the Teach the Controversy
campaign.
The Discovery Institute and leading proponents represent intelligent design as a revolutionary
scientific theory.[13][14][15][16] The overwhelming majority of the scientific community,[10] as represented
by the American Association for the Advancement of Science,[17] the National Academy of Sciences[18] and
nearly all scientific professional organizations, firmly rejects these claims, and insist that intelligent design is
not valid science, its proponents having failed to conduct an actual scientific research program.[10] This has
led the movement's critics to state that intelligent design is merely a public relations campaign and a political
campaign.[19]
According to critics of the intelligent design movement, the movement's purpose is political rather
than scientific or educational. They claim the movement's "activities betray an aggressive, systematic agenda
for promoting not only intelligent design creationism, but the religious worldview that undergirds it."[20]
Intelligent design is an attempt to recast religious dogma in an effort to reintroduce the teaching of biblical
creationism to public school science classrooms; the intelligent design movement is an effort to reshape
American society into a theocracy, primarily through education. As evidence, critics cite the Discovery
Institute's political activities, its "Wedge strategy" and statements made by leading intelligent design
proponents.
The scientific community's position, as represented by the National Academy of Sciences and the
National Center for Science Education, is that intelligent design is not science, but creationist pseudoscience.
Richard Dawkins, a biologist and professor at Oxford University, compares the intelligent design movement's
demand to "teach the controversy" with the demand to teach flat earthism; acceptable in terms of history, but
not in terms of science. "If you give the idea that there are two schools of thought within science, one that
says the earth is round and one that says the earth is flat, you are misleading children."[21]
Contents
[hide]
• 1 Philosophy
• 2 History of the movement
• 2.1 Origins
• 2.2 Center for the Renewal of Science and Culture
• 2.3 The Wedge strategy
• 2.4 Kansas evolution hearings
• 2.5 Kitzmiller v. Dover Area School District
• 3 Reception by the scientific community
• 4 Structure
• 4.1 The 'big tent' strategy
• 4.2 Obfuscation of religious motivation
• 4.3 Organizations
• 4.3.1 The Center for Science and Culture
• 4.3.2 Other organizations
• 5 Activism
• 5.1 Campaigns
• 5.2 Politics and public education
• 5.3 Higher education
• 5.4 The Web
• 5.5 International
[edit] Philosophy
At the 1999 "Reclaiming America for Christ Conference"[22] called by Reverend D. James Kennedy
of Coral Ridge Ministries, Johnson gave a speech called How the Evolution Debate Can Be Won. [23] In it he
sums up the theological and epistemological underpinnings of intelligent design and its strategy for winning
the battle:
"To talk of a purposeful or guided evolution is not to talk about evolution at all. That is slow
creation. When you understand it that way, you realize that the Darwinian theory of evolution
contradicts not just the Book of Genesis, but every word in the Bible from beginning to end. It
contradicts the idea that we are here because a creator brought about our existence for a
purpose. That is the first thing I realized, and it carries tremendous meaning." -- Phillip Johnson
"I have built an intellectual movement in the universities and churches that we call The Wedge,
which is devoted to scholarship and writing that furthers this program of questioning the
materialistic basis of science. One very famous book that's come out of The Wedge is
biochemist Michael Behe's book, Darwin's Black Box, which has had an enormous impact on
the scientific world." -- Phillip Johnson
"Now the way that I see the logic of our movement going is like this. The first thing you
understand is that the Darwinian theory isn't true. It's falsified by all of the evidence and the logic
is terrible. When you realize that, the next question that occurs to you is, well, where might you
get the truth? When I preach from the Bible, as I often do at churches and on Sundays, I don't
start with Genesis. I start with John 1:1. In the beginning was the word. In the beginning was
intelligence, purpose, and wisdom. The Bible had that right. And the materialist scientists are
deluding themselves." -- Phillip Johnson
[edit] History of the movement

The intelligent design movement grew out of a creationist tradition which argues against evolutionary
theory from a religious standpoint, usually that of evangelical or fundamentalistic Christianity. Although
intelligent design advocates often claim that they are arguing only for the existence of a designer who may or
may not be God, all the movement's leading advocates believe that this designer is God. They frequently
accompany their arguments with a discussion of religious issues, especially when addressing religious
audiences, but elsewhere downplay the religious aspects of their agenda.
[edit] Origins
The modern use of the words "intelligent design", as a term intended to describe a field of inquiry,
began after the Supreme Court of the United States, in the case of Edwards v. Aguillard (1987), ruled that
creationism is unconstitutional in public school science curricula. A Discovery Institute report says that
Charles Thaxton, editor of Of Pandas and People, had picked the phrase up from a NASA scientist, and
thought "That's just what I need, it's a good engineering term".[24] In drafts of the book over one hundred
uses of the root word "creation", such as "creationism" and "creation science", were changed, almost without
exception, to "intelligent design",[25] while "creationists" was changed to "design proponents" or, in one
instance, "cdesign proponentsists". [sic][26] In 1989 Of Pandas and People was published by the Foundation
for Thought and Ethics,[27] with the definition:
Intelligent design means that various forms of life began abruptly through an intelligent agency,
with their distinctive features already intact. Fish with fins and scales, birds with feathers, beaks,
wings, etc.[28]
Pandas was followed in 1991 by Darwin on Trial, a neo-creationist polemic by University of

California, Berkeley law professor emeritus Phillip E. Johnson, that is regarded as a central text of the
movement.[29] Darwin on Trial mentioned Pandas as "'creationist' only in the sense that it juxtaposes a
paradigm of 'intelligent design' with the dominant paradigm of (naturalistic) evolution", but his use of the term
as a focus for his wedge strategy promoting "theistic realism" came later.[page needed] The book was
reviewed by evolutionary biologist Stephen Jay Gould for Scientific American in July 1992, concluding that
the book contains "...no weighing of evidence, no careful reading of literature on all sides, no full citation of
sources (the book does not even contain a bibliography) and occasional use of scientific literature only to
score rhetorical points."[30] This "devastating" review led to the formation in 1992 or 1993 of an 'Ad Hoc
Origins Committee' of Johnson's supporters, which wrote a letter, circulated to thousands of university
professors, defending the book. Among the 39 signatories were nine who later became members of the
Center for the Renewal of Science and Culture.[31]
During the early 1990s Johnson worked to develop a 'big tent' movement to unify a wide range of
creationist viewpoints in opposition to evolution. In 1992, the first formal meeting devoted to intelligent design
was held in Southern Methodist University. It included a debate between Johnson and Michael Ruse (a key
witness in McLean v. Arkansas) and papers by William A. Dembski, Michael Behe and Stephen C. Meyer. In
1993 Johnson organized a follow-up meeting, including Dembski, Behe, Meyer, Dean H. Kenyon (co-author
of Pandas) and Walter Bradley (co-author with Thaxton and Kenyon of The Mystery of Life's Origin), as well
as two young Earth creationist graduate students, Paul A. Nelson and Jonathan Wells.[32]
[edit] Center for the Renewal of Science and Culture
On 6 December 1993 an article by Meyer was published in the Wall Street Journal, drawing national
attention to the controversy over Kenyon's teaching of creationism. This article also gained the attention of
Discovery Institute co-founder Bruce Chapman. On discovering that Meyer was developing the idea of
starting a scientific research center in conversations with conservative political scientist John G. West,
Chapman invited them to create a unit within the Discovery Institute called the Center for the Renewal of
Science and Culture (later renamed the Center for Science and Culture). This center was dedicated to
overthrowing "scientific materialism" and "fomenting nothing less than a scientific and cultural revolution".[33]
A 1995 conference, on "The Death of Materialism and the Renewal of Culture" served as a blueprint for the
center.[34] By 1996 they had nearly a million dollars in grants, the largest being from Howard Ahmanson, Jr.,
with smaller but still large contributions coming from the Stewardship Foundation established by C. Davis
Weyerhaeuser and the Maclellan Foundation, and appointed their first class of research fellows.[33]
[edit] The Wedge strategy

The Wedge strategy was formulated by Johnson to combat the "evil" of methodological naturalism.
[35] It first came to the general public's attention when a Discovery Institute internal memo now known as the
"Wedge Document" (believed to have been written in 1998) was leaked to the public in 1999. However it is
believed to have been update of an earlier document to be implemented between 1996 and 2001.[36]
The document begins with "the proposition that human beings are created in the image of God is one
of the bedrock principles on which Western civilization was built." and then goes on to outline the
movement's goal to exploit perceived discrepancies within evolutionary theory in order to discredit evolution
and scientific materialism in general. Much of the strategy is directed toward the broader public, as opposed
to the professional scientific community. The stated "governing goals" of the CSC's wedge strategy are:
1. To defeat scientific materialism and its destructive moral, cultural and political legacies
2. To replace materialistic explanations with the theistic understanding that nature and human
beings are created by God.
Critics of intelligent design movement argue that the wedge document and strategy demonstrate that
the intelligent design movement is motivated purely by religion and political ideology and that the Discovery
Institute as a matter of policy obfuscates its agenda. The Discovery Institute's official response was to
characterize the criticism and concern as "irrelevant," "paranoid," and "near-panic" while portraying the
wedge document as a "fund-raising document."[37]
Johnson in his 1997 book Defeating Darwinism by Opening Minds confirmed some of the concerns
voiced by the movement's gainsayers:
"If we understand our own times, we will know that we should affirm the reality of God by
challenging the domination of materialism and naturalism in the world of the mind. With the
assistance of many friends I have developed a strategy for doing this,...We call our strategy the
"wedge." -- Phillip Johnson[38]
[edit] Kansas evolution hearings

The Kansas evolution hearings were a series of hearings held in Topeka, Kansas, United States May
5 to May 12, 2005 by the Kansas State Board of Education and its State Board Science Hearing Committee
to change how evolution and the origin of life would be taught in the state's public high school science
classes. The hearings were arranged by the conservative Christian Board of Education with the intent of
introducing intelligent design into science classes via the Teach the Controversy method.[39][40]
The hearings raised the issues of creation and evolution in public education and were attended by all
the major participants in the intelligent design movement but were ultimately boycotted by the scientific
community over concern of lending credibility to the claim, made by proponents of intelligent design, that
evolution is purportedly the subject of wide dispute within the scientific and science education communities.
The Discovery Institute, hub of the intelligent design movement, played a central role in starting the
hearings by promoting its Critical Analysis of Evolution lesson plan[41] which the Kansas State Board of
Education eventually adopted over objections of the State Board Science Hearing Committee, and
campaigning on behalf of conservative Republican candidates for the Board.[42]
Local science advocacy group Kansas Citizens for Science organized a boycott of the hearings by
mainstream scientists, who accused it of being a kangaroo court and argued that their participation would
lend an undeserved air of legitimacy to the hearings.[43] Board member Kathy Martin declared at the
beginning of the hearings "Evolution has been proven false. ID (Intelligent Design) is science-based and
strong in facts." At their conclusion she proclaimed that evolution is "an unproven, often disproven" theory.
"ID has theological implications. ID is not strictly Christian, but it is theistic," asserted Martin.[44] The
scientific community rejects teaching intelligent design as science; a leading example being the United
States National Academy of Sciences, which issued a policy statement saying "Creationism, intelligent
design, and other claims of supernatural intervention in the origin of life or of species are not science
because they are not testable by the methods of science."[45]
On February 13, 2007, the Board voted 6 to 4 to reject the amended science standards enacted in
2005.[46]
[edit] Kitzmiller v. Dover Area School District
In the movement's sole major case, Kitzmiller v. Dover Area School District, it was represented by
the Thomas More Law Center,[47] which had been seeking a test-case on the issue for at least five years.
[48][49] However conflicting agendas resulted in the withdrawal of a number of Discovery Institute (DI)
Fellows as expert witnesses, at the request of DI director Bruce Chapman,[50] and mutual recriminations
with the DI after the case was lost.[51] The Alliance Defense Fund briefly represented the Foundation for
Thought and Ethics (FTE) in its unsuccessful motion to intervene in this case,[52] and prepared amicus
curiae briefs on behalf of the DI and FTE in it.[53] It has also made amicus curiae submissions[54] and
offered to pay for litigation,[55] in other (actual and potential) creationism-related cases. On a far smaller
scale, Larry Caldwell and his wife operate under the name Quality Science Education for All, and have made
a number of lawsuits in furtherance of the movement's anti-evolution agenda. In 2005 they brought at least
three separate lawsuits to further the intelligent design movement's agenda. One was later abandoned, two
were dismissed.[56][57][58]
[edit] Reception by the scientific community

Intelligent design advocates realize that their arguments have little chance of acceptance within the
mainstream scientific community, so they direct them toward politicians, philosophers and the general public.
[59][60][61] What prima facie "scientific" material they have produced has been attacked by critics as
containing factual misrepresentation and misleading, rhetorical and equivocal terminology. A number of
pseudoscientific documentaries that present intelligent design as an increasingly well-supported line of
scientific inquiry have been made.[62][63] The bulk of the material produced by the intelligent design
movement, however, is not intended to be scientific but rather to promote its social and political aims.[64][65]
[66] Polls indicate that intelligent design's main appeal to citizens comes from its link to religious concepts.
An August 2005 poll from The Pew Forum on Religion & Public Life showed 64% of Americans
favoring the teaching of creationism along with evolution in science classrooms, though only 38% favored
teaching it instead of evolution, with the results varying deeply by education level and religiosity. The poll
showed the educated were far less attached to intelligent design than the less educated. Evangelicals and
fundamentalists showed high rates of affiliation with intelligent design while other religious persons and the
secular were much lower.[67]
Scientists responding to a poll overwhelmingly said intelligent design is about religion, not science. A
2002 sampling of 460 Ohio science professors had 91% say it's primarily religion, 93% say there is not "any
scientifically valid evidence or an alternative scientific theory that challenges the fundamental principle of the
theory of evolution," and 97% say that they did not use intelligent design concepts in their own research.[68]
In October and November 2001 the Discovery Institute advertised A Scientific Dissent From
Darwinism listing what they claimed were "100 scientific dissenters" who had signed a statement that "We
are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of
life. Careful examination of the evidence for Darwinian theory should be encouraged."[69] Shortly afterwards
the NCSE described the wording as misleading, noting that a minority of the signatories were biologists and
some of the others were engineers, mathematicians and philosophers, and that some signatories did not fully
support the Discovery Institute's claims. The list was further criticized in a February 2006 New York Times
article[70] which pointed out that only 25% of the signatories by then were biologists and that signatories'
"doubts about evolution grew out of their religious beliefs." In 2003 as a humorous parody of such listings the
NCSE produced the pro-evolution Project Steve list of signatories, all with variations of the name Steve and
most of whom are trained biologists. As of July 31, 2006, the Discovery Institute lists "over 600 scientists",
while Project Steve reported 749 signatories; as of September 30, 2009, 1,112 Steves have signed the
statement.[71]
[edit] Structure
[edit] The 'big tent' strategy
The movement's strategy as set forth by Johnson states the replacement of "materialist science" with
"theistic science" as its primary goal; and, more generally, for intelligent design to become "the dominant
perspective in science" and to "permeate our religious, cultural, moral and political life." This agenda is now
being actively pursued by the Center for Science and Culture (CSC), which plays the leading role in the
promotion of intelligent design. Its fellows include most of the leading intelligent design advocates: William A.
Dembski, Michael Behe, Jonathan Wells and Stephen C. Meyer.
Intelligent design has been described by its proponents as a "big tent" belief, one in which all theists
united by a having some kind of creationist belief (but of differing opinions as regards details) can support. If
successfully promoted, it would reinstate creationism in the teaching of science, after which debates
regarding details could resume. In his 2002 article Big Tent: Traditional Creationism and the Intelligent
Design Community,[72] Discovery Institute fellow Paul A. Nelson credits Johnson for the "big tent" approach
and for reviving creationist debate since the Edwards v. Aguillard decision. According to Nelson, "The
promise of the big tent of ID is to provide a setting where Christians and others may disagree amicably and
fruitfully about how best to understand the natural world as well as scripture."
In his presentation to the 1999 Reclaiming America for Christ Conference, How the Evolution Debate
can be Won, Johnson affirmed this "big tent" role for "The Wedge" (without using the term intelligent design):
To talk of a purposeful or guided evolution is not to talk about evolution at all. That is "slow
creation." When you understand it that way, you realize that the Darwinian theory of evolution
contradicts not just the book of Genesis, but every word in the Bible from beginning to end. It
contradicts the idea that we are here because a Creator brought about our existence for a
purpose. That is the first thing I realized, and it carries tremendous meaning. [...]
So did God create us? Or did we create God? That's an issue that unites people across the
theistic world. Even religious, God-believing Jewish people will say, "That's an issue we really
have a stake in, so let's debate that question first. Let us settle that question first. There are
plenty of other important questions on which we may not agree, and we'll have a wonderful time
discussing those questions after we've settled the first one. We will approach those questions in
a better spirit because we have worked together for this important common end." [...]
[The Wedge is] inherently an ecumenical movement. Michael Behe is a Roman Catholic. The
next book that is coming out from Cambridge University Press by one of my close associates is
by an evangelical convert to Greek Orthodoxy. We have a lot of Protestants, too. The point is
that we have this broad-based intellectual movement that is enabling us to get a foothold in the
scientific and academic journals and in the journals of the various religious faiths.
– Phillip Johnson, The Evolution Debate Can Be Won[23]
The Discovery Institute consistently denies allegations that its intelligent design agenda has religious
foundations, and downplays the religious source of much of its funding. In an interview of Stephen C. Meyer
when ABC News'asked about the Discovery Institute's many evangelical Christian donors the institute's
public relations representative stopped the interview saying "I don't think we want to go down that path."[73]
[edit] Obfuscation of religious motivation
Phillip E. Johnson, largely regarded as the leader of the movement, positions himself as a "theistic
realist" against "methodological naturalism" and intelligent design as the method through which God created
life.[74] Johnson explicitly calls for intelligent design proponents to obfuscate their religious motivations so as
to avoid having intelligent design recognized "as just another way of packaging the Christian evangelical
message."[75] Hence intelligent design arguments are carefully formulated in secular terms and intentionally
avoid positing the identity of the designer. Johnson has stated that cultivating ambiguity by employing secular
language in arguments which are carefully crafted to avoid overtones of theistic creationism is a necessary
first step for ultimately introducing the Christian concept of God as the designer. Johnson emphasizes "the
first thing that has to be done is to get the Bible out of the discussion" and that "after we have separated
materialist prejudice from scientific fact" only then can "biblical issues" be discussed.[76] In the foreword to
Creation, Evolution, & Modern Science (2000) Johnson writes "The intelligent design movement starts with
the recognition that 'In the beginning was the Word.' and 'In the beginning God created.' Establishing that
point isn't enough, but it is absolutely essential to the rest of the gospel message."
[edit] Organizations
[edit] The Center for Science and Culture

Main article: Center for Science and Culture
The Center for Science and Culture (CSC), formerly known as the Center for Renewal of Science
and Culture (CRSC), is a division of the Discovery Institute. The Center consists of a tightly knit core of
people who have worked together for almost a decade to advance intelligent design as both a concept and a
movement as necessary adjuncts of its wedge strategy policy. This cadre includes Phillip E. Johnson,
Michael Behe, William A. Dembski and Stephen C. Meyer. They are united by a religious vision which,
although it varies among the members in its particulars and is seldom acknowledged outside of the Christian
press, is predicated on the shared conviction that America is in need of "renewal" which can be
accomplished only by unseating "Godless" materialism and instituting religion as its cultural foundation.
In his keynote address at the "Research and Progress in intelligent design" (RAPID) conference held
in 2002 at Biola University, William A. Dembski described intelligent design's "dual role as a constructive
scientific project and as a means for cultural renaissance." In a similar vein, the movement's hub, the
Discovery Institute's Center for Science and Culture had until 2002 been the "Center for the Renewal of
Science and Culture". Explaining the name change, a spokesperson for the CSC insisted that the old name
was simply too long. However, the change followed accusations that the center's real interest was not
science but reforming culture along lines favored by conservative Christians.
Critics of the movement cite the Wedge Document as confirmation of this criticism and assert that the
movement's leaders, particularly Phillip E. Johnson, view the subject as a culture war: "Darwinian evolution is
not primarily important as a scientific theory but as a culturally dominant creation story ... When there is
radical disagreement in a commonwealth about the creation story, the stage is set for intense conflict, the
kind ... known as 'culture war.' "
Recently the Center for Science and Culture's has moderated its previous overtly theistic mission
statements[77] to appeal to a broader, a more secular audience. It hopes to accomplish this by using less
overtly theistic messages and language.[78] Despite this, the Center for Science and Culture still states as a
goal a redefinition of science, and the philosophy on which it is based, particularly the exclusion of what it
calls the "unscientific principle of materialism", and in particular the acceptance of what it calls "the scientific
theory of intelligent design".
According to Reason magazine, promotional materials from the Discovery Institute acknowledge that
the Ahmanson family donated $1.5 million to the Center for Science and Culture, then known as the Center
for Renewal of Science and Culture, for a research and publicity program to "unseat not just Darwinism but
also Darwinism's cultural legacy". Mr. Ahmanson funds many causes important to the Christian religious
right, including Christian Reconstructionism, whose goal is to place the U.S. "under the control of biblical
law."[79] Until 1995, Ahmanson sat on the board of the Christian reconstructionist Chalcedon Foundation.[80]
[edit] Other organizations

• The Access Research Network (ARN), has become a comprehensive clearinghouse for ID
resources, including news releases, publications, multimedia products and an elementary school
science curriculum. It's stated mission is "providing accessible information on science, technology
and society issues from an intelligent design perspective."[81] Its directors are Dennis Wagner and
CSC Fellows Mark Hartwig, Stephen C. Meyer and Paul Nelson.[82] Its 'Friends of ARN' is also
dominated by CSC Fellows.[81]
• The Intelligent Design and Evolution Awareness Center (IDEA Center) is a Christian[83]
nonprofit organization formed originally as a student club promoting intelligent design at the
University of California, San Diego (UCSD). There are about 25 active chapters of this organization
in the United States, Kenya, Canada, Ukraine, and The Philippines. There have been a total of 35
active chapters formed and several others are currently pending. Six out of the listed 32 chapters in
the USA are located at high schools [84] In December 2008, biologist Allen MacNeill stated, on the
basis of analysis of the webpages of the national organization and local chapters, that it appeared
that the organization is moribund.[85]
• The Intelligent Design Network (IDnet) is a nonprofit organization formed in Kansas to
promote intelligent design. It is based in Shawnee Mission, Kansas. The Intelligent Design Network
was founded by John Calvert, a corporate finance lawyer with a bachelor's degree in geology and
nutritionist William S. Harris. Together, Calvert and Harris have published the article "Intelligent
Design: The Scientific Alternative to Evolution" in the National Catholic Bioethics Quarterly.[86]
Calvert also has written a play about intelligent design in a high school biology class with Daniel
Schwabauer.[87]
• The Foundation for Thought and Ethics (FTE) is a Christian non-profit organization[88] based
in Richardson, Texas that publishes textbooks and articles promoting intelligent design, abstinence,
and Christian nationism. In addition, the foundation's officers and editors are some of the leading
proponents of intelligent design. The FTE has close associations with the Discovery Institute, hub of
the intelligent design movement and other religious Christian groups.
[edit] Activism
The intelligent design movement primarily campaigns on two fronts: a public relations campaign
meant to influence the popular media and sway public opinion; and an aggressive lobbying campaign to
cultivate support for the teaching of intelligent design amongst policymakers and the wider educational
community. Both these activities are largely funded and directed by the Discovery Institute, from national to
grassroots levels. The movement's first goal is to establish an acceptance of intelligent design at the expense
of evolution in public school science; its long-term goal is no less than the "renewal" of American culture
through the shaping of public policy to reflect conservative Christian values. As the Discovery Institute states,
intelligent design is central to this agenda: "Design theory promises to reverse the stifling dominance of the
materialist worldview, and to replace it with a science consonant with Christian and theistic convictions."
The Discovery Institute has also relied on several polls to indicate the acceptance of intelligent
design. A 2005 Harris poll identified ten percent of adults in the United States as taking what they called the
intelligent design position, that "human beings are so complex that they required a powerful force or
intelligent being to help create them". (64% agreed with the creationist view that "human beings were created
directly by God" and 22% believed that "human beings evolved from earlier species". However, 49%
accepted plant and animal evolution, while 45% did not.)[89] Although some polls commissioned by the
Discovery Institute show more support, these polls have been criticized as suffering from considerable flaws,
such as having a low response rate (248 out of 16,000), being conducted on behalf of an organization with an
expressed interest in the outcome of the poll, and containing leading questions.[90]
Critics of intelligent design and its movement contend that intelligent design is a specific form of
creationism, neo-creationism, a viewpoint rejected by intelligent design advocates. It was bolstered by the
2005 ruling in United States federal court that a public school district requirement for science classes to teach
that intelligent design is an alternative to evolution was a violation of the Establishment Clause of the First
Amendment to the United States Constitution. In Kitzmiller v. Dover Area School District (2005), United
States District Judge John E. Jones III also ruled that intelligent design is not science and is essentially
religious in nature.
In pursuing the goal of establishing intelligent design at the expense of evolution in public school
science, intelligent design groups have threatened and isolated high school science teachers, school board
members and parents who opposed their efforts.[91][92][93] Responding to the well-organized curricular
challenges of intelligent design proponents to local school boards have been disruptive and divisive in the
communities where they've taken place. The campaigns run by intelligent design groups place teachers in
the difficult position of arguing against their employers while the legal challenges to local school districts are
costly and divert scarce funds away from education into court battles. Although these court battles have
almost invariably resulted in the defeat of intelligent design proponents, they are draining and divisive to local
schools. For example, as a result of Kitzmiller v. Dover Area School District trial, the Dover Area School
District was forced to pay $1,000,011 in legal fees and damages for pursuing a policy of teaching the
controversy - presenting intelligent design as an allegedly scientific alternative to evolution. [94]
Leading members of the intelligent design movement are also associated with denialism, both Phillip
Johnson and Jonathan Wells have signed an AIDS denialism petition.[95][96][97][98]
[edit] Campaigns
Main article: Discovery Institute intelligent design campaigns
The Discovery Institute, through its Center for Science and Culture, has formulated a number of
campaigns to promote intelligent design, while discrediting evolutionary biology, which the Institute terms
"Darwinism."[99]
Prominent Institute campaigns have been to 'Teach the Controversy' and, more recently, to allow
Critical Analysis of Evolution. Other prominent campaigns have claimed that intelligent design advocates
(most notably Richard Sternberg) have been discriminated against, and thus that Academic Freedom bills
are needed to protect academics' and teachers' ability to criticise evolution, and that there is a link from
evolution to ideologies such as Nazism and eugenics. These three claims are all publicised in the pro-ID
movie Expelled: No Intelligence Allowed. Other campaigns have included petitions, most notably A Scientific
Dissent From Darwinism.
The response of the scientific community has been to reiterate that the theory of evolution is
overwhelmingly accepted as a matter of scientific consensus[100] whereas intelligent design has been
rejected by the overwhelming majority of the scientific community (see list of scientific societies explicitly
rejecting intelligent design).
[edit] Politics and public education

Main articles: Intelligent design in politics and creation and evolution in public education
The main battlefield for this culture war has been U.S. regional and state school boards. Courts have
also become involved as those campaigns to include intelligent design or weaken the teaching of evolution in
public school science curricula are challenged on First Amendment grounds.[101] In Kitzmiller v. Dover Area
School District the plaintiffs successfully argued that intelligent design is a form of creationism, and that the
school board policy thus violated the Establishment Clause of the First Amendment.
Intelligent design is an integral part of a political campaign by cultural conservatives, largely from
evangelical religious convictions, that seek to redefine science to suit their own ideological agenda.[102]
Though numerically a minority of Americans,.[67] the politics of intelligent design is based less on numbers
than on intensive mobilization of ideologically committed followers and savvy public relations campaigns.
[103] Political repercussions from the culturally conservative sponsorship of the issue has been divisive and
costly to the effected communities, polarizing and dividing not only those directly charged with educating
young people but entire local communities.
With a doctrine that calls itself science among non-scientists but is rejected by the vast majority of
the real practitioners, an amicable coexistence and collaboration between intelligent design advocates and
upholders of mainstream science education standards is rare. With mainstream scientific and educational
organizations saying the theory of evolution is not "in crisis" or a subject doubted by scientists, nor intelligent
design the emergent scientific paradigm or rival theory its proponents proclaim,[104] "teaching the
controversy" is suitable for classes on politics, history, culture, or theology they say, but not science. By
attempting to force the issue into science classrooms, intelligent design proponents create a charged
environment that forces participants and bystanders alike to declare their positions, which has resulted in
intelligent design groups threatening and isolating high school science teachers, school board members and
parents who opposed their efforts.[91][92][93][105][106]
In a round table discussion entitled "Science Wars: Should Schools Teach Intelligent Design?"[107]
at the American Enterprise Institute on 21 October 2005 and televised on C-SPAN, the Discovery Institute's
Mark Ryland and the Thomas More Law Center's Richard Thompson had a frank disagreement, in which
Ryland claimed the Discovery Institute has always cautioned against the teaching of intelligent design, and
Thompson responded that the institute's leadership had not only advocated the teaching of intelligent design,
but encouraged others to do so, and that the Dover Area School District had merely followed the institute's
calls for action.[51] As evidence, Thompson cited the Discovery Institute's guidebook Intelligent Design in
Public School Science Curricula[108] written by the institute's director and co-founder, Stephen C. Meyer and
David DeWolf, a fellow of the institute, which stated in its closing paragraphs: " Moreover, as the previous
discussion demonstrates, school boards have the authority to permit, and even encourage, teaching about
design theory as an alternative to Darwinian evolution -- and this includes the use of textbooks such as Of
Pandas and People that present evidence for the theory of intelligent design. "
[edit] Higher education

This section needs additional citations for verification.
Please help improve this article by adding reliable references. Unsourced material may be
challenged and removed. (January 2011)
The battle to bring intelligent design and its social and political agenda the high school science
classroom is well established. Bringing intelligent design to higher education is also an active part of
Discovery Institute's strategy, though it has not taken the normal path of emergent scientific paradigms,
through graduate schools and leading professional journals of science. It has been out of the question for
intelligent design to be successfully introduced to the public via higher education venues and gain standing in
such scientific courts as long as the evidence for evolution continues to grow in the view of the scientific
community. The Discovery Institute acknowledges that if intelligent design is to become part of college and
university science curricula, it will come to campus via students, their parents, sympathetic faculty, and the
impositions of consumer-conscious college administrators. To that end the institute has supported 'IDEA'
intelligent design student groups[109] at various campuses,[110] and reports having faculty supporters on
every university campus in this country including the Ivy League schools. Academics who are Discovery
Institute fellows include Robert Kaita of Princeton University, Henry F. Schaefer of the University of Georgia,
Robert Koons and J. Budziszewski of the University of Texas at Austin, and Guillermo Gonzalez of Iowa
State University. Prominent academics who, although not officially associated with the Discovery Institute,
sympathize with its aims, include Alvin Plantinga at Notre Dame, Christopher Macosko at University of
Minnesota, Jed Macosko at Wake Forest University, and Frank Tipler at Tulane University.
A number of religious schools offer Discovery Institute-recommended curricula. Biola University and
Oklahoma Baptist University are listed on the Access Research Network website as "ID Colleges." The
intelligent design and Undergraduate Research Center, ARN’s student division, also recruits and supports
followers at universities. Campus youth ministries play an active role in bringing intelligent design to
university campuses through lectures by intelligent design leaders Phillip Johnson, William Dembski,
Jonathan Wells, Michael Behe and others. This activity takes place outside university science departments.
The few university presses (such as Cambridge and Michigan State) that have published intelligent
design books classify them as philosophy, rhetoric, or public affairs, not science.[111] There are no peer-
reviewed studies supporting intelligent design in the scientific research literature. With the scientific
community as a whole unmoved or unconvinced by proponents' works and rhetoric and the absence of
intelligent design scientific research programs, Dembski conceded that "the scientific research part" of
intelligent design is now "lagging behind" its success in influencing popular opinion.
In 2005 the American Association of University Professors issued a strongly worded statement
asserting that the theory of evolution is nearly universally accepted in the community of scholars, and
criticizing the intelligent design movement's attempts to weaken or undermine the teaching of evolution as
"inimical to principles of academic freedom."[112]
The Discovery Institute organizes on-campus intelligent design conferences across the US for
students. In the beginning, these were generally held at Christian universities and often sponsored by the
administration or other faculty as an official university function. Lateron, Yale and the University of San
Francisco have seen proponents of intelligent design speak on their campuses. Not only did these succeed
in reaching out to a more secular group of students, but the backdrop of prestigious universities achieved a
goal set forth in the Wedge strategy; to lend an aura of academic legitimacy to the proceedings and by
extension, the intelligent design movement. Commenting on the Yale conference, for example, a student
auxiliary of the Access Research Network stated, "Basically, the conference, beside being a statement (after
all we were meeting at Yale University), proved to be very promising." These conferences were not
sponsored by the universities at which they were held. They were sponsored by associated religious
organizations — at Yale, the Rivendell Institute for Christian Thought and Learning.
[edit] The Web

Much of the actual debate over intelligent design between intelligent design proponents and
members of the scientific community has taken place on the Web, primarily blogs and message boards,
instead of the scientific journals and symposia where traditionally much science is discussed and settled. In
promoting intelligent design the actions of its proponents have been more like a political pressure group than
like researchers entering an academic debate as described by movement critic Taner Edis.[113] In the
absence of any verifiable scientific research program and concomitant debates in academic circles,[114] the
most vibrant venues for intelligent design debate are websites such as Pandas Thumb [7], Dembski's blogs
at UncommonDescent.com [8] and DesignInference.com [9] and the Discovery Institute's Evolutionnews.org
[10] , often with discussions and their various responses taking place on two or more sites at a time.
[improper synthesis?]
The Web continues to play a central role in the Discovery Institute's strategy of promotion of
intelligent design and it adjunct campaigns. On September 6, 2006, on the center's evolutionnews.org blog
Discovery Institute staffer Casey Luskin published a post entitled "Putting Wikipedia On Notice About Their
Biased Anti-ID Intelligent Design Entries." There Luskin reprinted a letter from a reader complaining that he
believed Wikipedia's coverage of ID to be "one sided" and that pro-intelligent design editors were censored
and attacked. Along with the letter Luskin published a Wikipedia email address for general information and
urged readers to "to contact Wikipedia to express your feelings about the biased nature of the entries on
intelligent design."[115]
[edit] International
Despite being primarily based in the United States, there have been efforts to introduce pro
Intelligent Design teaching material into educational facilities in other countries. In the United Kingdom, the
group Truth in Science has used material from the Discovery Institute to create free teaching packs which
have been mass-mailed to all UK schools.[116] Shortly after this emerged, government ministers announced
that they regarded intelligent design to be creationism and unsuitable for teaching in the classroom. They
also announced that the teaching of the material in science classes was to be prohibited.[117]
[edit] Criticisms of the movement

One of the most common criticisms of the movement and its leadership is that of intellectual
dishonesty, in the form of misleading impressions created by the use of rhetoric, intentional ambiguity, and
misrepresented evidence.[118] It is alleged that its goal is to lead an unwary public to reach certain
conclusions, and that many have been deceived as a result. Critics of the movement, such as Eugenie Scott,
Robert Pennock and Barbara Forrest, claim that leaders of the Intelligent Design movement, and the
Discovery Institute in particular, knowingly misquote scientists and other experts, deceptively omit contextual
text through ellipsis, and make unsupported amplifications of relationships and credentials. Theologian and
molecular biophysicist Alister McGrath has a number of criticisms of the Intelligent design movement, stating
that "those who adopt this approach make Christianity deeply... vulnerable to scientific progress" and defining
it as just another "god-of-the-gaps" theory. He went on to criticize the movement on theological grounds as
well, stating "It is not an approach I accept, either on scientific or theological grounds."[119]
Critics claim that the institute uses academic credentials and affiliations opportunistically. In 2001,
the Discovery Institute purchased advertisements in three national publications (the New York Review of
Books, the New Republic and the Weekly Standard) to proclaim the adherence of approximately 100
scientists to the following statement: "We are skeptical of claims for the ability of random mutation and
natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian
theory should be encouraged."
Such statements commonly note the institutional affiliations of signatories for purposes of
identification. But this statement strategically listed either the institution that granted a signatory's PhD or the
institutions with which the individual is presently affiliated. Thus the institutions listed for Raymond G. Bohlin,
Fazale Rana, and Jonathan Wells, for example, were the University of Texas, Ohio University, and the
University of California, Berkeley, where they earned their degrees, rather than their current affiliations:
Probe Ministries for Bohlin, The Reasons to Believe Ministry for Rana, and The Discovery Institute's Center
for Science and Culture for Wells. Similarly confusing lists of local scientists were circulated during
controversies over evolution education in Georgia, New Mexico, Ohio, and Texas. In another instance, the
Discovery Institute frequently mentions the Nobel Prize in connection with Henry F. Schaefer, a Discovery
Institute fellow, and chemist at the University of Georgia. Critics allege that Discovery Institute is inflating his
reputation by constantly referring to him as a "five-time nominee for the Nobel Prize" because Nobel Prize
nominations remain confidential for fifty years.
This criticism is not reserved only to the institute; individual intelligent design proponents have been
accused of using their own credentials and those of others in a misleading or confusing fashion. For
example, critics allege William Dembski gratuitously invokes his laurels by boasting of his correspondence
with a Nobel laureate, bragging that one of his books was published in a series whose editors include a
Nobel laureate, and exulting that the publisher of the intelligent design book The Mystery of Life's Origin,
Philosophical Library Inc., also published books by eight Nobel laureates. Critics claim that Dembski
purposefully omits relevant facts which he fails to mention to his audience that in 1986, during the Edwards v.
Aguillard hearings, 72 Nobel laureates endorsed an amicus curiae brief that noted that the "evolutionary
history of organisms has been as extensively tested and as thoroughly corroborated as any biological
concept."
Another common criticism is that since no intelligent design research has been published in
mainstream, peer-reviewed scientific journals, the Discovery Institute often misuses the work of mainstream
scientists by putting out lists of articles that allegedly support their arguments for intelligent design drawing
from mainstream scientific literature. Often, the original authors respond that their articles cited by the center
don't support their arguments at all. Many times, the original authors have publicly refuted them for distorting
the meaning of something they've written for their own purposes.
Sahotra Sarkar, a molecular biologist at the University of Texas, has testified that intelligent design
advocates, and specifically the Discovery Institute, have misused his work by misrepresenting its conclusions
to bolster their own claims, has gone on to allege that the extent of the misrepresentations rises to the level
of professional malfeasance:[120]
"When testifying before the Texas State Board of Education in 2003 (in a battle over textbook
adoption that we won hands down), I claimed that my work had been maliciously misused by
members of the Discovery Institute. ... The trouble is that it says nothing of the sort that Meyer
claims. I don't mention Dembski, ID, or "intelligent" information whatever that may be. I don't talk
about assembly instructions. In fact what the paper essentially does is question the value of
informational notions altogether, which made many molecular biologists unhappy, but which is
also diametrically opposed to the "complex specified information" project of the ID
creationists. ... Notice how my work is being presented as being in concordance with ID when
Meyer knows very well where I stand on this issue. If Meyer were an academic, this kind of
malfeasance would rightly earn him professional censure. Unfortunately he's not. He's only the
Director of the Discovery Institute's Center for Science and Culture." -- Sahotra Sarkar
An October 2005 conference called "When Christians and Cultures Clash" was held at the
Pennsylvania Evangelical School of Theology. Attorney Randy Wenger, who is affiliated with the Alliance
Defense Fund, and a close ally of the Discovery Institute, and one of the presenters at the conference
advocated the use of subterfuge for advancing the movement's religious goals: "But even with God’s
blessing, it’s helpful to consult a lawyer before joining the battle. For instance, the Dover area school board
might have had a better case for the intelligent design disclaimer they inserted into high school biology
classes had they not mentioned a religious motivation at their meetings. Give us a call before you do
something controversial like that, I think we need to do a better job at being clever as serpents."[121]
[edit] See also

• Intelligent design in politics
• Kitzmiller v. Dover Area School District
• Expelled: No Intelligence Allowed
• Wedge strategy
• Intelligent Design and Evolution Awareness Center
• Intelligent design network

• Discovery Institute - Center for Science and Culture
• The Wedge Breaking the Modernist Monopoly on Science by Phillip E. Johnson. Touchstone,
A Journal of Mere Christianity. Volume 12, Issue 4. July/August 1999
• The Wedge at Work: How Intelligent Design Creationism Is Wedging Its Way into the Cultural
and Academic Mainstream Chapter 1 of the book Intelligent Design Creationism and Its Critics by
Barbara Forrest, Ph.D. MIT Press, 2001
• Does "Intelligent Design" Threaten the Definition of Science? John Roach. National
Geographic News. April 27, 2005
• Over 500 Scientists Proclaim Their Doubts About Darwin’s Theory Discovery Institute
February 20, 2006
• Design & the Discriminating Public Gaining a Hearing from Ordinary People by Nancy
Pearcey. Touchstone, A Journal of Mere Christianity. Volume 12, Issue 4. July/August 1999
• The Newest Evolution of Creationism Intelligent design is about politics and religion, not
science. Barbara Forrest Ph.D. From Natural History, April, 2002, page 80
• "Inferior Design" Chris Mooney, The American Prospect Online, 10 August 2005.
• Show Me the Science Daniel C. Dennett. At Tufts University, tufts.edu. An editorial originally
published in the New York Times. 28 August 2005
• Should Creationism Be Taught in the Public Schools? (PDF) Robert T. Pennock. March 2002
• Politicized Scholars Put Evolution on the Defensive Jody Wilgoren. Originally published in
the New York Times. 21 August 2005
• Intelligent design opponents invoke US constitution . Donald MacLeod, The Guardian, 18
October 2005.
• Devolution - Why intelligent design isn’t. H. Allen Orr. Annals of Science. New Yorker. May
2005
• Intelligent design network .org
• Intelligent Judging — Evolution in the Classroom and the Courtroom George J. Annas, J.D.,
M.P.H. New England Journal of Medicine. Volume 354:2277-2281, Number 21 May 25, 2006
• The Political Design of Intelligent Design Russell D. Renka, Professor of Political Science,
Southeast Missouri State University November, 2005
• Intelligent Design vs. Evolution debate between paleontologist Peter Ward and Stephen
Meyer co-founder of the Discovery Institute
• Haran Yahya Islamic creationist site
• Intelligent Design Network Australia
• Finnish Intelligent Design site
• Italian Intelligent Design site
[edit] Notes
1. ^ Creationism's Trojan Horse Forrest & Gross, p7
2. ^ Forrest, Barbara (May,2007) (PDF). Understanding the Intelligent Design Creationist
Movement: Its True Nature and Goals. A Position Paper from the Center for Inquiry, Office of Public
Policy. Washington, D.C.: Center for Inquiry, Inc..
http://www.centerforinquiry.net/uploads/attachments/intelligent-design.pdf. Retrieved 2007-08-06 .
3. ^ a b Wedge Strategy Discovery Institute, 1999.
4. ^ Barbara Forrest. 2001. "The Wedge at Work: Intelligent Design Creationism and Its Critics
5. ^ "An Objective Observer Would Know that ID and Teaching About 'Gaps' and 'Problems' in
Evolutionary Theory are Creationist, Religious Strategies that Evolved from Earlier Forms of
Creationism: The concept of intelligent design (hereinafter "ID"), in its current form, came into
existence after the Edwards case was decided in 1987. For the reasons that follow, we conclude that
the religious nature of ID would be readily apparent to an objective observer, adult or child." (page
18) "...we find that ID's religious nature would be further evident to our objective observer because it
directly involves a supernatural designer." (page 24) "A 'hypothetical reasonable observer,' adult or
child, who is 'aware of the history and context of the community and forum' is also presumed to know
that ID is a form of creationism. (page 31) "The evidence at trial demonstrates that ID is nothing less
than the progeny of creationism." (page 31) Context Ruling, Kitzmiller v. Dover Area School District.
Pages 17-35
6. ^ "Q. Has the Discovery Institute been a leader in the intelligent design movement? A. Yes,
the Discovery Institute's Center for Science and Culture. Q. And are almost all of the individuals who
are involved with the intelligent design movement associated with the Discovery Institute? A. All of
the leaders are, yes." Barbara Forrest, 2005, testifying in the Kitzmiller v. Dover Area School District
trial. "Kitzmiller v. Dover Area School District Trial transcript: Day 6 (October 5), PM Session, Part
1.". The TalkOrigins Archive. 2005. http://www.talkorigins.org/faqs/dover/day6pm.html. Retrieved
2007-07-19.
• "The Discovery Institute is the ideological and strategic backbone behind the eruption of skirmishes
over science in school districts and state capitals across the country." In: Wilgoren, J (2005-08-21).
"Politicized Scholars Put Evolution on the Defensive" (PDF). The New York Times.
http://www.msu.edu/course/te/407/FS05Sec3/te408/files/Politicized%20Scholars%20Put
%20Evolution%20on%20the%20Defensive%20-%20New%20York%20Times.pdf. Retrieved 2007-
07-19.
• "Who is behind the ID movement?". Frequently Asked Questions About "Intelligent Design" .
American Civil Liberties Union. 2005-09-16.
http://www.aclu.org/religion/schools/16371res20050916.html. Retrieved 2007-07-20.
• Kahn, JP (2005-07-27). "The Evolution of George Gilder. The Author And Tech-Sector Guru Has A
New Cause To Create Controversy With: Intelligent Design". The Boston Globe.
http://www.discovery.org/scripts/viewDB/index.php?command=view&program=DI%20Main%20Page
%20-%20News&id=2745. Retrieved 2007-07-19.
• "Who's Who of Intelligent Design Proponents". Science & Religion Guide. Science & Theology
News. November 2005. http://www.discovery.org/scripts/viewDB/filesDB-download.php?
command=download&id=602. Retrieved 2007-07-20. (PDF file from Discovery Institute).
• "The engine behind the ID movement is the Discovery Institute." Attie, Alan D.; Elliot Sober, Ronald
L. Numbers, Richard M. Amasino, Beth Cox4, Terese Berceau, Thomas Powell and Michael M. Cox
(2006). "Defending science education against intelligent design: a call to action". Journal of Clinical
Investigation 116:1134–1138. doi:10.1172/JCI28449. A publication of the American Society for
Clinical Investigation.. http://www.jci.org/cgi/content/full/116/5/1134. Retrieved 2007-07-20.
7. ^ "Science and Policy: Intelligent Design and Peer Review". American Association for the
Advancement of Science. 2007.
http://www.aaas.org/spp/dser/03_Areas/evolution/issues/peerreview.shtml. Retrieved 2007-07-19.
8. ^ AAAS Denounces Anti-Evolution Laws American Association for the Advancement of
Science News, February 19, 2006.
9. ^ Ruling, Kitzmiller v. Dover, page 70
10.^ a b c Ruling, Kitzmiller v. Dover page 83
11.^ Defending science education against intelligent design: a call to action Journal of Clinical
Investigation 116:1134-1138 (2006). doi:10.1172/JCI28449. A publication of the American Society for
Clinical Investigation.
12.^ Patricia O’Connell Killen, a religion professor at Pacific Lutheran University in Tacoma
whose work centers around the regional religious identity of the Pacific Northwest, recently wrote that
"religiously inspired think tanks such as the conservative evangelical Discovery Institute" are part of
the "religious landscape" of that area. [1]
13.^ The Wedge Strategy Center for the Renewal of Science and Culture. 1998
14.^ The Design Revolution: Answering the Toughest Questions about Intelligent Design
William A. Dembski. Intervarsity Press, 2004.
15.^ Why scientists dismiss 'intelligent design' Ker Than. MSNBC, September 23, 2005.
16.^ Q&A: Darwin on Trial Margaret Talbot. The New Yorker, November 28, 2005.
17.^ AAAS Board Resolution on Intelligent Design Theory American Association for the
Advancement of Science.
18.^ National Academy of Sciences, 1999 Science and Creationism: A View from the National
Academy of Sciences, Second Edition
19.^ DI's New Talking Point Ed Brayton. Dispatches from the Culture Wars, December 11, 2006.
20.^ The Wedge at Work: How Intelligent Design Creationism Is Wedging Its Way into the
Cultural and Academic Mainstream Barbara Forrest. Chapter 1 of the book Intelligent Design
Creationism and Its Critics (MIT Press, 2001).
21.^ The Evolution Wars Claudia Wallis. TIME magazine. August 15, 2005.
22.^ Reclaim America .org
23.^ a b The Evolution Debate Can Be Won. Phillip Johnson. Truths that Transform.
24.^ Jonathan Witt. Discovery Institute. Evolution News & Views: Dover Judge Regurgitates
Mythological History of Intelligent Design; December 20, 2005 [cited 2007-10-05].
25.^ Kitzmiller v. Dover Area School District, 04 cv 2688 (December 20, 2005)., pp. 31 – 33.
26.^ Nick Matzke. National Center for Science Education. NCSE Resource -- 9.0. Matzke
(2006): The Story of the Pandas Drafts; 2006 [cited 2009-11-18]. *Nick Matzke. National Center for
Science Education. Missing Link discovered!; 2006 [archived 2007-01-14; cited 2009-11-18].
27.^ Book thrown at proponents of Intelligent Design Celeste Biever. NewScientist.com, October
6, 2005,
28.^ Kitzmiller v Dover day 6 a.m. (Barbara Forrest's testimony)
29.^ Stewart, Robert (2007). Intelligent design: William A. Dembski Michael Ruse in dialogue .
Minneapolis, MN: Fortress Press. pp. 2. ISBN 0-8006-6218-0.
30.^ Gould SJ (1992). "Impeaching a Self-Appointed Judge". Scientific American 267 (1).
http://www.stephenjaygould.org/ctrl/gould_darwin-on-trial.html. Retrieved 2009-04-01.
31.^ Forrest & Gross(2004), p18
32.^ Numbers(2006) p380
33.^ a b Numbers(2006) pp381-382
34.^ Forrest&Gross(2004) p19
35.^ Numbers(2006) p377
36.^ Forrest&Gross(2004) pp 25-29
37.^ The Wedge Document: So What? Discovery Institute. (PDF file)
38.^ Defeating Darwinism by Opening Minds Phillip Johnson. pg. 91-92, 1997.
39.^ Transcripts, Kansas Evolution Hearings Page 6. Via Talk Origins Archive.
40.^ A Real Monkey Trial Peter Dizikes. Salon, May 13, 2005.
41.^ CSC - Key Resources for Parents and School Board Members
42.^ 6News Lawrence: Some question group's move with elections nearing
43.^ Wichita Eagle, "Scientists Right to Boycott Evolution Hearings," March 30, 2005; "Evolution
Hearings Rejected by Scientists," April 12, 2005.
44.^ Reason Magazine - Unintelligent Design
45.^ [2].
46.^ "Evolution of Kansas science standards continues as Darwin's theories regain
prominence". International Herald-Tribune. 2007-02-13.
http://www.iht.com/articles/ap/2007/02/13/america/NA-GEN-US-Kansas-Evolution-History.php.
Retrieved 2007-02-14.
47.^ Intelligent designer Gordy Slack. Salon.com, October 2005.
48.^ "For years, a lawyer for the Thomas More Law Center in Michigan visited school boards
around the country searching for one willing to challenge evolution by teaching intelligent design, and
to face a risky, high-profile trial." In Intelligent Design Case, a Cause in Search of a Lawsuit Laurie
Goodstein. The New York Times, November 4, 2005.
49.^ "TMLC representatives traveled the country from at least early 2000, encouraging school
boards to teach ID in science classrooms. From Virginia to Minnesota, TMLC recommended the
textbook Of Pandas and People (Pandas) as a supplement to regular biology textbooks, promising to
defend the schools free of charge when the ACLU filed the inevitable lawsuit. Finally, in summer
2004, they found a willing school board in Dover, Pennsylvania, a board known to have been
searching for a way to get creationism inserted into its science classrooms for years. " Kitzmiller et al.
versus Dover Area School District Burt Humburg, Ed Brayton. Skeptic magazine, July–December
2005.
50.^ Seattle's Discovery Institute scrambling to rebound after intelligent-design ruling, David
Postman, The Seattle Times, April 26, 2006
51.^ a b Discovery Institute and Thomas More Law Center Squabble in AEI Forum, October
23rd, 2005 National Center for Science Education
52.^ ADF attorneys seek to supply missing link in intelligent design curriculum case Alliance
Defense Fund, May 24, 2005.
53.^ Plaintiffs' Response to Amicus Briefs, Kitzmiller v. Dover Area School District
54.^ Circuit Court Sends 'Textbook Sticker' Case Back to Lower Court at the Wayback Machine
(archived August 22, 2006)., Jim Brown, 2006Agape Press, June 1, 2006
55.^ Focus on religion a central ADF tenet, Michael Moore, Missoulian, 29 February 2004
56.^ Nuisance Lawsuit Against Scott and NCSE Withdrawn, Eugenie Scott, The Pandas Thumb,
September 14, 2005
57.^ Caldwell vs Roseville, NO. CIV. S-05-0061 FCD JFM September 17, 2007
58.^ Court dismisses lawsuit targeting evolution website, Robert Sanders, UC Berkeley News,
15 March 2006
59.^ "Whether educational authorities allow the schools to teach about the controversy or not,
public recognition that there is something seriously wrong with Darwinian orthodoxy is going to keep
on growing. While the educators stonewall, our job is to continue building the community of people
who understand the difference between a science that tests its theories against the evidence, and a
pseudoscience that protects its key doctrines by imposing philosophical rules and erecting legal
barriers to freedom of thought. The Pennsylvania Controversy Phillip E. Johnson, Phillip Johnson's
Weekly Wedge Update. June 11, 2001
60.^ "If the science educators continue to pretend that there is no controversy to teach, perhaps
the television networks and the newspapers will take over the responsibility of informing the public."
Icons of Evolution exposed on CNN Phillip E. Johnson, Phillip Johnson's Weekly Wedge Update.
May 2001
61.^ "If the public school educators will not "teach the controversy," our informal network can do
the job for them. In time, the educators will be running to catch up." Passing the Torch Phillip E.
Johnson, Phillip Johnson's Weekly Wedge Update. April 9, 2002
62.^ Privileged Planet - New science documentary explores Earth’s extraordinary place in the
cosmos Staff, Discovery Institute, August 20, 2004
63.^ Unlocking the Mystery of Life - Documentary reveals growing number of scientific
challenges to Darwinian evolution Stephen C. Meyer and W. Peter Allen. Illustra Media, July 15,
2004
64.^ Ruling - whether ID is science, pg.83 Kitzmiller v. Dover Area School District.
65.^ Ruling - whether ID is science, pg.89 Kitzmiller v. Dover Area School District.
66.^ Ruling - disclaimer, pg. 49 Kitzmiller v. Dover Area School District.
67.^ a b Public Divided on Origins of Life The Pew Forum on Religion & Public Life. August 30,
2005
68.^ Ohio Scientists' Intelligent Design Poll Internet Public Opinion Laboratory, Department of
Political Science University of Cincinnati. October 2002.
69.^ A Scientific Dissent from Darwinism Discovery Institute — Center for Science and Culture
accessed July 27, 2006
70.^ Few Biologists But Many Evangelicals Sign Anti-Evolution Petition Kenneth Chang. The
New York Times, February 21, 2006
71.^ The List of Steves, National Center for Science Education
72.^ Life In The Big Tent: Traditional Creationism And The Intelligent Design Community Paul A.
Nelson. Christian Research Institute. (PDF file)
73.^ Small Group Wields Major Influence in Intelligent Design Debate ABC News, November 9,
2005
74.^ "A theistic realist assumes that the universe and all its creatures were brought into
existence for a purpose by God. Theistic realists expect this "fact" of creation to have empirical,
observable consequences that are different from the consequences one would observe if the
universe were the product of nonrational causes . . . . God always has the option of working through
regular secondary mechanisms, and we observe such mechanisms frequently. On the other hand,
many important questions--including the origin of genetic information and human consciousness--
may not be explicable in terms of unintelligent causes, just as a computer or a book cannot be
explained that way." Phillip Johnson. Reason in the Balance: The Case Against Naturalism in
Science, Law and Education. 1995. InterVarsity Press pg. 208-209.
75.^ "Intelligent Design is an intellectual movement, and the Wedge strategy stops working
when we are seen as just another way of packaging the Christian evangelical message. ... The
evangelists do what they do very well, and I hope our work opens up for them some doors that have
been closed." Phillip Johnson. "Keeping the Darwinists Honest", an interview with Phillip Johnson. In
Citizen Magazine. April 1999.
76.^ "...the first thing that has to be done is to get the Bible out of the discussion. ...This is not to
say that the biblical issues are unimportant; the point is rather that the time to address them will be
after we have separated materialist prejudice from scientific fact." Phillip Johnson. "The Wedge",
Touchstone: A Journal of Mere Christianity. July/August 1999.
77.^ About The CRSC recovered from the Internet Archive.
78.^ About the CSC Discovery Institute
79.^ Avenging angel of the religious right Max Blumenthal. Salon.com, January 1, 2004.
80.^ Theocratic Dominionism Gains Influence Part 3 - No Longer Without Sheep Frederick
Clarkson. The Public Eye Magazine, Vol. 8, No. 1. Political Research Associates, March/June 1994.
81.^ a b Barbara Forrest and Paul R. Gross, Creationism's Trojan Horse. Oxford University
Press, (January 8, 2004) ISBN 0195157427 (pp 165-167)
82.^ "About the Access Research Network". Access Research Network. 2008.
http://www.arn.org/infopage/info.htm. Retrieved 2008-05-17.
83.^ "Luskin explained that as a Christian group, 'we wanted to be totally open about who we
thought the designer was.'" Intelligent Design Gains Momentum, Raises Eyebrows on Campuses at
the Wayback Machine (archived September 2, 2006).
84.^ http://www.ideacenter.org/clubs/locations.php
85.^ The "Intelligent Design" Movement on College and University Campuses is Dead, Allen
MacNeill
86.^ Intelligent Design: The Scientific Alternative to Evolution , John H. Calvert and William S.
Harris, National Catholic Bioethics Quarterly, Autumn 2003
87.^ The Rule, Daniel Schwabauer and John Calvert
88.^ Kitzmiller v. Dover: July 14 Hearing: Jon A. Buell
89.^ Nearly Two-thirds of U.S. Adults Believe Human Beings Were Created by God The Harris
Poll #52, July 6, 2005.
90.^ Mooney, Chris (2003-09-11). "Polling for ID". Doubt and About. Committee for Skeptical
Inquiry. Archived from the original on February 3, 2007.
http://web.archive.org/web/20070203135805/http://www.csicop.org/doubtandabout/polling/.
91.^ a b Testimony, Aralene Callahan Kitzmiller v. Dover Area School District September 27,
2005
92.^ a b Testimony, Julie Smith Kitzmiller v. Dover Area School District September 28, 2005
93.^ a b Defending science education against intelligent design: a call to action Journal of
Clinical Investigation 116:1134-1138 (2006). American Society for Clinical Investigation.
94.^ Dover gets a million-dollar bill Christina Kauffman. The York Dispatch, February 22, 2006
95.^ Is It Science Yet?: Intelligent Design Creationism And The Constitution Matthew J. Brauer,
Barbara Forrest, Steven G. Gey. Washington University Law Quarterly, Volume 83, Number 1, 2005.
(PDF file)
96.^ The Group for the Scientific Reappraisal of the HIV-AIDS Hypothesis
97.^ "His personal peculiarities include membership in the Moonies and support for AIDS
reappraisal - the theory that the HIV is not the primary cause of AIDS" Undercover at the Discovery
Institute Beth Quittman. Seattlest, September 8, 2006.
98.^ "some leading lights of anti-evolution Intelligent Design theory, including ID godfather
Phillip Johnson and Moonie Jonathan Wells, have joined the AIDS denialist camp." AIDS 'Denialism'
Gathers Strange Bedfellows Peter McKnight. Originally published in the Vancouver Sun, June 17,
2006.
99.^ Understanding the Intelligent Design Creationist Movement: Its True Nature and Goals. A
Position Paper from the Center for Inquiry, Office of Public Policy Barbara Forrest. May, 2007.
100.^ "99.9 percent of scientists accept evolution" Finding the Evolution in Medicine National
Institutes of Health
101.^ Teaching Evolution: A State-by-State Debate National Public Radio, December 20, 2005.
102.^ The Political Design of Intelligent Design Russell D. Renka, Professor of Political Science.
Southeast Missouri State University. November 16, 2005
103.^ The institute spends more than $1 million a year for research, polls, lobbying and media
pieces that support intelligent design and their Teach the Controversy campaign Battle on Teaching
Evolution Sharpens Peter Slevin Washington Post, March 14, 2005, and is employing the same
Washington, D.C. public relations firm that promoted the Contract with America Politicized Scholars
Put Evolution on the Defensive By Jodi Wilgoren, New York Times, August 21, 2005
104.^ Faculty Association Speaks Out on Three Top Issues American Association of University
Professors. June 17, 2005.
105.^ "Moreover, Board members and teachers opposing the curriculum change and its
implementation have been confronted directly. First, Casey Brown testified that following her
opposition to the curriculum change on October 18, 2004, Buckingham called her an atheist and
Bonsell told her that she would go to hell. Second, Angie Yingling was coerced into voting for the
curriculum change by Board members accusing her of being an atheist and un- Christian. In addition,
both Bryan Rehm and Fred Callahan have been confronted in similarly hostile ways, as have
teachers in the DASD." Ruling, conclusion - Effect of Board’s Actions on Plaintiffs Kitzmiller v. Dover
Area School District.
106.^ In July 2006 a moderator of the blog of intelligent design proponent William A. Dembski,
uncommondescent.com, endorsed bullying the children of the plaintiffs in the Kitzmiller v. Dover Area
School District trial and committing vandalism to drive them out of town and that he intends to publish
their names on the Web to that end.[3][4][5][6]
107.^ Science Wars Should Schools Teach Intelligent Design? Video of American Enterprise
Institute forum that took place during the Kitzmiller case, originally broadcast on C-SPAN
108.^ Intelligent Design in Public School Science Curricula: A Legal Guidebook Access
Research Network
109.^ Intelligent Design and Evolution Awareness IDEA.org
110.^ IDEA chapter locations IDEA.org
111.^ Darwinism, Design, and Public Education, Rhetoric and Public Affairs Series, Michigan
State University Press
112.^ Faculty Association Speaks Out on Three Top Issues at the Wayback Machine (archived
February 10, 2006)., American Association of University Professors, June 17, 2005
113.^ Why ID Fails Taner Edis. 2005.
114.^ The Wedge at Work Chapter 1 of Intelligent Design Creationism and Its Critics . Barbara
Forrest. MIT Press, 2001.
115.^ Putting Wikipedia On Notice About Their Biased Anti-ID Intelligent Design Entries Casey
Luskin. EvolutionNews.org, September 6, 2006.
116.^ Revealed: rise of creationism in the UK Guardian Unlimited. November 27, 2006.
117.^ Ministers to ban creationist teaching aids in science lessons Guardian Unlimited.
December 7, 2006.
118.^ "ID supporters present fallacious arguments, use dishonest rhetoric, and often present
non-contemptuous responses as evidence that their theories are gaining acceptance." Leaders and
Followers in the Intelligent Design Movement Jason Rosenhouse. BioScience, Vol. 53 No. 1, January
2003.
119.^ McGrath, A: The Dawkins Delusion?, page 30. InterVarsity Press, 2007.
120.^ Fraud from the Discovery Institute Sahotra Sarkar. Sarkar Lab WebLog. December 3,
2005.
121.^ "'Bring us your legal issues,' clergy told" Daniel Burke. Lancaster New Era, October 20,
2005
[edit] References
• Forrest, Barbara; Gross, Paul R. (8 January 2004). Creationism's Trojan Horse. Oxford
University Press. ISBN 0195157427.
• Numbers, Ronald (November 30, 2006). The Creationists: From Scientific Creationism to
Intelligent Design, Expanded Edition. Harvard University Press. ISBN 0674023390.
Retrieved from "http://en.wikipedia.org/wiki/Intelligent_design_movement"
Categories: Intelligent design movement | Intelligent design advocates | Religion and politics |
Religion and education | Discovery Institute campaigns
W000
Evolution of sexual reproduction


The evolution of sexual reproduction is currently described by several competing scientific
hypotheses. Many groups of organisms, notably the majority of animals and plants, reproduce sexually. The
evolution of sex contains two related, yet distinct, themes: its origin and its maintenance. However, since the
hypotheses for the origins of sex are difficult to test experimentally, most current work has been focused on
the maintenance of sexual reproduction.
It seems that a sexual cycle is maintained because it improves the quality of progeny (fitness),
despite reducing the overall number of offspring (the twofold cost of sex). In order for sex to be evolutionarily
advantageous, it must be associated with a significant increase in the fitness of offspring. One of the most
widely accepted explanations for the advantage of sex lies in the creation of genetic variation. Another
explanation is based on two molecular advantages. First is the advantage of recombinational DNA repair
(promoted during meiosis because homologous chromosomes pair at that time), and second is the
advantage of complementation (also known as hybrid vigor, heterosis or masking of mutations).
For the advantage due to creation of genetic variation, there are three possible reasons this might
happen. First, sexual reproduction can bring together mutations that are beneficial into the same individual
(sex aids in the spread of advantageous traits). Second, sex acts to bring together currently deleterious
mutations to create severely unfit individuals that are then eliminated from the population ( sex aids in the
removal of deleterious genes). Last, sex creates new gene combinations that may be more fit than previously
existing ones, or may simply lead to reduced competition among relatives.
For the advantage due to DNA repair, there is an immediate large benefit to removal of DNA damage
by recombinational DNA repair during meiosis, since this removal allows greater survival of progeny with
undamaged DNA. The advantage of complementation to each sexual partner is avoidance of the bad effects
of their deleterious recessive genes in progeny by the masking effect of normal dominant genes contributed
by the other partner.
The classes of hypotheses based on the creation of variation are further broken down below. It is
important to realise that any number of these hypotheses may be true in any given species (they are not
mutually exclusive), and that different hypotheses may apply in different species. However, a research
framework based on creation of variation has yet to be found that allows one to determine whether the
reason for sex is universal for all sexual species, and, if not, which mechanism is acting in each species.
On the other hand, the maintenance of sex based on DNA repair and complementation applies
widely to all sexual species. This explanation for the maintenance of sex is explored further in Section 6.2.
Contents
[hide]
• 1 Historical perspective
• 2 Two-fold cost of sex
• 3 Promotion of genetic variation
• 4 Spread of advantageous traits
• 4.1 Novel genotypes
• 4.2 Increased resistance to parasites
• 5 Deleterious mutation clearance
• 5.1 Maintenance of mutation-free individuals
• 5.2 Removal of deleterious genes
• 6 Other explanations
• 6.1 Speed of evolution
• 6.2 DNA repair and complementation
• 7 Origin of sexual reproduction
• 8 Mechanistic origin of sexual reproduction
• 8.1 Viral eukaryogenesis
• 8.2 Neomuran revolution
• 9 See also
• 10 References
• 12 External links
[edit] Historical perspective
Modern philosophical-scientific thinking on the problem can be traced back to Erasmus Darwin in the
18th century; it also features in Aristotle's writings. The thread was later picked up by August Weismann in
1889, who understood that the purpose of sex was to generate genetic variation, as is detailed in the majority
of the explanations below. On the other hand, Charles Darwin, also in 1889, concluded that the effects of
hybrid vigor (complementation) “is amply sufficient to account for the ... genesis of the two sexes.” This is
consistent with the repair and complementation hypothesis, given below under “Other explanations.”
Several explanations have been suggested by biologists including W. D. Hamilton, Alexey
Kondrashov, George C. Williams, Harris Bernstein, Carol Bernstein, Michael M. Cox, Frederic A. Hopf and
Richard E. Michod to explain how sexual reproduction is maintained in a vast array of different living
organisms.
[edit] Two-fold cost of sex

This diagram illustrates the twofold cost of sex. If each individual were to contribute to the same
number of offspring (two), (a) the sexual population remains the same size each generation, where the (b)
asexual population doubles in size each generation.
In all multicellular sexual species, the population consists of two sexes, only one of which is capable
of bearing young (with the exception of simultaneous hermaphrodites). In an asexual species, each member
of the population is capable of bearing young. This implies that an asexual population has an intrinsic
capacity to grow more rapidly each generation. The cost was first described in mathematical terms by John
Maynard Smith.[1] He imagined an asexual mutant arising in a sexual population, half of which comprises
males that cannot themselves produce offspring. With female-only offspring, the asexual lineage doubles its
representation in the population each generation, all else being equal. Often all else is not equal, however, in
which case the realised fitness cost to sex may be much less than this intrinsic twofold cost of producing
males. For example, an asexual mutant arising in a sexual population occupies a niche frozen to that of its
parental genotype because the asexual descendants are genetically self-identical. Analysis of competitive
Lotka-Volterra equations suggests that the asexual lineage may never realise its full twofold advantage in
population growth capacity, if the broader niche of the sexual population confers even a small competitive
edge.[2]
An additional cost is that males and females must search for each other in order to mate, and sexual
selection often favours traits that reduce the survival of individuals.[1]
Evidence that the cost is not insurmountable comes from George C. Williams, who noted the
existence of species which are capable of both asexual and sexual reproduction. These species time their
sexual reproduction with periods of environmental uncertainty, and reproduce asexually when conditions are
more favourable. The important point is that these species are observed to reproduce sexually when they
could choose not to, implying that there is a selective advantage to sexual reproduction.[3]
Another disadvantage of sexual reproduction is that a sexually reproducing organism will only be
able to pass on 50% of its genes to each offspring. This is a consequence of the fact that gametes from
sexually reproducing species are haploid.[4]
[edit] Promotion of genetic variation

August Weismann proposed in 1889[5] an explanation for the evolution of sex, where the advantage
of sex is the creation of variation among siblings. It was then subsequently explained in genetics terms by
Fisher[6] and Muller[7] and has been recently summarised by Burt in 2000.[8]
George C. Williams gave an example based around the elm tree. In the forest of this example, empty
patches between trees can support one individual each. When a patch becomes available because of the
death of a tree, other trees' seeds will compete to fill the patch. Since the chance of a seed's success in
occupying the patch depends upon its genotype, and a parent cannot anticipate which genotype is most
successful, each parent will send many seeds, creating competition between siblings. Natural selection
therefore favours parents which can produce a variety of offspring.
A similar hypothesis is named the tangled bank hypothesis after a passage in Charles Darwin's The
Origin of Species:
"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds,
with birds singing on the bushes, with various insects flitting about, and with worms crawling through
the damp earth, and to reflect that these elaborately constructed forms, so different from each other,
and dependent on each other in so complex a manner, have all been produced by laws acting around
us."
The hypothesis, proposed by Michael Ghiselin in his 1974 book, The Economy of Nature and the
Evolution of Sex, suggests that a diverse set of siblings may be able to extract more food from its
environment than a clone, because each sibling uses a slightly different niche. One of the main proponents of
this hypothesis is Graham Bell of McGill University. The hypothesis has been criticised for failing to explain
how asexual species developed sexes. In his book, Evolution and Human Behavior (MIT Press, 2000), John
Cartwright comments:
"Although once popular, the tangled bank hypothesis now seems to face many problems, and
former adherents are falling away. The theory would predict a greater interest in sex among animals
that produce lots of small offspring that compete with each other. In fact, sex is invariably associated
with organisms that produce a few large offspring, whereas organisms producing small offspring
frequently engage in parthenogenesis [asexual reproduction]. In addition, the evidence from fossils
suggests that species go for vast periods of [geologic] time without changing much."
[edit] Spread of advantageous traits
[edit] Novel genotypes
This diagram illustrates how sex might create novel genotypes more rapidly. Two advantageous
alleles A and B occur at random. The two alleles are recombined rapidly in a sexual population (top), but in
an asexual population (bottom) the two alleles must independently arise because of clonal interference.
Sex could be a method by which novel genotypes are created. Since sex combines genes from two
individuals, sexually reproducing populations can more easily combine advantageous genes than can
asexual populations. If, in a sexual population, two different advantageous alleles arise at different loci on a
chromosome in different members of the population, a chromosome containing the two advantageous alleles
can be produced within a few generations by recombination. However, should the same two alleles arise in
different members of an asexual population, the only way that one chromosome can develop the other allele
is to independently gain the same mutation, which would take much longer.
Ronald Fisher also suggested that sex might facilitate the spread of advantageous genes by allowing
them to escape their genetic surroundings, if they should arise on a chromosome with deleterious genes.
But these explanations depend upon the rate of mutation. If favourable mutations are so rare that
each will become fixed in the population before the next arises (bearing in mind that mutation is a Poisson
process), then sexual and asexual populations would evolve at the same rate.
Additionally, these explanations depend upon group selection, which most theorists maintain is a
weak selective force relative to individual selection – sex is still disadvantageous to the individual due to the
twofold cost of sex. Therefore, these explanations do not explain why heterogonic species choose to adopt
sexual reproduction, as George C. Williams pointed out in his balance argument, and hence are insufficient
to explain the evolution of sex.
Supporters of these theories respond to the balance argument that the individuals produced by
sexual and asexual reproduction may differ in other respects too – which may influence the persistence of
sexuality. For example, in water fleas of the genus Cladocera, sexual offspring form eggs which are better
able to survive the winter.
[edit] Increased resistance to parasites

One of the most widely accepted theories to explain the persistence of sex is that it is maintained to
assist sexual individuals in resisting parasites, also known as the Red Queen's Hypothesis.[4][9][10]
When an environment changes, previously neutral or deleterious alleles can become favourable. If
the environment changed sufficiently rapidly (i.e. between generations), these changes in the environment
can make sex advantageous for the individual. Such rapid changes in environment are caused by the co-
evolution between hosts and parasites.
Imagine, for example that there is one gene in parasites with two alleles p and P conferring two types
of parasitic ability, and one gene in hosts with two alleles h and H, conferring two types of parasite
resistance, such that parasites with allele p can attach themselves to hosts with the allele h, and P to H. Such
a situation will lead to cyclic changes in allele frequency - as p increases in frequency, h will be disfavoured.
In reality, there will be several genes involved in the relationship between hosts and parasites. In an
asexual population of hosts, offspring will only have the different parasitic resistance if a mutation arises. In a
sexual population of hosts, however, offspring will have a new combination of parasitic resistance alleles.
In other words, like Lewis Carroll's Red Queen, sexual hosts are continually adapting in order to stay
ahead of their parasites.
Evidence for this explanation for the evolution of sex is provided by comparison of the rate of
molecular evolution of genes for kinases and immunoglobulins in the immune system with genes coding
other proteins. The genes coding for immune system proteins evolve considerably faster.[11][12]
Critics of the Red Queen hypothesis question whether the constantly-changing environment of hosts
and parasites is sufficiently common to explain the evolution of sex.
[edit] Deleterious mutation clearance

Mutations can have many different effects upon an organism. It is generally believed that the majority
of non-neutral mutations are deleterious, which means that they will cause a decrease in the organism's
overall fitness.[13] If a mutation has a deleterious effect, it will then usually be removed from the population
by the process of natural selection. Sexual reproduction is believed to be more efficient than asexual
reproduction in removing those mutations from the genome.[14]
There are two main hypotheses which explain how sex may act to remove deleterious genes from
the genome.
[edit] Maintenance of mutation-free individuals

Main article: Muller's ratchet
In a finite asexual population under the pressure of deleterious mutations, the random loss of
individuals without such mutations is inevitable. This is known as Muller's ratchet. In a sexual population,
however, mutation-free genotypes can be restored by recombination of genotypes containing deleterious
mutations.
This comparison will only work for a small population - in a large population, random loss of the most
fit genotype becomes unlikely even in an asexual population.
[edit] Removal of deleterious genes
Diagram illustrating different relationships between numbers of mutations and fitness. Kondrashov's
model requires synergistic epistasis, which is represented by the blue line - each mutation has a
disproproportionately large effect on the organism's fitness.
This hypothesis was proposed by Alexey Kondrashov, and is sometimes known as the deterministic
mutation hypothesis.[14] It assumes that the majority of deleterious mutations are only slightly deleterious,
and affect the individual such that the introduction of each additional mutation has an increasingly large effect
on the fitness of the organism. This relationship between number of mutations and fitness is known as
synergistic epistasis.
By way of analogy, think of a car with several minor faults. Each is not sufficient alone to prevent the
car from running, but in combination, the faults combine to prevent the car from functioning.
Similarly, an organism may be able to cope with a few defects, but the presence of many mutations
could overwhelm its backup mechanisms.
Kondrashov argues that the slightly deleterious nature of mutations means that the population will
tend to be composed of individuals with a small number of mutations. Sex will act to recombine these
genotypes, creating some individuals with fewer deleterious mutations, and some with more. Because there
is a major selective disadvantage to individuals with more mutations, these individuals die out. In essence,
sex compartmentalises the deleterious mutations.
There has been much criticism of Kondrashov's theory, since it relies on two key restrictive
conditions. The first requires that the rate of deleterious mutation should exceed one per genome per
generation in order to provide a substantial advantage for sex. While there is some empirical evidence for it
(for example in Drosophila[15] and E. coli[16]), there is also strong evidence against it.[ citation needed]
Secondly, there should be strong interactions among loci (synergistic epistasis), a mutation-fitness relation
for which there is only limited evidence. Conversely, there is also the same amount of evidence that
mutations show no epistasis (purely additive model) or antagonistic interactions (each additional mutation
has a disproportionally small effect).
[edit] Other explanations

[edit] Speed of evolution
Ilan Eshel suggested that sex prevents rapid evolution. He suggests that recombination breaks up
favourable gene combinations more often than it creates them, and sex is maintained because it ensures
selection is longer-term than in asexual populations - so the population is less affected by short-term
changes.[citation needed] This explanation is not widely accepted, as its assumptions are very restrictive.
It has recently been shown in experiments with Chlamydomonas algae that sex can remove the
speed limit on evolution.[17]
[edit] DNA repair and complementation

As discussed in the earlier part of this article, sexual reproduction is conventionally explained as an
adaptation for producing genetic variation through allelic recombination. As acknowledged above, however,
serious problems with this explanation have led many biologists to conclude that the benefit of sex is a major
unsolved problem in evolutionary biology.
An alternative “informational” approach to this problem has led to the view that the two fundamental
aspects of sex, genetic recombination and outcrossing, are adaptive responses to the two major sources of
“noise” in transmitting genetic information. Genetic noise can occur as either physical damage to the genome
(e.g. chemically altered bases of DNA or breaks in the chromosome) or replication errors (mutations)[18][19]
[20] This alternative view is referred to as the repair and complementation hypothesis, to distinguish it from
the traditional variation hypothesis.
The repair and complementation hypothesis assumes that genetic recombination is fundamentally a
DNA repair process, and that when it occurs during meiosis it is an adaptation for repairing the genomic DNA
which is passed on to progeny. Recombinational repair is the only repair process known which can
accurately remove double-strand damages in DNA, and such damages are both common in nature and
ordinarily lethal if not repaired. Recombinational repair is prevalent from the simplest viruses to the most
complex multicellular eukaryotes. It is effective against many different types of genomic damage, and in
particular is highly efficient at overcoming double-strand damages. Studies of the mechanism of meiotic
recombination indicate that meiosis is an adaptation for repairing DNA.[21] These considerations form the
basis for the first part of the repair and complementation hypothesis.
In some lines of descent from the earliest organisms, the diploid stage of the sexual cycle, which was
at first transient, became the predominant stage, because it allowed complementation — the masking of
deleterious recessive mutations (i.e. hybrid vigor or heterosis). Outcrossing, the second fundamental aspect
of sex, is maintained by the advantage of masking mutations and the disadvantage of inbreeding (mating
with a close relative) which allows expression of recessive mutations (commonly observed as inbreeding
depression). This is in accord with Charles Darwin,[22] who concluded that the adaptive advantage of sex is
hybrid vigor; or as he put it, “the offspring of two individuals, especially if their progenitors have been
subjected to very different conditions, have a great advantage in height, weight, constitutional vigor and
fertility over the self fertilised offspring from either one of the same parents.”
However, outcrossing may be abandoned in favor of parthogenesis or selfing (which retain the
advantage of meiotic recombinational repair) under conditions in which the costs of mating are very high. For
instance, costs of mating are high when individuals are rare in a geographic area, such as when there has
been a forest fire and the individuals entering the burned area are the initial ones to arrive. At such times
mates are hard to find, and this favors parthenogenic species.
In the view of the repair and complementation hypothesis, the removal of DNA damage by
recombinational repair produces a new, less deleterious form of informational noise, allelic recombination, as
a by-product. This lesser informational noise generates genetic variation, viewed by some as the major effect
of sex, as discussed in the earlier parts of this article.
[edit] Origin of sexual reproduction

This section requires expansion.
All sexually reproducing organisms derive from a common ancestor which was a single celled
eukaryotic species[citation needed]. Many protists reproduce sexually, as do the multicellular plants, animals,
and fungi. There are a few species which have secondarily lost this feature, such as Bdelloidea and some
parthenocarpic plants.
Organisms need to replicate their genetic material in an efficient and reliable manner. The necessity
to repair genetic damage is one of the leading theories explaining the origin of sexual reproduction. Diploid
individuals can repair a mutated section of its DNA via homologous recombination, since there are two
copies of the gene in the cell and one copy is presumed to be undamaged. A mutation in an haploid
individual, on the other hand, is more likely to become resident, as the DNA repair machinery has no way of
knowing what the original undamaged sequence was.[18] The most primitive form of sex may have been one
organism with damaged DNA replicating an undamaged strand from a similar organism in order to repair
itself.[23]
Another theory is that sexual reproduction originated from selfish parasitic genetic elements that
exchange genetic material (that is: copies of their own genome) for their transmission and propagation. In
some organisms, sexual reproduction has been shown to enhance the spread of parasitic genetic elements
(e.g.: yeast, filamentous fungi).[24] Bacterial conjugation, a form of genetic exchange that some sources
describe as sex, is not a form of reproduction, but rather an example of horizontal gene transfer. However, it
does support the selfish genetic element theory, as it is propagated through such a "selfish gene", the F-
plasmid.[23] Similarly, it has been proposed that sexual reproduction evolved from ancient haloarchaea
through a combination of jumping genes, and swapping plasmids.[25]
A third theory is that sex evolved as a form of cannibalism. One primitive organism ate another one,
but rather than completely digesting it, some of the 'eaten' organism's DNA was incorporated into the 'eater'
organism.[23]
Sex may also be derived from prokaryotic processes. A comprehensive 'origin of sex as vaccination'
theory proposes that eukaryan sex-as-syngamy (fusion sex) arose from prokaryan unilateral sex-as-infection
when infected hosts began swapping nuclearised genomes containing coevolved, vertically transmitted
symbionts that provided protection against horizontal superinfection by more virulent symbionts. Sex-as-
meiosis (fission sex) then evolved as a host strategy to uncouple (and thereby emasculate) the acquired
symbiont genomes.[26]
[edit] Mechanistic origin of sexual reproduction

Though theories positing benefits that lead to the origin of sex are often problematic, several credible
theories on the evolution of the mechanisms of sexual reproduction have been proposed.
[edit] Viral eukaryogenesis

The viral eukaryogenesis (VE) theory proposes that eukaryotic cells arose from a combination of a
lysogenic virus, an archaeon and a bacterium. This model suggests that the nucleus originated when the
lysogenic virus incorporated genetic material from the archaeon and the bacterium and took over the role of
information storage for the amalgam. The archaeal host transferred much of its functional genome to the
virus during the evolution of cytoplasm but retained the function of gene translation and general metabolism.
The bacterium transferred most of its functional genome to the virus as it transitioned into a mitochondrion.
[27]
For these transformations to lead to the eukaryotic cell cycle, the VE hypothesis specifies a pox-like
virus as the lysogenic virus. A pox-like virus is a likely ancestor because of its fundamental similarities with
eukaryotic nuclei. These include a double stranded DNA genome, a linear chromosome with short telomeric
repeats, a complex membrane bound capsid, the ability to produce capped mRNA, and the ability to export
the capped mRNA across the viral membrane into the cytoplasm. The presence of a lysogenic pox-like virus
ancestor explains the development of meiotic division, an essential component of sexual reproduction.[28]
Meiotic division in the VE hypothesis arose because of the evolutionary pressures placed on the
lysogenic virus as a result of its inability to enter into the lytic cycle. This selective pressure resulted in the
development of processes allowing the viruses to spread horizontally throughout the population. The
outcome of this selection was cell-to-cell fusion. (This is distinct from the conjugation methods used by
bacterial plasmids under evolutionary pressure, with important consequences.)[27] The possibility of this kind
of fusion is supported by the presence of fusion proteins in the envelopes of the pox viruses that allow them
to fuse with host membranes. These proteins could have been transferred to the cell membrane during viral
reproduction, enabling cell-to-cell fusion between the virus host and an uninfected cell. The theory proposes
meiosis originated from the fusion between two cells infected with related but different viruses which
recognised each other as uninfected. After the fusion of the two cells, incompatibilities between the two
viruses result in a meiotic-like cell division.[28]
The two viruses established in the cell would initiate replication in response to signals from the host
cell. A mitosis-like cell cycle would proceed until the viral membranes dissolved, at which point linear
chromosomes would be bound together with centromeres. The homologous nature of the two viral
centromeres would incite the grouping of both sets into tetrads. It is speculated that this grouping may be the
origin of crossing over, characteristic of the first division in modern meiosis. The partitioning apparatus of the
mitotic-like cell cycle the cells used to replicate independently would then pull each set of chromosomes to
one side of the cell, still bound by centromeres. These centromeres would prevent their replication in
subsequent division, resulting in four daughter cells with one copy of one of the two original pox-like viruses.
The process resulting from combination of two similar pox viruses within the same host closely mimics
meiosis.[28]
[edit] Neomuran revolution
An alternative theory, proposed by Thomas Cavalier-Smith, was labeled the Neomuran revolution.
The designation "Neomuran revolution" refers to the appearances of the common ancestors of eukaryotes
and archaea. Cavalier-Smith proposes that the first neomurans emerged 850 million years ago. Other
molecular biologists assume that this group appeared much earlier, but Cavalier-Smith dismisses these
claims because they are based on the "theoretically and empirically" unsound model of molecular clocks.
Cavalier-Smith's theory of the Neomuran revolution has implications for the evolutionary history of the cellular
machinery for recombination and sex. It suggests that this machinery evolved in two distinct bouts separated
by a long period of stasis; first the appearance of recombination machinery in a bacterial ancestor which was
maintained for 3 Gy, until the neomuran revolution when the mechanics were adapted to the presence of
nucleosomes. The archaeal products of the revolution maintained recombination machinery that was
essentially bacterial, whereas the eukaryotic products broke with this bacterial continuity. They introduced
cell fusion and ploidy cycles into cell life histories. Cavalier-Smith argues that both bouts of mechanical
evolution were motivated by similar selective forces: the need for accurate DNA replication without loss of
viability.[29]
[edit] See also

Book:Sex
Books are collections of articles that can be downloaded or ordered in print.

• Asexual reproduction
• Biological reproduction
• Epistasis
• Genetic recombination
• Mutation
• Sexual reproduction
[edit] References
1. ^ a b John Maynard Smith The Evolution of Sex 1978.
2. ^ Doncaster, C. P. et al.; Pound, GE; Cox, SJ (2000). "The ecological cost of sex". Nature
404 (6775): 281–285. doi:10.1038/35005078. PMID 10749210.
3. ^ George C. Williams Sex and Evolution 1975, Princeton University Press, ISBN 0-691-
08152-2
4. ^ a b Matt Ridley 1995 The Red Queen: Sex and the Evolution of Human Nature 1995
Penguin.
5. ^ Weismann, A. 1889. Essays on heredity and kindred biological subjects. Oxford Univ.
Press, Oxford, UK
6. ^ Fisher, R. A. 1930. The genetical theory of natural selection. Clarendon Press, Oxford, UK
7. ^ Muller, H. J. (1932). "Some genetic aspects of sex". Am. Nat. 8: 118–138.
8. ^ Burt, A. (2000). "Perspective: sex, recombination, and the efficacy of selection—was
Weismann right?". Evolution 54 (2): 337–351. PMID 10937212.
9. ^ Van Valen, L. (1973). "A New Evolutionary Law". Evolutionary Theory 1: 1–30.
10.^ Hamilton, W. D. et al. (1990). "Sexual reproduction as an adaptation to resist parasites".
Proceedings of the National Academy of Sciences 87: 3566–3573. doi:10.1073/pnas.87.9.3566.
11.^ Kuma, K.; Iwabe, N.; Miyata, T. (1995). "Functional constraints against variations on
molecules from the tissue-level - slowly evolving brain-specific genes demonstrated by protein-
kinase and immunoglobulin supergene families". Molecular Biology and Evolution 12 (1): 123–130.
PMID 7877487.
12.^ Wolfe KH & Sharp PM. 1993. Mammalian gene evolution - nucleotide-sequence divergence
between mouse and rat. Journal of molecular evolution 37 (4): 441-456 OCT 1993
13.^ Griffiths et al. 1999. Gene mutations, p197-234, in Modern Genetic Analysis, New York,
W.H. Freeman and Company.
14.^ a b Kondrashov, A. S. (1988). "Deleterious mutations and the evolution of sexual
reproduction". Nature 336: 435–440. doi:10.1038/336435a0.
15.^ Whitlock, M. C.; Bourget, D. (2000). "Factors affecting the genetic load in Drosophila:
synergistic epistasis and correlations among fitness components". Evolution 54 (5): 1654–1660.
PMID 11108592.
16.^ Elena, S. F.; Lenski, R. E. (1997). "Test of synergistic interactions among deleterious
mutations in bacteria". Nature 390 (6658): 395–398. doi:10.1038/37108. PMID 9389477.
17.^ Colegrave, N. (2002). "Sex releases the speed limit on evolution". Nature 420 (6916): 664–
666. doi:10.1038/nature01191. PMID 12478292.
18.^ a b Bernstein H, Byerly HC, Hopf FA, Michod RE (1984). "Origin of sex". J. Theor. Biol. 110
(3): 323–51. doi:10.1016/S0022-5193(84)80178-2. PMID 6209512.
19.^ Bernstein H, Byerly HC, Hopf FA, Michod RE (1985). "Genetic damage, mutation, and the
evolution of sex". Science 229 (4719): 1277–81. doi:10.1126/science.3898363. PMID 3898363.
20.^ Bernstein H, Hopf FA, Michod RE (1987). "The molecular basis of the evolution of sex".
Adv. Genet. 24: 323–70. doi:10.1016/S0065-2660(08)60012-7. PMID 3324702.
21.^ Cox MM (2001). "Historical overview: searching for replication help in all of the rec places".
Proc. Natl. Acad. Sci. U.S.A. 98 (15): 8173–80. doi:10.1073/pnas.131004998. PMID 11459950.
22.^ Darwin C. 1889. The effects of cross and self fertilisation in the vegetable kingdom.
Chapter XII. General Results pp. 436-463. D. Appleton and Company, New York
23.^ a b c Olivia Judson (2002). Dr. Tatiana's sex advice to all creation. New York: Metropolitan
Books. pp. 233–4. ISBN 0-8050-6331-5.
24.^ Hickey D (1982). "Selfish DNA: a sexually-transmitted nuclear parasite". Genetics 101 (3-
4): 519–31. PMID 6293914.
25.^ DasSarma, Shiladitya (2007). "Extreme Microbes". American Scientist. 95. pp. 224–231
26.^ Sterrer W (2002). "On the origin of sex as vaccination". Journal of Theoretical Biology 216
(4): 387–396. doi:10.1006/jtbi.2002.3008. PMID 12151256.
27.^ a b PJ Bell (2001). "Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA
virus?". J Molec Biol 53 (3): 251–6.
28.^ a b c PJ Bell (2006). "Sex and the eukaryotic cell cycle is consistent with a viral ancestry for
the eukaryotic nucleus". J Theor Biol 243 (1): 54–63. doi:10.1016/j.jtbi.2006.05.015. PMID 16846615.
29.^ Cavalier-Smith, Thomas (2006). "Cell evolution and Earth history: stasis and revolution".
Royal Society of Biol Sci 361 (1470): 969–1006. doi:10.1098/rstb.2006.1842. PMID 16754610.

• Bell, Graham (1982). The masterpiece of nature: the evolution and genetics of sexuality.
Berkeley: University of California Press. ISBN 0-520-04583-1.
• Bernstein, Harris; Carol Bernstein (1991). Aging, sex, and DNA repair. Boston: Academic
Press. ISBN 0-12-092860-4.
• Hurst, L.D.; J.R. Peck (1996). "Recent advances in the understanding of the evolution and
maintenance of sex". Trends in Ecology and Evolution 11: 46–52. doi:10.1016/0169-5347(96)81041-
X.
• Levin, Bruce R.; Richard E. Michod (1988). The Evolution of sex: an examination of current
ideas. Sunderland, Mass: Sinauer Associates. ISBN 0-87893-459-6.
• Maynard Smith, John (1978). The evolution of sex. Cambridge, UK: Cambridge University
Press. ISBN 0-521-21887-X.
• Michod, Richard E. (1995). Eros and evolution: a natural philosophy of sex. Reading, Mass:
Addison-Wesley Pub. Co. ISBN 0-201-40754-X.
• "Scientists put sex origin mystery to bed, Wild strawberry research provides evidence on
when gender emerges". MSNBC. http://www.msnbc.msn.com/id/27927661/. Retrieved 2008-11-25.
• Ridley, Mark (1993). Evolution. Oxford: Blackwell Scientific. ISBN 0-632-03481-5.
• Ridley, Mark (2000). Mendel's demon: gene justice and the complexity of life . London:
Weidenfeld & Nicolson. ISBN 0-297-64634-6.
• Ridley, Matt (1995). The Red Queen: sex and the evolution of human nature . New York:
Penguin Books. ISBN 0-14-024548-0.
• Szathmáry, Eörs; John Maynard Smith (1995). The Major Transitions in Evolution. Oxford:
W.H. Freeman Spektrum. ISBN 0-7167-4525-9.
• Taylor, Timothy (1996). The prehistory of sex: four million years of human sexual culture .
New York: Bantam Books. ISBN 0-553-09694-X.
• Williams, George (1975). Sex and evolution. Princeton, N.J: Princeton University Press.
ISBN 0-691-08147-6.

• The Origin of Sex: Cosmic Solution to an Ancient Mystery
• Why Sex is Good
• An essay summarising the different theories , dating from around 2001
[hide]v · d · eThe development of phenotype
Key concepts Genotype-phenotype distinction · Norms of reaction · Gene-

environment interaction · Heritability · Quantitative genetics
Dominance relationship · Epistasis · Polygenic inheritance ·

Genetic architecture Pleiotropy · Plasticity · Canalisation · Fitness landscape · Transgressive
phenotype
Non-genetic
influences Epigenetics · Maternal effect · Dual inheritance theory
Developmental
architecture Segmentation · Modularity
Evolution of genetic
systems Evolvability · Mutational robustness · Evolution of sex
Influential figures C. H. Waddington · Richard Lewontin

Debates Nature versus nurture · Morphogenetic field
List of evolutionary biology topics
[hide]v · d · e Basic topics in evolutionary biology
Evidence of common descent
Processes of
evolution Adaptation · Macroevolution · Microevolution · Speciation
Population genetic
mechanisms Genetic drift · Gene flow · Mutation · Natural selection
Evolutionary
developmental
biology (Evo-devo) Canalisation · Inversion · Modularity · Phenotypic plasticity
concepts
Evolution of organs Aging · Cellular · DNA · The Ear · The Eye · Flagella · Flight · Hair ·
and biological processes Human intelligence · Modular · Multicellular · Sex
Birds · Butterflies · Cephalopods · Dinosaurs · Dolphins and whales ·

Taxa evolution Fungi · Horses · Humans · Influenza · Insects · Lemur · Life · Molluscs · Plants ·
Sirenians (sea cows) · Spiders · Viruses
Modes of
speciation Anagenesis · Catagenesis · Cladogenesis
History of Charles Darwin · On the Origin of Species ·

evolutionary thought Modern evolutionary synthesis · Gene-centered view of evolution · Life
(classification trees)
Other subfields Ecological genetics · Molecular evolution · Phylogenetics · Systematics
List of evolutionary biology topics · Timeline of evolution
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction"
Categories: Evolutionary biology | Sex

W000
Flower

For other uses, see Flower (disambiguation).
A poster with twelve species of flowers or clusters of flowers of different families
A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering
plants (plants of the division Magnoliophyta, also called angiosperms). The biological function of a flower is to
effect reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may
facilitate outcrossing (fusion of sperm and eggs from different individuals in a population) or allow selfing
(fusion of sperm and egg from the same flower). Some flowers produce diaspores without fertilization
(parthenocarpy). Flowers contain sporangia and are the site where gametophytes develop. Flowers give rise
to fruit and seeds. Many flowers have evolved to be attractive to animals, so as to cause them to be vectors
for the transfer of pollen.
In addition to facilitating the reproduction of flowering plants, flowers have long been admired and
used by humans to beautify their environment but also as objects of romance, ritual, religion, medicine and
as a source of food.
Contents
[hide]
• 1 Morphology
• 2 Development
• 2.1 Flowering transition
• 2.2 Organ development
• 3 Flower specialization and pollination
• 3.1 Floral formula
• 4 Pollination
• 4.1 Attraction methods
• 4.2 Pollination mechanism
• 4.3 Flower-pollinator relationships
• 5 Fertilization and dispersal
• 6 Evolution
• 7 Symbolism
• 8 Usage
• 9 See also
• 10 References
Morphology
Diagram showing the main parts of a mature flower

Flowering plants are heterosporous, producing two types of spores. Microspores are produced by
meiosis inside anthers while megaspores are produced inside ovules, inside an ovary. In fact, anthers
typically consist of four microsporangia and an ovule is an integumented megasporangium. Both types of
spores develop into gametophytes inside sporangia. As with all heterosporous plants, the gametophytes also
develop inside the spores (are endosporic).
A flower is a modified stem tip with compressed internodes, bearing structures that are highly
modified leaves.[1] In essence, a flower develops on a modified shoot or axis from a determinate apical
meristem (determinate meaning the axis grows to a set size).
Flowers may be directly attached to the plant at their base (sessile--the supporting stalk or stem is
highly reduced or absent). The stem or stalk subtending a flower is called a peduncle. If a peduncle supports
more than one flower, the stems connecting each flower to the main axis are called pedicels. The apex of a
flowering stem forms a terminal swelling which is called the torus or receptacle. The parts of a flower are
arranged in whorls on the receptacle. The four main whorls (starting from the base of the flower or lowest
node and working upwards) are as follows:
An example of a "perfect flower", this Crateva religiosa flower has both stamens (outer ring) and a
pistil (center).
• Calyx: the outermost whorl consisting of units called sepals; these are typically green and
enclose the rest of the flower in the bud stage, however, they can be absent or prominent and petal-
like in some species.
• Corolla: the next whorl toward the apex, composed of units called petals, which are typically
thin, soft and colored to attract animals that help the process of pollination.
• Androecium (from Greek andros oikia: man's house): the next whorl (sometimes multiplied
into several whorls), consisting of units called stamens. Stamens consist of two parts: a stalk called a
filament, topped by an anther where pollen is produced by meiosis and eventually dispersed.
• Gynoecium (from Greek gynaikos oikia: woman's house): the innermost whorl of a flower,
consisting of one or more units called carpels. The carpel or multiple fused carpels form a hollow
structure called an ovary, which produces ovules internally. Ovules are megasporangia and they in
turn produce megaspores by meiosis which develop into female gametophytes. These give rise to
egg cells. The gynoecium of a flower is also described using an alternative terminology wherein the
structure one sees in the innermost whorl (consisting of an ovary, style and stigma) is called a pistil.
A pistil may consist of a single carpel or a number of carpels fused together. The sticky tip of the
pistil, the stigma, is the receptor of pollen. The supportive stalk, the style, becomes the pathway for
pollen tubes to grow from pollen grains adhering to the stigma.
Although the arrangement described above is considered "typical", plant species show a wide
variation in floral structure. These modifications have significance in the evolution of flowering plants and are
used extensively by botanists to establish relationships among plant species.
In the majority of species, individual flowers have both functional carpels and stamens. These flowers
are described by botanists as being perfect or bisexual. Some flowers lack one or the other reproductive
organ and called imperfect or unisexual If unisex flowers are found on the same individual plant but in
different locations, the species is said to be monoecious. If each type of unisex flower is found only on
separate individuals, the plant is dioecious.
Additional discussions on floral modifications from the basic plan are presented in the articles on
each of the basic parts of the flower. In those species that have more than one flower on an axis, the
collection of flowers is termed an inflorescence. Some inflorescences are composed of many small flowers
arranged in a formation that resembles a single flower. The common example of this is most members of the
very large composite (Asteraceae) group. A single daisy or sunflower, for example, is not a flower but a
flower head—an inflorescence composed of numerous flowers (or florets).
Many flowers have a symmetry, if the perianth is bisected through the central axis from any point,
symmetrical halves are produced—the flower is called regular or actinomorphic, e.g. rose or trillium. When
flowers are bisected and produce only one line that produces symmetrical halves the flower is said to be
irregular or zygomorphic. e.g. snapdragon or most orchids.
Christmas Lillium (Lilium longiflorum). 1. Stigma, 2. Style, 3. Stamens, 4. Filament, 5. Petal
Development
Flowering transition
The transition to flowering is one of the major phase changes that a plant makes during its life cycle.
The transition must take place at a time that is favorable for fertilization and the formation of seeds, hence
ensuring maximal reproductive success. To meet these needs a plant is able to interpret important
endogenous and environmental cues such as changes in levels of plant hormones and seasonable
temperature and photoperiod changes.[2] Many perennial and most biennial plants require vernalization to
flower. The molecular interpretation of these signals is through the transmission of a complex signal known
as florigen, which involves a variety of genes, including CONSTANS, FLOWERING LOCUS C and
FLOWERING LOCUS T. Florigen is produced in the leaves in reproductively favorable conditions and acts in
buds and growing tips to induce a number of different physiological and morphological changes.[3] The first
step is the transformation of the vegetative stem primordia into floral primordia. This occurs as biochemical
changes take place to change cellular differentiation of leaf, bud and stem tissues into tissue that will grow
into the reproductive organs. Growth of the central part of the stem tip stops or flattens out and the sides
develop protuberances in a whorled or spiral fashion around the outside of the stem end. These
protuberances develop into the sepals, petals, stamens, and carpels. Once this process begins, in most
plants, it cannot be reversed and the stems develop flowers, even if the initial start of the flower formation
event was dependent of some environmental cue.[4] Once the process begins, even if that cue is removed
the stem will continue to develop a flower.
Organ development
The ABC model of flower development

The molecular control of floral organ identity determination is fairly well understood. In a simple
model, three gene activities interact in a combinatorial manner to determine the developmental identities of
the organ primordia within the floral meristem. These gene functions are called A, B and C-gene functions. In
the first floral whorl only A-genes are expressed, leading to the formation of sepals. In the second whorl both
A- and B-genes are expressed, leading to the formation of petals. In the third whorl, B and C genes interact
to form stamens and in the center of the flower C-genes alone give rise to carpels. The model is based upon
studies of homeotic mutants in Arabidopsis thaliana and snapdragon, Antirrhinum majus. For example, when
there is a loss of B-gene function, mutant flowers are produced with sepals in the first whorl as usual, but also
in the second whorl instead of the normal petal formation. In the third whorl the lack of B function but
presence of C-function mimics the fourth whorl, leading to the formation of carpels also in the third whorl. See
also The ABC Model of Flower Development.
Most genes central in this model belong to the MADS-box genes and are transcription factors that
regulate the expression of the genes specific for each floral organ.
Flower specialization and pollination

Further information: Pollination syndrome
Flowering plants usually face selective pressure to optimize the transfer of their pollen, and this is
typically reflected in the morphology of the flowers and the behaviour of the plants. Pollen may be transferred
between plants via a number of 'vectors'. Some plants make use of abiotic vectors — namely wind
(anemophily) or, much less commonly, water (hydrophily). Others use biotic vectors including insects
(entomophily), birds (ornithophily), bats (chiropterophily) or other animals. Some plants make use of multiple
vectors, but many are highly specialised.
Cleistogamous flowers are self pollinated, after which they may or may not open. Many Viola and
some Salvia species are known to have these types of flowers.
The flowers of plants that make use of biotic pollen vectors commonly have glands called nectaries
that act as an incentive for animals to visit the flower. Some flowers have patterns, called nectar guides, that
show pollinators where to look for nectar. Flowers also attract pollinators by scent and color. Still other
flowers use mimicry to attract pollinators. Some species of orchids, for example, produce flowers resembling
female bees in color, shape, and scent. Flowers are also specialized in shape and have an arrangement of
the stamens that ensures that pollen grains are transferred to the bodies of the pollinator when it lands in
search of its attractant (such as nectar, pollen, or a mate). In pursuing this attractant from many flowers of the
same species, the pollinator transfers pollen to the stigmas—arranged with equally pointed precision—of all of
the flowers it visits.
Anemophilous flowers use the wind to move pollen from one flower to the next. Examples include
grasses, birch trees, ragweed and maples. They have no need to attract pollinators and therefore tend not to
be "showy" flowers. Male and female reproductive organs are generally found in separate flowers, the male
flowers having a number of long filaments terminating in exposed stamens, and the female flowers having
long, feather-like stigmas. Whereas the pollen of animal-pollinated flowers tends to be large-grained, sticky,
and rich in protein (another "reward" for pollinators), anemophilous flower pollen is usually small-grained,
very light, and of little nutritional value to animals.
Floral formula
A floral formula is a way to represent the structure of a flower using specific letters, numbers, and
symbols. Typically, a general formula will be used to represent the flower structure of a plant family rather
than a particular species. The following representations are used:
Ca = calyx (sepal whorl; e. g. Ca5 = 5 sepals)
Co = corolla (petal whorl; e. g., Co 3(x) = petals some multiple of three )
Z = add if zygomorphic (e. g., CoZ6 = zygomorphic with 6 petals)
A = androecium (whorl of stamens; e. g., A∞ = many stamens)
G = gynoecium (carpel or carpels; e. g., G1 = monocarpous)
x: to represent a "variable number"
∞: to represent "many"
A floral formula would appear something like this:
Ca5Co5A10 - ∞G1
Several additional symbols are sometimes used (see Key to Floral Formulas).
The four main parts of a flower are generally defined by their positions on the receptacle and not by
their function. Many flowers lack some parts or parts may be modified into other functions and/or look like
what is typically another part. In some families, like Ranunculaceae, the petals are greatly reduced and in
many species the sepals are colorful and petal-like. Other flowers have modified stamens that are petal-like,
the double flowers of Peonies and Roses are mostly petaloid stamens.[5] Flowers show great variation and
plant scientists describe this variation in a systematic way to identify and distinguish species.
Specific terminology is used to descried flowers and their parts. Many flower parts are fused
together; fused parts originating from the same whorl are connate, while fused parts originating from different
whorls are adnate, parts that are not fused are free. When petals are fused into a tube or ring that falls away
as a single unit, they are sympetalous (also called gamopetalous.) Petals that are connate may have
distinctive regions: the cylindrical base is the tube, the expanding region is the throat and the flaring outer
region is the limb. A sympetalous flower, with bilateral symmetry with an upper and lower lip, is bilabiate.
Flowers with connate petals or sepals may have various shaped corolla or calyx including: campanulate,
funnelform, tubular, urceolate, salverform or rotate.
Pollination
Main article: pollination
Grains of pollen sticking to this bee will be transferred to the next flower it visits
Tip of a tulip stamen. Note the grains of pollen
The primary purpose of a flower is reproduction. Since the flowers are the reproductive organs of
plant, they mediate the joining of the sperm, contained within pollen, to the ovules — contained in the ovary.
Pollination is the movement of pollen from the anthers to the stigma. The joining of the sperm to the ovules is
called fertilization. Normally pollen is moved from one plant to another, but many plants are able to self
pollinate. The fertilized ovules produce seeds that are the next generation. Sexual reproduction produces
genetically unique offspring, allowing for adaptation. Flowers have specific designs which encourages the
transfer of pollen from one plant to another of the same species. Many plants are dependent upon external
factors for pollination, including: wind and animals, and especially insects. Even large animals such as birds,
bats, and pygmy possums can be employed. The period of time during which this process can take place (the
flower is fully expanded and functional) is called anthesis.
Attraction methods
A Bee orchid has evolved over many generations to better mimic a female bee to attract male bees
as pollinators.
Plants can not move from one location to another, thus many flowers have evolved to attract animals
to transfer pollen between individuals in dispersed populations. Flowers that are insect-pollinated are called
entomophilous; literally "insect-loving" in Greek. They can be highly modified along with the pollinating
insects by co-evolution. Flowers commonly have glands called nectaries on various parts that attract animals
looking for nutritious nectar. Birds and bees have color vision, enabling them to seek out "colorful" flowers.
Some flowers have patterns, called nectar guides, that show pollinators where to look for nectar; they may be
visible only under ultraviolet light, which is visible to bees and some other insects. Flowers also attract
pollinators by scent and some of those scents are pleasant to our sense of smell. Not all flower scents are
appealing to humans, a number of flowers are pollinated by insects that are attracted to rotten flesh and have
flowers that smell like dead animals, often called Carrion flowers including Rafflesia, the titan arum, and the
North American pawpaw (Asimina triloba). Flowers pollinated by night visitors, including bats and moths, are
likely to concentrate on scent to attract pollinators and most such flowers are white.
Still other flowers use mimicry to attract pollinators. Some species of orchids, for example, produce
flowers resembling female bees in color, shape, and scent. Male bees move from one such flower to another
in search of a mate.
Pollination mechanism
The pollination mechanism employed by a plant depends on what method of pollination is utilized.
Most flowers can be divided between two broad groups of pollination methods:
Entomophilous: flowers attract and use insects, bats, birds or other animals to transfer pollen from
one flower to the next. Often they are specialized in shape and have an arrangement of the stamens that
ensures that pollen grains are transferred to the bodies of the pollinator when it lands in search of its
attractant (such as nectar, pollen, or a mate). In pursuing this attractant from many flowers of the same
species, the pollinator transfers pollen to the stigmas—arranged with equally pointed precision—of all of the
flowers it visits. Many flowers rely on simple proximity between flower parts to ensure pollination. Others,
such as the Sarracenia or lady-slipper orchids, have elaborate designs to ensure pollination while preventing
self-pollination.
Anthers detached from a Meadow Foxtail flower.

A grass flower head (Meadow Foxtail) showing the plain coloured flowers with large anthers.
Anemophilous: flowers use the wind to move pollen from one flower to the next, examples include
the grasses, Birch trees, Ragweed and Maples. They have no need to attract pollinators and therefore tend
not to be "showy" flowers. Whereas the pollen of entomophilous flowers tends to be large-grained, sticky,
and rich in protein (another "reward" for pollinators), anemophilous flower pollen is usually small-grained,
very light, and of little nutritional value to insects, though it may still be gathered in times of dearth.
Honeybees and bumblebees actively gather anemophilous corn (maize) pollen, though it is of little value to
them.
Some flowers are self pollinated and use flowers that never open or are self pollinated before the
flowers open, these flowers are called cleistogamous. Many Viola species and some Salvia have these types
of flowers.
Flower-pollinator relationships
Many flowers have close relationships with one or a few specific pollinating organisms. Many flowers,
for example, attract only one specific species of insect, and therefore rely on that insect for successful
reproduction. This close relationship is often given as an example of coevolution, as the flower and pollinator
are thought to have developed together over a long period of time to match each other's needs.
This close relationship compounds the negative effects of extinction. The extinction of either member
in such a relationship would mean almost certain extinction of the other member as well. Some endangered
plant species are so because of shrinking pollinator populations.
Fertilization and dispersal

Main article: biological dispersal
Cassia Fistula. A hermaphrodite flower showing both male and female parts.
Some flowers with both stamens and a pistil are capable of self-fertilization, which does increase the
chance of producing seeds but limits genetic variation. The extreme case of self-fertilization occurs in flowers
that always self-fertilize, such as many dandelions. Conversely, many species of plants have ways of
preventing self-fertilization. Unisexual male and female flowers on the same plant may not appear or mature
at the same time, or pollen from the same plant may be incapable of fertilizing its ovules. The latter flower
types, which have chemical barriers to their own pollen, are referred to as self-sterile or self-incompatible
(see also: Plant sexuality).
Evolution
Further information: Evolution of flowers
Archaefructus liaoningensis, one of the earliest known flowering plants

Amborella trichopoda, the sister group to the rest of the flowering plants
While land plants have existed for about 425 million years, the first ones reproduced by a simple
adaptation of their aquatic counterparts: spores. In the sea, plants—and some animals—can simply scatter out
genetic clones of themselves to float away and grow elsewhere. This is how early plants reproduced. But
plants soon evolved methods of protecting these copies to deal with drying out and other abuse which is
even more likely on land than in the sea. The protection became the seed, though it had not yet evolved the
flower. Early seed-bearing plants include the ginkgo and conifers. The earliest fossil of a flowering plant,
Archaefructus liaoningensis, is dated about 125 million years old.[6] Several groups of extinct gymnosperms,
particularly seed ferns, have been proposed as the ancestors of flowering plants but there is no continuous
fossil evidence showing exactly how flowers evolved. The apparently sudden appearance of relatively
modern flowers in the fossil record posed such a problem for the theory of evolution that it was called an
"abominable mystery" by Charles Darwin. Recently discovered angiosperm fossils such as Archaefructus,
along with further discoveries of fossil gymnosperms, suggest how angiosperm characteristics may have
been acquired in a series of steps.
Recent DNA analysis (molecular systematics)[7][8] shows that Amborella trichopoda, found on the
Pacific island of New Caledonia, is the sister group to the rest of the flowering plants, and morphological
studies[9] suggest that it has features which may have been characteristic of the earliest flowering plants.
The general assumption is that the function of flowers, from the start, was to involve animals in the
reproduction process. Pollen can be scattered without bright colors and obvious shapes, which would
therefore be a liability, using the plant's resources, unless they provide some other benefit. One proposed
reason for the sudden, fully developed appearance of flowers is that they evolved in an isolated setting like
an island, or chain of islands, where the plants bearing them were able to develop a highly specialized
relationship with some specific animal (a wasp, for example), the way many island species develop today.
This symbiotic relationship, with a hypothetical wasp bearing pollen from one plant to another much the way
fig wasps do today, could have eventually resulted in both the plant(s) and their partners developing a high
degree of specialization. Island genetics is believed to be a common source of speciation, especially when it
comes to radical adaptations which seem to have required inferior transitional forms. Note that the wasp
example is not incidental; bees, apparently evolved specifically for symbiotic plant relationships, are
descended from wasps.
Likewise, most fruit used in plant reproduction comes from the enlargement of parts of the flower.
This fruit is frequently a tool which depends upon animals wishing to eat it, and thus scattering the seeds it
contains.
While many such symbiotic relationships remain too fragile to survive competition with mainland
organisms, flowers proved to be an unusually effective means of production, spreading (whatever their actual
origin) to become the dominant form of land plant life.
While there is only hard proof of such flowers existing about 130 million years ago, there is some
circumstantial evidence that they did exist up to 250 million years ago. A chemical used by plants to defend
their flowers, oleanane, has been detected in fossil plants that old, including gigantopterids,[10] which
evolved at that time and bear many of the traits of modern, flowering plants, though they are not known to be
flowering plants themselves, because only their stems and prickles have been found preserved in detail; one
of the earliest examples of petrification.
The similarity in leaf and stem structure can be very important, because flowers are genetically just
an adaptation of normal leaf and stem components on plants, a combination of genes normally responsible
for forming new shoots.[11] The most primitive flowers are thought to have had a variable number of flower
parts, often separate from (but in contact with) each other. The flowers would have tended to grow in a spiral
pattern, to be bisexual (in plants, this means both male and female parts on the same flower), and to be
dominated by the ovary (female part). As flowers grew more advanced, some variations developed parts
fused together, with a much more specific number and design, and with either specific sexes per flower or
plant, or at least "ovary inferior".
Flower evolution continues to the present day; modern flowers have been so profoundly influenced
by humans that many of them cannot be pollinated in nature. Many modern, domesticated flowers used to be
simple weeds, which only sprouted when the ground was disturbed. Some of them tended to grow with
human crops, and the prettiest did not get plucked because of their beauty, developing a dependence upon
and special adaptation to human affection.[12]
Symbolism
Lilies are often used to denote life or resurrection

Flowers are common subjects of still life paintings, such as this one by Ambrosius Bosschaert the
Elder
Chinese Jade ornament with flower design, Jin Dynasty (1115-1234 AD), Shanghai Museum.
Many flowers have important symbolic meanings in Western culture. The practice of assigning
meanings to flowers is known as floriography. Some of the more common examples include:
• Red roses are given as a symbol of love, beauty, and passion.
• Poppies are a symbol of consolation in time of death. In the United Kingdom, New Zealand,
Australia and Canada, red poppies are worn to commemorate soldiers who have died in times of war.
• Irises/Lily are used in burials as a symbol referring to "resurrection/life". It is also associated
with stars (sun) and its petals blooming/shining.
• Daisies are a symbol of innocence.
Flowers within art are also representative of the female genitalia, as seen in the works of artists such
as Georgia O'Keeffe, Imogen Cunningham, Veronica Ruiz de Velasco, and Judy Chicago, and in fact in
Asian and western classical art. Many cultures around the world have a marked tendency to associate
flowers with femininity.
The great variety of delicate and beautiful flowers has inspired the works of numerous poets,
especially from the 18th-19th century Romantic era. Famous examples include William Wordsworth's I
Wandered Lonely as a Cloud and William Blake's Ah! Sun-Flower.
Because of their varied and colorful appearance, flowers have long been a favorite subject of visual
artists as well. Some of the most celebrated paintings from well-known painters are of flowers, such as Van
Gogh's sunflowers series or Monet's water lilies. Flowers are also dried, freeze dried and pressed in order to
create permanent, three-dimensional pieces of flower art.
The Roman goddess of flowers, gardens, and the season of Spring is Flora. The Greek goddess of
spring, flowers and nature is Chloris.
In Hindu mythology, flowers have a significant status. Vishnu, one of the three major gods in the
Hindu system, is often depicted standing straight on a lotus flower.[13] Apart from the association with
Vishnu, the Hindu tradition also considers the lotus to have spiritual significance.[14] For example, it figures
in the Hindu stories of creation.[15]
Usage
Flower market, Detroit's Eastern Market.

Female hand spreading flowers over a Lingam temple in Varanasi
In modern times, people have sought ways to cultivate, buy, wear, or otherwise be around flowers
and blooming plants, partly because of their agreeable appearance and smell. Around the world, people use
flowers for a wide range of events and functions that, cumulatively, encompass one's lifetime:
• For new births or Christenings
• As a corsage or boutonniere to be worn at social functions or for holidays
• As tokens of love or esteem
• For wedding flowers for the bridal party, and decorations for the hall
• As brightening decorations within the home
• As a gift of remembrance for bon voyage parties, welcome home parties, and "thinking of
you" gifts
• For funeral flowers and expressions of sympathy for the grieving
• For worshiping goddesses. in Hindu culture it is very common to bring flowers as a gift to
temples.
People therefore grow flowers around their homes, dedicate entire parts of their living space to flower
gardens, pick wildflowers, or buy flowers from florists who depend on an entire network of commercial
growers and shippers to support their trade.
Flowers provide less food than other major plants parts (seeds, fruits, roots, stems and leaves) but
they provide several important foods and spices. Flower vegetables include broccoli, cauliflower and
artichoke. The most expensive spice, saffron, consists of dried stigmas of a crocus. Other flower spices are
cloves and capers. Hops flowers are used to flavor beer. Marigold flowers are fed to chickens to give their
egg yolks a golden yellow color, which consumers find more desirable. Dandelion flowers are often made into
wine. Bee Pollen, pollen collected from bees, is considered a health food by some people. Honey consists of
bee-processed flower nectar and is often named for the type of flower, e.g. orange blossom honey, clover
honey and tupelo honey.
Hundreds of fresh flowers are edible but few are widely marketed as food. They are often used to
add color and flavor to salads. Squash flowers are dipped in breadcrumbs and fried. Edible flowers include
nasturtium, chrysanthemum, carnation, cattail, honeysuckle, chicory, cornflower, Canna, and sunflower.
Some edible flowers are sometimes candied such as daisy and rose (you may also come across a candied
pansy).
Flowers can also be made into herbal teas. Dried flowers such as chrysanthemum, rose, jasmine,
camomile are infused into tea both for their fragrance and medical properties. Sometimes, they are also
mixed with tea leaves for the added fragrance.
See also
• Gardening
• Garden
• List of garden plants
• Plant evolutionary developmental biology
• Plant sexuality
• Sowing
References
1. ^ Eames, A. J. (1961) Morphology of the Angiosperms McGraw-Hill Book Co., New York.
2. ^ Ausín, I., et al. (2005). "Environmental regulation of flowering". Int J Dev Biol 49 (5-6): 689–
705. doi:10.1387/ijdb.052022ia. PMID 16096975.
3. ^ Turck, F., Fornara, F., Coupland, G. (2008). "Regulation and Identity of Florigen:
FLOWERING LOCUS T Moves Centre Stage". Annual Review of Plant Biology 59: 573–594.
doi:10.1146/annurev.arplant.59.032607.092755. PMID 18444908.
4. ^ Searle, I., et al. (2006). "The transcription factor FLC confers a flowering response to
vernalization by repressing meristem competence and systemic signaling in Arabidopsis". Genes &
Dev. 20 (7): 898–912. doi:10.1101/gad.373506. PMID 16600915.
5. ^ Reynolds, Joan; Tampion, John (1983). Double flowers: a scientific study. London:
[Published for the] Polytechnic of Central London Press [by] Pembridge Press. p. 41. ISBN 978-0-
86206-004-6.
6. ^ "Flowers Modern & Ancient". Pbs.org. http://www.pbs.org/wgbh/nova/flower/anatomy.html.
7. ^ "First Flower". Pbs.org. 2007-04-17.
http://www.pbs.org/wgbh/nova/transcripts/3405_flower.html. Retrieved 2010-08-30.
8. ^ "Amborella not a "basal angiosperm"? Not so fast". Amjbot.org. doi:10.3732/ajb.91.6.997.
http://www.amjbot.org/cgi/content/full/91/6/997. Retrieved 2010-08-30.
9. ^ "South Pacific plant may be missing link in evolution of flowering plants". Eurekalert.org.
2006-05-17. http://www.eurekalert.org/pub_releases/2006-05/uoca-spp051506.php. Retrieved 2010-
08-30.
10.^ "Oily Fossils Provide Clues To The Evolution Of Flowers". Sciencedaily.com. 2001-04-05.
http://www.sciencedaily.com/releases/2001/04/010403071438.htm. Retrieved 2010-08-30.
11.^ "Age-Old Question On Evolution Of Flowers Answered". Unisci.com. 2001-06-15.
http://unisci.com/stories/20012/0615015.htm. Retrieved 2010-08-30.
12.^ "Human Affection Altered Evolution of Flowers". Livescience.com.
http://www.livescience.com/othernews/050526_flower_power.html. Retrieved 2010-08-30.
13.^ "Vishnu". Bbc.co.uk. 2009-08-24.
http://www.bbc.co.uk/religion/religions/hinduism/deities/vishnu.shtml. Retrieved 2010-08-30.
14.^ "God's Favorite Flower". Hinduism Today.
http://www.hinduismtoday.com/archives/1999/7/1999-7-13.shtml. Retrieved 2010-08-30.
15.^ "The Lotus". Theosociety.org. http://www.theosociety.org/pasadena/sunrise/49-99-0/ge-
mrook.htm. Retrieved 2010-08-30.
• Esau, Katherine (1965) Plant Anatomy (2nd ed.) John Wiley & Sons, New York.
External links
Wikiquote has a collection of quotations related to: Flowers
Look up flower in Wiktionary, the free dictionary.
Wikimedia Commons has media related to: flowers
• Media related to Flowers at Wikimedia Commons

• Native Plant Information Network
• Garden Guide UK - Information on Flowers and Colours
• Israeli researchers bring scent back to our flowers [VIDEO]
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W000
Plant defense against herbivory


Poison ivy produces urushiol to protect the plant from herbivores. In humans this chemical produces
an allergic skin rash, known as urushiol-induced contact dermatitis.
Foxgloves produce several deadly chemicals, namely cardiac and steroidal glycosides. Ingestion can
cause nausea, vomiting, hallucinations, convulsions, or death.
Plant defense against herbivory or host-plant resistance (HPR) describes a range of adaptations
evolved by plants which improve their survival and reproduction by reducing the impact of herbivores. Plants
use several strategies to defend against damage caused by herbivores. Many plants produce secondary
metabolites, known as allelochemicals, that influence the behavior, growth, or survival of herbivores. These
chemical defenses can act as repellents or toxins to herbivores, or reduce plant digestibility.
Other defensive strategies used by plants include escaping or avoiding herbivores in time or in place,
for example by growing in a location where plants are not easily found or accessed by herbivores, or by
changing seasonal growth patterns. Another approach diverts herbivores toward eating non-essential parts,
or enhances the ability of a plant to recover from the damage caused by herbivory. Some plants encourage
the presence of natural enemies of herbivores, which in turn protect the plant. Each type of defense can be
either constitutive (always present in the plant), or induced (produced in reaction to damage or stress caused
by herbivores).
Historically, insects have been the most significant herbivores, and the evolution of land plants is
closely associated with the evolution of insects. While most plant defenses are directed against insects, other
defenses have evolved that are aimed at vertebrate herbivores, such as birds and mammals. The study of
plant defenses against herbivory is important, not only from an evolutionary view point, but also in the direct
impact that these defenses have on agriculture, including human and livestock food sources; as beneficial
'biological control agents' in biological pest control programs; as well as the in the search for plants of
medical importance.
Contents
[hide]
• 1 Evolution of defensive traits
• 1.1 Records of herbivores
• 1.2 Co-evolution
• 2 Types
• 2.1 Chemical defenses
• 2.1.1 Types of chemical defenses
• 2.2 Mechanical defenses
• 2.2.1 Thigmonasty
• 2.3 Mimicry and camouflage
• 2.4 Indirect defenses
• 2.5 Leaf shedding and colour
• 3 Costs and benefits
• 3.1 Optimal defense hypothesis
• 3.2 Carbon:nutrient balance hypothesis
• 3.3 Growth rate hypothesis
• 3.4 Growth-differentiation balance hypothesis
• 4 Importance to humans
• 4.1 Agriculture
• 4.2 Pharmaceutical
• 4.3 Biological pest control
[edit] Evolution of defensive traits
Timeline of plant evolution and the beginnings of different modes of insect herbivory
Main article: Evolutionary history of plants
The earliest land plants evolved from aquatic plants around 450 million years ago (Ma) in the
Ordovician period. These early land plants had no vascular system and required free water for their
reproduction. Vascular plants appeared later and their diversification began in the Devonian era (about 400
Ma). Their reduced dependence on water resulted from adaptations such as protective coatings to reduce
evaporation from their tissues. Reproduction and dispersal of vascular plants in these dry conditions was
achieved through the evolution of specialized seed structures. The diversification of flowering plants
(angiosperms) during the Cretaceous period is associated with the sudden burst of speciation in insects.[1]
This diversification of insects represented a major selective force in plant evolution, and led to selection of
plants that had defensive adaptations. Early insect herbivores were mandibulate and bit or chewed
vegetation; but the evolution of vascular plants lead to the co-evolution of other forms of herbivory, such as
sap-sucking, leaf mining, gall forming and nectar-feeding.[2]
[edit] Records of herbivores
Viburnum lesquereuxii leaf with insect damage; Dakota Sandstone (Cretaceous) of Ellsworth County,
Kansas. Scale bar is 10 mm.
Our understanding of herbivory in geological time comes from three sources: fossilised plants, which
may preserve evidence of defence (such as spines), or herbivory-related damage; the observation of plant
debris in fossilised animal faeces; and the construction of herbivore mouthparts.[3]
Long thought to be a Mesozoic phenomenon, evidence for herbivory is found almost as soon as
fossils which could show it. Within under 20 million years of the first fossils of sporangia and stems towards
the close of the Silurian, around 420 million years ago, there is evidence that they were being consumed.[4]
Animals fed on the spores of early Devonian plants, and the Rhynie chert also provides evidence that
organisms fed on plants using a "pierce and suck" technique.[3] Many plants of this time are preserved with
spine-like enations, which may have performed a defensive role before being co-opted to develop into
leaves.
During the ensuing 75 million years, plants evolved a range of more complex organs - from roots to
seeds. There was a gap of 50 to 100 million years between each organ evolving, and it being fed upon.[4]
Hole feeding and skeletonisation are recorded in the early Permian, with surface fluid feeding evolving by the
end of that period.[3]
A Plain Tiger Danaus chrysippus caterpillar making a moat to block defensive chemicals of
Calotropis before feeding
[edit] Co-evolution
Herbivores depend on plants for food, and have evolved mechanisms to obtain this food despite the
evolution of a diverse arsenal of plant defenses. Herbivore adaptations to plant defense have been likened to
offensive traits and consist of adaptations that allow increased feeding and use of a host plant.[5]
Relationships between herbivores and their host plants often results in reciprocal evolutionary change, called
co-evolution. When a herbivore eats a plant it selects for plants that can mount a defensive response. In
cases where this relationship demonstrates specificity (the evolution of each trait is due to the other), and
reciprocity (both traits must evolve), the species are thought to have co-evolved.[6] The "escape and
radiation" mechanism for co-evolution presents the idea that adaptations in herbivores and their host plants
have been the driving force behind speciation,[1][7] and have played a role in the radiation of insect species
during the age of angiosperms.[8] Some herbivores have evolved ways to hijack plant defenses to their own
benefit, by sequestering these chemicals and using them to protect themselves from predators.[1]
[edit] Types
Plant defenses can be classified generally as constitutive or induced. Constitutive defenses are
always present in the plant, while induced defenses are produced or mobilized to the site where a plant is
injured. There is wide variation in the composition and concentration of constitutive defenses and these
range from mechanical defenses to digestibility reducers and toxins. Many external mechanical defenses and
large quantitative defenses are constitutive, as they require large amounts of resources to produce and
difficult to mobilize.[9]
Induced defenses include secondary metabolic products, as well as morphological and physiological
changes.[10] An advantage of inducible, as opposed to constitutive defenses, is that they are only produced
when needed, and are therefore potentially less costly, especially when herbivory is variable..[10]
[edit] Chemical defenses
Persimmon, genus Diospyros, has a high tannin content which gives immature fruit, seen above, an
astringent and bitter flavor.
The evolution of chemical defenses in plants is linked to the emergence of chemical substances that
are not involved in the essential photosynthetic and metabolic activities. These substances, secondary
metabolites, are organic compounds that are not directly involved in the normal growth, development or
reproduction of organisms,[11] and often produced as by-products during the synthesis of primary metabolic
products.[12] These secondary metabolites play a major role in defenses against herbivores.[1][11][13]
Secondary metabolites are often characterized as either qualitative or quantitative. Qualitative
metabolites are defined as toxins that interfere with an herbivore’s metabolism, often by blocking specific
biochemical reactions. Qualitative chemicals are present in plants in relatively low concentrations (often less
than 2% dry weight), and are not dosage dependent. They are usually small, water soluble molecules, and
therefore can be rapidly synthesized, transported and stored with relatively little energy cost to the plant.
Qualitative allelochemicals are usually effective against non-adapted specialists and generalist herbivores.
Quantitative chemicals are those that are present in high concentration in plants (5 – 40% dry weight)
and are equally effective against all specialists and generalist herbivores. Most quantitative metabolites are
digestibility reducers that make plant cell walls indigestible to animals. The effects of quantitative metabolites
are dosage dependent and the higher these chemicals’ proportion in the herbivore’s diet, the less nutrition
the herbivore can gain from ingesting plant tissues. Because they are typically large molecules, these
defenses are energetically expensive to produce and maintain, and often take longer to synthesise and
transport.[14]
The geranium, for example, produces a unique chemical compound in its petals to defend itself from
Japanese beetles. Within 30 minutes of ingestion the chemical paralyzes the herbivore. While the chemical
usually wears off within a few hours, during this time the beetle is often consumed by its own predators.[2]
• See Toxalbumin
[edit] Types of chemical defenses
Plants have evolved many secondary metabolites involved in plant defense, which are collectively
known as antiherbivory compounds and can be classified into three sub-groups: nitrogen compounds
(including alkaloids, cyanogenic glycosides and glucosinolates), terpenoids, and phenolics.[15]
Alkaloids are derived from various amino acids. Over 3000 known alkaloids exist, examples include
nicotine, caffeine, morphine, colchicine, ergolines, strychnine, and quinine.[16] Alkaloids have
pharmacological effects on humans and other animals. Some alkaloids can inhibit or activate enzymes, or
alter carbohydrate and fat storage by inhibiting the formation phosphodiester bonds involved in their
breakdown.[17] Certain alkaloids bind to nucleic acids and can inhibit synthesis of proteins and affect DNA
repair mechanisms. Alkaloids can also affect cell membrane and cytoskeletal structure causing the cells to
weaken, collapse, or leak, and can affect nerve transmission.[18] Although alkaloids act on a diversity of
metabolic systems in humans and other animals, they almost uniformly invoke an aversively bitter taste.[19]
Cyanogenic glycosides are stored in inactive forms in plant vacuoles. They become toxic when
herbivores eat the plant and break cell membranes allowing the glycosides to come into contact with
enzymes in the cytoplasm releasing hydrogen cyanide which blocks cellular respiration.[20] Glucosinolates
are activated in much the same way as cyanogenic glucosides, and the products can cause gastroenteritis,
salivation, diarrhea, and irritation of the mouth.[19]
The terpenoids, sometimes referred to as isoprenoids, are organic chemicals similar to terpenes,
derived from five-carbon isoprene units. There are over 10,000 known types of terpenoids.[21] Most are
multicyclic structures which differ from one another in both functional groups, and in basic carbon skeletons.
[22] Monoterpenoids, continuing 2 isoprene units, are volatile essential oils such as citronella, limonene,
menthol, camphor, and pinene. Diterpenoids, 4 isoprene units, are widely distributed in latex and resins, and
can be quite toxic. Diterpenes are responsible for making Rhododendron leaves poisonous. Plant steroids
and sterols are also produced from terpenoid precursors, including vitamin D, glycosides (such as digitalis)
and saponins (which lyse red blood cells of herbivores).[23]
Phenolics, sometimes called phenols, consist of an aromatic 6-carbon ring bonded to a hydroxy
group. Some phenols have antiseptic properties, while others disrupt endocrine activity. Phenolics range
from simple tannins to the more complex flavonoids that give plants much of their red, blue, yellow, and white
pigments. Complex phenolics called polyphenols are capable of producing many different types of effects on
humans, including antioxidant properties. Some examples of phenolics used for defense in plants are: lignin,
silymarin and cannabinoids.[24] Condensed tannins, polymers composed of 2 to 50 (or more) flavonoid
molecules, inhibit herbivore digestion by binding to consumed plant proteins and making them more difficult
for animals to digest, and by interfering with protein absorption and digestive enzymes.[25] Silica and lignins,
which are completely indigestible to animals, grind down insect mandibles (appendages necessary for
feeding).
In addition to the three larger groups of substances mentioned above, fatty acid derivates, amino
acids and even peptides[26] are used as defence. The cholinergic toxine, cicutoxin of water hemlock, is an
polyyne derived from the fatty acid metabolism.[27] β-N-Oxalyl-L-α,β-diaminopropionic acid as simple amino
acid is used by the sweet pea which leads also to intoxication in humans.[28] The synthesis of fluoroacetate
in several plants is an example for the use of small molecules to disturb the metabolism of the herbivore, in
this case the citric acid cycle.[29]
[edit] Mechanical defenses
The thorns on the stem of this raspberry plant, serve as a mechanical defense against herbivory.
Plants have many external structural defenses that discourage herbivory.[30] Depending on the
herbivore’s physical characteristics (i.e. size and defensive armor), plant structural defenses on stems and
leaves can deter, injure, or kill the grazer. Some defensive compounds are produced internally but are
released onto the plant’s surface; for example, resins, lignins, silica, and wax cover the epidermis of
terrestrial plants and alter the texture of the plant tissue. The leaves of holly plants, for instance, are very
smooth and slippery making feeding difficult. Some plants produce gummosis or sap that traps insects.
A plant's leaves and stem may be covered with sharp prickles, spines, thorns, or trichomes- hairs on
the leaf often with barbs, sometimes containing irritants or poisons. Plant structural features like spines and
thorns reduce feeding by large ungulate herbivores (e.g. kudu, impala, and goats) by restricting the
herbivores' feeding rate, or by wearing down the molars as in pears.[31] The structure of a plant, its
branching and leaf arrangement may also be evolved to reduce herbivore impact. The shrubs of New
Zealand have evolved special wide branching adaptations believed to be a response to browsing birds such
as the moas.[32] Similarly, African Acacias have long spines low in the canopy, but very short spines high in
the canopy, which is comparatively safe from herbivores such as giraffes.[33][34]
Coconut palms protect their fruit by surrounding it with multiple layers of armour.
Trees such as coconut and other palms, may protect their fruit by multiple layers of armour, needing
efficient tools to break through to the seed contents, and special skills to climb the tall and relatively smooth
trunk.
[edit] Thigmonasty
Thigmonastic movements, those that occur in response to touch, are used as a defense in some
plants. The leaves of the sensitive plant, Mimosa pudica, close up rapidly in response to direct touch,
vibration, or even electrical and thermal stimuli. The proximate cause of this mechanical response is an
abrupt change in the turgor pressure in the pulvini at the base of leaves resulting from osmotic phenomena.
This is then spread via both electrical and chemical means through the plant; only a single leaflet need be
disturbed.[35]
This response lowers the surface area available to herbivores, which are presented with the
underside of each leaflet, and results in a wilted appearance. It may also physically dislodge small
herbivores, such as insects.
[edit] Mimicry and camouflage

Some plants mimic the presence of insect eggs on their leaves, dissuading insect species from
laying their eggs there. Because female butterflies are less likely to lay their eggs on plants that already have
butterfly eggs, some species of neotropical vines of the genus Passiflora (Passion flowers) contain physical
structures resembling the yellow eggs of Heliconius butterflies on their leaves, which discourage oviposition
by butterflies.[36]
[edit] Indirect defenses
The large thorn-like stipules of Acacia collinsii are hollow and afford shelter for ants, which in return
protect the plant against herbivores.
Another category of plant defenses are those features that indirectly protect the plant by enhancing
the probability of attracting the natural enemies of herbivores. Such an arrangement is known as mutualism,
in this case of the "enemy of my enemy" variety. One such feature are semiochemicals, given off by plants.
Semiochemicals are a group of volatile organic compounds involved in interactions between organisms. One
group of semiochemicals are allelochemicals; consisting of allomones, which play a defensive role in
interspecies communication, and kairomones, which are used by members of higher trophic levels to locate
food sources. When a plant is attacked it releases allelochemics containing an abnormal ratio of volatiles.[37]
[38] Predators sense these volatiles as food cues, attracting them to the damaged plant, and to feeding
herbivores. The subsequent reduction in the number of herbivores confers a fitness benefit to the plant and
demonstrates the indirect defensive capabilities of semiochemicals. Induced volatiles also have drawbacks,
however; some studies have suggested that these volatiles also attract herbivores.[37]
Plants also provide housing and food items for natural enemies of herbivores, known as “biotic”
defense mechanisms, as a means to maintain their presence. For example, trees from the genus Macaranga
have adapted their thin stem walls to create ideal housing for an ant species (genus Crematogaster), which,
in turn, protects the plant from herbivores.[39] In addition to providing housing, the plant also provides the ant
with its exclusive food source; from the food bodies produced by the plant. Similarly, some Acacia tree
species have developed thorns that are swollen at the base, forming a hollowing structure that acts as
housing. These Acacia trees also produce nectar in extrafloral nectaries on their leaves as food for the ants.
[40]
Most plants have endophytes, microbial organisms that live within them. While some cause disease,
others protect plants from herbivores and pathogenic microbes. Endophytes can help the plant by producing
toxins harmful to other organisms that would attack the plant, such as alkaloid producing fungi which are
common in grasses such as tall fescue (Festuca arundinacea).[35]
[edit] Leaf shedding and colour

There have been suggestions that leaf shedding may be a response that provides protection against
diseases and certain kinds of pests such as leaf miners and gall forming insects.[41] Other responses such
as the change of leaf colours prior to fall have also been suggested as adaptations that may help undermine
the camouflage of herbivores.[42] Autumn leaf color has also been suggested to act as an honest warning
signal of defensive commitment towards insect pests that migrate to the trees in autumn.[43][44]
[edit] Costs and benefits

Defensive structures and chemicals are costly as they require resources that could otherwise be
used by plants to maximize growth and reproduction. Many models have been proposed to explore how and
why some plants make this investment in defenses against herbivores.
[edit] Optimal defense hypothesis

The optimal defense hypothesis attempts to explain how the kinds of defenses a particular plant
might use reflect the threats each individual plant faces.[45] This model considers three main factors,
namely: risk of attack, value of the plant part, and the cost of defense.[46][47]
The first factor determining optimal defense is risk: how likely is it that a plant or certain plant parts
will be attacked? This is also related to the plant apparency hypothesis, which states that a plant will invest
heavily in broadly effective defenses when the plant is easily found by herbivores.[48] Examples of apparent
plants that produce generalized protections include long-living trees, shrubs, and perennial grasses.[48]
Unapparent plants, such as short-lived plants of early successional stages, on the other hand, preferentially
invest in small amounts of qualitative toxins that are effective against all but the most specialized herbivores.
[48]
The second factor is the value of protection: would the plant be less able to survive and reproduce
after removal of part of its structure by a herbivore? Not all plant parts are of equal evolutionary value, thus
valuable parts contain more defenses. A plant’s stage of development at the time of feeding also affects the
resulting change in fitness. Experimentally, the fitness value of a plant structure is determined by removing
that part of the plant and observing the effect.[49] In general, reproductive parts are not as easily replaced as
vegetative parts, terminal leaves have greater value than basal leaves, and the loss of plant parts mid-
season has a greater negative effect on fitness than removal at the beginning or end of the season.[50][51]
Seeds in particular tend to be very well protected. For example, the seeds of many edible fruits and nuts
contain cyanogenic glycosides such as amygdalin. This results from the need to balance the effort needed to
make the fruit attractive to animal dispersers while ensuring that the seeds are not destroyed by the animal.
[52][53]
The final consideration is cost: how much will a particular defensive strategy cost a plant in energy
and materials? This is particularly important, as energy spent on defense cannot be used for other functions,
such as reproduction and growth. The optimal defense hypothesis predicts that plants will allocate more
energy towards defense when the benefits of protection outweigh the costs, specifically in situations where
there is high herbivore pressure.[54]
[edit] Carbon:nutrient balance hypothesis
The carbon:nutrient balance hypothesis, also known as the environmental constraint hypothesis,
states that the various types of plant defenses are responses to variations in the levels of nutrients in the
environment.[55][56] This hypothesis predicts the Carbon/Nitrogen ratio in plants determines which
secondary metabolites will be synthesized. For example, plants growing in nitrogen-poor soils will use
carbon-based defenses (mostly digestibility reducers), while those growing in low-carbon environments (such
as shady conditions) are more likely to produce nitrogen-based toxins. The hypothesis further predicts that
plants can change their defences in response to changes in nutrients. For example, if plants are grown in
low-nitrogen conditions, then these plants will implement a defensive strategy composed of constitutive
carbon-based defenses. If nutrient levels subsequently increase, by for example the addition of fertilizers,
these carbon-based defenses will decrease.
[edit] Growth rate hypothesis

The growth rate hypothesis, also known as the resource availability hypothesis, states that defense
strategies are determined by the inherent growth rate of the plant, which is in turn determined by the
resources available to the plant. A major assumption is that available resources are the limiting factor in
determining the maximum growth rate of a plant species. This model predicts that the level of defense
investment will increase as the potential of growth decreases.[57] Additionally, plants in resource-poor areas,
with inherently slow-growth rates, tend to have long-lived leaves and twigs, and the loss of plant appendages
may result in a loss of scarce and valuable nutrients.[58]
A recent test of this model involved a reciprocal transplants of seedlings of 20 species of trees
between clay soils (nutrient rich) and white sand (nutrient poor) to determine whether trade-offs between
growth rate and defenses restrict species to one habitat. Seedlings originating from the nutrient-poor sand
had higher levels of constitutive carbon-based defenses, but when they were transplanted into nutrient-rich
clay soils, they experienced higher mortality from herbivory. These finding suggest that defensive strategies
limit the habitats of some plants.[59]
[edit] Growth-differentiation balance hypothesis

The growth-differentiation balance hypothesis states that plant defenses are a result of a tradeoff
between “growth-related processes” and “differentiation-related processes” in different environments.[60]
Differentiation-related processes are defined as “processes that enhance the structure or function of existing
cells (i.e. maturation and specialization).”[45] A plant will produce chemical defenses only when energy is
available from photosynthesis, and plants with the highest concentrations of secondary metabolites are the
ones with an intermediate level of available resources.[60] The GDBH also accounts for tradeoffs between
growth and defense over a resource availability gradient. In situations where resources (e.g. water and
nutrients) limit photosynthesis, carbon supply is predicted to limit both growth and defense. As resource
availability increases, the requirements needed to support photosynthesis are met, allowing for accumulation
of carbohydrate in tissues. As resources are not sufficient to meet the large demands of growth, these carbon
compounds can instead be partitioned into the synthesis of carbon based secondary metabolites (phenolics,
tannins, etc.). In environments where the resource demands for growth are met, carbon is allocated to rapidly
dividing meristems (high sink strength) at the expense of secondary metabolism. Thus rapidly growing plants
are predicted to contain lower levels of secondary metabolites and vice versa. In addition, the tradeoff
predicted by the GDBH may change over time, as evidenced by a recent study on Salix spp. Much support
for this hypothesis is present in the literature, and some scientists consider the GDBH the most mature of the
plant defense hypotheses.
[edit] Importance to humans
[edit] Agriculture
The variation of plant susceptibility to pests was probably known even in the early stages of
agriculture in humans. In historic times, the observation of such variations in susceptibility have provided
solutions for major socio-economic problems. The grape phylloxera was introduced from North America to
France in 1860 and in 25 years it destroyed nearly a third (100,000 km²) of the French grape yards. Charles
Valentine Riley noted that the American species Vitis labrusca was resistant to Phylloxera. Riley, with J. E.
Planchon, helped save the French wine industry by suggesting the grafting of the susceptible but high quality
grapes onto Vitis labrusca root stocks.[61] The formal study of plant resistance to herbivory was first covered
extensively in 1951 by Reginald (R.H.) Painter, who is widely regarded as the founder of this area of
research, in his book Plant Resistance to Insects.[62] While this work pioneered further research in the US,
the work of Chesnokov was the basis of further research in the USSR.[63]
Fresh growth of grass is sometimes high in prussic acid content and can cause poisoning of grazing
livestock. The production of cyanogenic chemicals in grasses is primarily a defense against herbivores.[64]
[65]
The human innovation of cooking may have been particularly helpful in overcoming many of the
defensive chemicals of plants. Many enzyme inhibitors in cereal grains and pulses, such as trypsin inhibitors
prevalent in pulse crops, are denatured by cooking, making them digestible.[66][67]
It has been known since the late 17th century that plants contain noxious chemicals which are
avoided by insects. These chemicals have been used by man as early insecticides; in 1690 nicotine was
extracted from tobacco and used as a contact insecticide. In 1773, insect infested plants were treated with
nicotine fumigation by heating tobacco and blowing the smoke over the plants.[68] The flowers of
Chrysanthemum species contain pyrethrin which is a potent insecticide. In later years, the applications of
plant resistance became an important area of research in agriculture and plant breeding, particularly because
they can serve as a safe and low-cost alternative to the use of pesticides.[69] The important role of
secondary plant substances in plant defense was described in the late 1950s by Vincent Dethier and G.S.
Fraenkel.[11][70] The use of botanical pesticides is widespread and notable examples include Azadirachtin
from the neem (Azadirachta indica), d-Limonene from Citrus species, Rotenone from Derris, Capsaicin from
Chili Pepper and Pyrethrum.[71]
Natural materials found in the environment also induce plant resistance as well.[72] Chitosan derived
from chitin induce a plant's natural defense response against pathogens, diseases and insects including cyst
nematodes, both are approved as an biopesticide by the EPA to reduce the dependence on toxic pesticides.
The selective breeding of crop plants often involves selection against the plant's intrinsic resistance
strategies. This makes crop plant varieties particularly susceptible to pests unlike their wild relatives. In
breeding for host-plant resistance, it is often the wild relatives that provide the source of resistance genes.
These genes are incorporated using conventional approaches to plant breeding, but have also been
augmented by recombinant techniques, which allow introduction of genes from completely unrelated
organisms. The most famous transgenic approach is the introduction of genes from the bacterial species,
Bacillus thuringiensis, into plants. The bacterium produces proteins that, when ingested, kill lepidopteran
caterpillars. The gene encoding for these highly toxic proteins, when introduced into the host plant genome,
confers resistance against caterpillars, when the same toxic proteins are produced within the plant. This
approach is controversial, however, due to the possibility of ecological and toxicological side effects.[73]
[edit] Pharmaceutical
Illustration from the 15th century manuscript Tacuinum Sanitatis detailing the beneficial and harmful
properties of Mandrakes.
Many currently available pharmaceuticals are derived from the secondary metabolites plants use to
protect themselves from herbivores, including opium, aspirin, cocaine, and atropine.[74] These chemicals
have evolved to affect the biochemistry of insects in very specific ways. However, many of these biochemical
pathways are conserved in vertebrates, including humans, and the chemicals act on human biochemistry in
ways similar to that of insects. It has therefore been suggested that the study of plant-insect interactions may
help in bioprospecting.[75]
There is evidence that humans began using plant alkaloids in medical preparations as early as 3000
B.C.[17] Although the active components of most medicinal plants have been isolated only recently
(beginning in the early 19th century) these substances have been used as drugs throughout the human
history in potions, medicines, teas and as poisons. For example, to combat herbivory by the larvae of some
Lepidoptera species, Cinchona trees produce a variety of alkaloids, the most familiar of which is quinine.
Quinine is extremely bitter, making the bark of the tree quite unpalatable, it is also an anti-fever agent, known
as Jesuit's bark, and is especially useful in treating malaria.[76]
Throughout history mandrakes (Mandragora officinarum) have been highly sought after for their
reputed aphrodisiac properties. However, the roots of the mandrake plant also contain large quantities of the
alkaloid scopolamine, which, at high doses, acts as a central nervous system depressant, and makes the
plant highly toxic to herbivores. Scopolamine was later found to be medicinal use in pain management before
and during labor; in smaller doses it is used to prevent motion sickness.[77] One of the most well-known
medicinally valuable terpenes is an anticancer drug, taxol, isolated from the bark of the Pacific yew, Taxus
brevifolia, in the early 1960s.[78]
[edit] Biological pest control

Repellent companion planting, defensive live fencing hedges, and "obstructive-repellent"
interplanting, with host-plant resistance species as beneficial 'biological control agents' is a technique in
biological pest control programs for: organic gardening, wildlife gardening, sustainable gardening, and
sustainable landscaping; in organic farming and sustainable agriculture; and in restoration ecology methods
for habitat restoration projects.
[edit] See also
• Alarm signal#Other • List of repellent • Raphide
alarm signals plants • Plant
• Aposematism • List of pest- disease resistance
• Chemical ecology regulating plants • Pollination
• Canavanine • List of beneficial • Phytoalexin
• Druse (botany) weeds • Rapid plant
• Laticifer • List of movement
• Lectin companion plants • Seed
predation
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54.^ Pennings, Steven C.; Erin L. Siska, Mark D. Bertness (May 2001). "Latitudinal differences
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57.^ Colley, Phyllis D.; John P. Bryant, and F. Stuart Chapin III (1985). "Resource availability
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58.^ Chapin, F. Stuart, III (1980). "The Mineral Nutrition of Wild Plants". Annual Review of
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specialization by trees in Amazonian forests". Science 305 (5684): 663–5.
doi:10.1126/science.1098982. PMID 15286371.
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F. Wareing and I. D. J. Phillips. Growth and differentiation in plants. New York: Pergamon Press.
pp. 1–17. ISBN 0-08-026351-8.
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63.^ Chesnokov, Pavel G. (1953). Methods of Investigating Plant Resistance to Pests .
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64.^ Gleadow, Roslyn M.; Ian E. Woodrow (2002). "Constraints on effectiveness of cyanogenic
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65.^ Vough, Lester R.; E. Kim Cassel (July 2002). "Prussic Acid Poisoning of Livestock: Causes
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69.^ Michael Smith, C. (2005). Plant Resistance to Arthropods: Molecular and Conventional
Approaches. Berlin: Springer. ISBN 1-4020-3701-5.
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71.^ Russ, Karen. "Less toxic insecticides". Clemson University Home & Garden Information
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[edit] Further references

• Robert S. Fritz and Ellen L. Simms (editors) (1992). Plant resistance to herbivores and
pathogens: ecology, evolution, and genetics. Chicago: University of Chicago Press. ISBN 0-226-
26553-6. http://books.google.com/?id=NkF0xuz664gC&dq=Herbivores:
+Their+interaction+with+secondary+plant.
• Hartley, Sue (2010) The 300 Million Years War: Plant Biomass v Herbivores Royal Institution
Christmas Lecture.
• Howe, H. F., and L. C. Westley. 1988. Ecological relationships of plants and animals. Oxford
University Press, Oxford, UK.
• Pierre Jolivet, (1998). Interrelationship Between Insects and Plants . Boca Raton: CRC.
ISBN 1-57444-052-7. http://books.google.com/?id=J5sTAB_mymwC&dq=Herbivores:
• Richard Karban and Ian T. Baldwin (1997). Induced responses to herbivory. Chicago:
University of Chicago Press. ISBN 0-226-42495-2. http://books.google.com/?
id=thHTfR3ICZAC&dq=Herbivores:+Their+interaction+with+secondary+plant.
• Martin R. Speight, Mark D. Hunter, Allan D. Watt (1999). Ecology of insects: concepts and
applications. Oxford: Blackwell Science. ISBN 0-86542-745-3. http://books.google.com/?
id=JiO_Nnk5Y8AC&pg=PP1&lpg=PP1&dq=%22Insect+ecology%22.
• John N. Thompson (1994). The coevolutionary process. Chicago: University of Chicago
Press. ISBN 0-226-79759-7. http://books.google.com/?id=InCAChmWM1QC&dq=Herbivores:
• Wiens, D. (1978). "Mimicry in plants". Evolutionary Biology 11: 365–403.

• Bruce A. Kimball Evolutionary Plant Defense Strategies Life Histories and Contributions to
Future Generations
• Plant Defense Systems & Medicinal Botany
• Herbivore Defenses of Senecio viscosus L.
[hide] Modelling ecosystems - trophic components

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plankton · Trophic cascade · Trophic level ·
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r against herbivores · Predator avoidance in
schooling fish
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Categories: Herbivory | Plant physiology | Biological pest control | Ecological restoration | Habitat
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W000
Fern

This article is about the group of pteridophyte plants. For other uses, see Fern (disambiguation).
Ferns (Pteridophyta)
Temporal range: Mid Devonian[1]—Recent
PreЄ
g
Athyrium filix-femina unrolling young frond
Scientific classification
Kingdom: Plantae
Division: Pteridophyta
Classes[2]
• †Cladoxylopsida
• Psilotopsida
• Equisetopsida (alias Sphenopsida)
• Marattiopsida
• Polypodiopsida (alias Pteridopsida,
Filicopsida)
A fern is any one of a group of about 12,000 species of plants.[3] Unlike mosses, they have xylem
and phloem (making them vascular plants). They have stems, leaves, and roots like other vascular plants.
Ferns do not have either seeds or flowers (they reproduce via spores).
By far the largest group of ferns are the leptosporangiate ferns, but ferns as defined here (also called
monilophytes) include horsetails, whisk ferns, marattioid ferns, and ophioglossoid ferns. The term
pteridophyte also refers to ferns (and possibly other seedless vascular plants; see classification section
below). A pteridologist is a specialist in the study of ferns and lycophytes.
Ferns first appear in the fossil record 360 million years ago in the Carboniferous but many of the
current families and species did not appear until roughly 145 million years ago in the late Cretaceous (after
flowering plants came to dominate many environments).
Ferns are not of major economic importance, but some are grown or gathered for food, as
ornamental plants, or for remediating contaminated soils. Some are significant weeds. They also featured in
mythology, medicine, and art.
Contents
[hide]
• 1 Life cycle
• 2 Fern ecology
• 3 Fern structure
• 4 Evolution and classification
• 5 Smith's Classification
• 6 Uses
• 7 Cultural connotations
• 8 Misunderstood names
• 9 Gallery
• 10 See also
• 11 References
[edit] Life cycle
Gametophyte (thalloid green mass) and sporophyte (ascendent frond) of Onoclea sensibilis
Ferns are vascular plants differing from lycophytes by having true leaves (megaphylls). They differ
from seed plants (gymnosperms and angiosperms) in their mode of reproduction—lacking flowers and seeds.
Like all other vascular plants, they have a life cycle referred to as alternation of generations, characterized by
a diploid sporophytic and a haploid gametophytic phase. Unlike the gymnosperms and angiosperms, the
ferns' gametophyte is a free-living organism.
Life cycle of a typical fern:
1. A sporophyte (diploid) phase produces haploid spores by meiosis.
2. A spore grows by mitosis into a gametophyte, which typically consists of a photosynthetic
prothallus.
3. The gametophyte produces gametes (often both sperm and eggs on the same prothallus) by
mitosis.
4. A mobile, flagellate sperm fertilizes an egg that remains attached to the prothallus.
5. The fertilized egg is now a diploid zygote and grows by mitosis into a sporophyte (the typical
"fern" plant).
[edit] Fern ecology
Ferns at Muir Woods, California

The stereotypic image of ferns growing in moist shady woodland nooks is far from being a complete
picture of the habitats where ferns can be found growing. Fern species live in a wide variety of habitats, from
remote mountain elevations, to dry desert rock faces, to bodies of water or in open fields. Ferns in general
may be thought of as largely being specialists in marginal habitats, often succeeding in places where various
environmental factors limit the success of flowering plants. Some ferns are among the world's most serious
weed species, including the bracken fern growing in the Scottish highlands, or the mosquito fern ( Azolla)
growing in tropical lakes, both species forming large aggressively spreading colonies. There are four
particular types of habitats that ferns are found in: moist, shady forests; crevices in rock faces, especially
when sheltered from the full sun; acid wetlands including bogs and swamps; and tropical trees, where many
species are epiphytes (something like a quarter to a third of all fern species[4]).
Many ferns depend on associations with mycorrhizal fungi. Many ferns only grow within specific pH
ranges; for instance, the climbing fern (Lygodium) of eastern North America will only grow in moist, intensely
acid soils, while the bulblet bladder fern ( Cystopteris bulbifera), with an overlapping range, is only found on
limestone.
The spores are rich in lipids, protein and calories, so some vertebrates eat these. The European
woodmouse (Apodemus sylvaticus) has been found to eat the spores of Culcita macrocarpa and the bullfinch
(Pyrrhula murina) and the New Zealand lesser short-tailed bat (Mystacina tuberculata) also eat fern spores.
[5]
[edit] Fern structure

Ferns at the Royal Melbourne Botanical Gardens
Tree ferns, probably Dicksonia antarctica, growing in Nunniong, Australia

Like the sporophytes of seed plants, those of ferns consist of:
• Stems: Most often an underground creeping rhizome, but sometimes an above-ground
creeping stolon (e.g., Polypodiaceae), or an above-ground erect semi-woody trunk (e.g.,
Cyatheaceae) reaching up to 20 m in a few species (e.g., Cyathea brownii on Norfolk Island and
Cyathea medullaris in New Zealand).
• Leaf: The green, photosynthetic part of the plant. In ferns, it is often referred to as a frond, but
this is because of the historical division between people who study ferns and people who study seed
plants, rather than because of differences in structure. New leaves typically expand by the unrolling
of a tight spiral called a crozier or fiddlehead. This uncurling of the leaf is termed circinate vernation.
Leaves are divided into three types:
• Trophophyll: A leaf that does not produce spores, instead only producing sugars by
photosynthesis. Analogous to the typical green leaves of seed plants.
• Sporophyll: A leaf that produces spores. These leaves are analogous to the scales of
pine cones or to stamens and pistil in gymnosperms and angiosperms, respectively. Unlike
the seed plants, however, the sporophylls of ferns are typically not very specialized, looking
similar to trophophylls and producing sugars by photosynthesis as the trophophylls do.
• Brophophyll: A leaf that produces abnormally large amounts of spores. Their leaves
are also larger than the other leaves but bear a resemblance to trophophylls.
• Roots: The underground non-photosynthetic structures that take up water and nutrients from
soil. They are always fibrous and are structurally very similar to the roots of seed plants.
The gametophytes of ferns, however, are very different from those of seed plants. They typically
consist of:
• Prothallus: A green, photosynthetic structure that is one cell thick, usually heart or kidney
shaped, 3–10 mm long and 2–8 mm broad. The prothallus produces gametes by means of:
• Antheridia: Small spherical structures that produce flagellate sperm.
• Archegonia: A flask-shaped structure that produces a single egg at the bottom,
reached by the sperm by swimming down the neck.
• Rhizoids: root-like structures (not true roots) that consist of single greatly elongated cells,
water and mineral salts are absorbed over the whole structure. Rhizoids anchor the prothallus to the
soil.
One difference between sporophytes and gametophytes might be summed up by the saying that
"Nothing eats ferns, but everything eats gametophytes." This is an over-simplification, but it is true that
gametophytes are often difficult to find in the field because they are far more likely to be food than are the
sporophytes.
[edit] Evolution and classification

Ferns first appear in the fossil record in the early-Carboniferous period. By the Triassic, the first
evidence of ferns related to several modern families appeared. The "great fern radiation" occurred in the late-
Cretaceous, when many modern families of ferns first appeared.
One problem with fern classification is the problem of cryptic species. A cryptic species is a species
that is morphologically similar to another species, but differs genetically in ways that prevent fertile
interbreeding. A good example of this is the currently designated species Asplenium trichomanes, the
maidenhair spleenwort. This is actually a species complex that includes distinct diploid and tetraploid races.
There are minor but unclear morphological differences between the two groups, which prefer distinctly
differing habitats. In many cases such as this, the species complexes have been separated into separate
species, thus raising the number of overall fern species. Possibly many more cryptic species are yet to be
discovered and designated.
Ferns have traditionally been grouped in the Class Filices, but modern classifications assign them
their own phylum or division in the plant kingdom, called Pteridophyta, also known as Filicophyta. The group
is also referred to as Polypodiophyta, (or Polypodiopsida when treated as a subdivision of tracheophyta
(vascular plants), although Polypodiopsida sometimes refers to only the leptosporangiate ferns). The term
"pteridophyte" has traditionally been used to describe all seedless vascular plants, making it synonymous
with "ferns and fern allies". This can be confusing since members of the fern phylum Pteridophyta are also
sometimes referred to as pteridophytes. The study of ferns and other pteridophytes is called pteridology, and
one who studies ferns and other pteridophytes is called a pteridologist.
Traditionally, three discrete groups of plants have been considered ferns: two groups of
eusporangiate ferns—families Ophioglossaceae (adders-tongues, moonworts, and grape-ferns) and
Marattiaceae—and the leptosporangiate ferns. The Marattiaceae are a primitive group of tropical ferns with a
large, fleshy rhizome, and are now thought to be a sibling taxon to the main group of ferns, the
leptosporangiate ferns. Several other groups of plants were considered "fern allies": the clubmosses,
spikemosses, and quillworts in the Lycopodiophyta, the whisk ferns in Psilotaceae, and the horsetails in the
Equisetaceae. More recent genetic studies have shown that the Lycopodiophyta are more distantly related to
other vascular plants, having radiated evolutionarily at the base of the vascular plant clade, while both the
whisk ferns and horsetails are as much "true" ferns as are the Ophioglossoids and Marattiaceae. In fact, the
whisk ferns and Ophioglossoids are demonstrably a clade, and the horsetails and Marattiaceae are arguably
another clade. Molecular data—which remain poorly constrained for many parts of the plants' phylogeny —
have been supplemented by recent morphological observations supporting the inclusion of Equisetaceae
within the ferns, notably relating to the construction of their sperm, and peculiarities of their roots.[2]
However, there are still differences of opinion about the placement of the Equisetum species (see
Equisetopsida for further discussion). One possible means of treating this situation is to consider only the
leptosporangiate ferns as "true" ferns, while considering the other three groups as "fern allies". In practice,
numerous classification schemes have been proposed for ferns and fern allies, and there has been little
consensus among them.
A 2006 classification by Smith et al. is based on recent molecular systematic studies, in addition to
morphological data. Their phylogeny is a consensus of a number of studies, and is shown below (to the level
of orders).[2]
Trachaeophyta
euphyllophytes
ferns
Psilotopsida
Psilotales
Ophioglossales
Equisetopsida
Equisetales
Marattiopsida
Marattiales
Polypodiopsida
Osmundales
Hymenophyllales
Gleicheniales
Schizaeales
core
leptosporangiates
Salviniales
Cyatheales
Polypodiales
Their classification based on this phylogeny divides extant ferns into four classes:
• Psilotopsida (whisk ferns and ophioglossoid ferns), about 92 species[6]
• Equisetopsida (horsetails), about 15 species[6]
• Marattiopsida, about 150 species[6]
• Polypodiopsida (leptosporangiate ferns), over 9000 species[6]
The last group includes most plants familiarly known as ferns. Modern research supports older ideas
based on morphology that the Osmundaceae diverged early in the evolutionary history of the
leptosporangiate ferns; in certain ways this family is intermediate between the eusporangiate ferns and the
leptosporangiate ferns.
[edit] Smith's Classification

The complete classification scheme proposed by Smith et al. (2006) is shown below (alternative
names in brackets).[2]
• Class Psilotopsida
• Order Ophioglossales
• Family Ophioglossaceae (incl. Botrychiaceae, Helminthostachyaceae)
• Order Psilotales
• Family Psilotaceae (incl. Tmesipteridaceae)
• Class Equisetopsida [=Sphenopsida]
• Order Equisetales
• Family Equisetaceae
• Class Marattiopsida
• Order Marattiales
• Family Marattiaceae (incl. Angiopteridaceae, Christenseniaceae,
Danaeaceae, Kaulfussiaceae)
• Class Pteridopsida [=Filicopsida, Polypodiopsida]
• Order Osmundales
• Family Osmundaceae
• Order Hymenophyllales
• Family Hymenophyllaceae (incl. Trichomanaceae)
• Order Gleicheniales
• Family Gleicheniaceae (incl. Dicranopteridaceae, Stromatopteridaceae)
• Family Dipteridaceae (incl. Cheiropleuriaceae)
• Family Matoniaceae
• Order Schizaeales
• Family Lygodiaceae
• Family Anemiaceae (incl. Mohriaceae)
• Family Schizaeaceae
• Order Salviniales
• Family Marsileaceae (incl. Pilulariaceae)
• Family Salviniaceae (incl. Azollaceae)
• Order Cyatheales
• Family Thyrsopteridaceae
• Family Loxsomataceae
• Family Culcitaceae
• Family Plagiogyriaceae
• Family Cibotiaceae
• Family Cyatheaceae (incl. Alsophilaceae, Hymenophyllopsidaceae)
• Family Dicksoniaceae (incl. Lophosoriaceae)
• Family Metaxyaceae
• Order Polypodiales
Adiantum lunulatum from Family Pteridaceae
• Family Lindsaeaceae (incl. Cystodiaceae, Lonchitidaceae)
• Family Saccolomataceae
• Family Dennstaedtiaceae (incl. Hypolepidaceae, Monachosoraceae,
Pteridiaceae)
• Family Pteridaceae (incl. Pellaeaceae, Adiantaceae, Ceratopteridaceae,
Cryptogrammaceae)
• Family Aspleniaceae
• Family Thelypteridaceae
• Family Woodsiaceae (incl. Athyriaceae, Cystopteridaceae)
• Family Blechnaceae (incl. Stenochlaenaceae)
• Family Onocleaceae
• Family Dryopteridaceae (incl. Aspidiaceae, Bolbitidaceae,
Elaphoglossaceae, Hypodematiaceae, Peranemataceae)
• Family Oleandraceae
• Family Davalliaceae
• Family Lomariopsidaceae (incl. Nephrolepis)
• Family Polypodiaceae (incl. Drynariaceae, Grammitidaceae,
Gymnogrammitidaceae, Loxogrammaceae, Platyceriaceae, Pleurisoriopsidaceae)
• Family Tectariaceae
[edit] Uses
Ferns are not as important economically as seed plants but have considerable importance in some
societies. Some ferns are used for food, including the fiddleheads of bracken, Pteridium aquilinum, ostrich
fern, Matteuccia struthiopteris, and cinnamon fern, Osmunda cinnamomea. Diplazium esculentum is also
used by some tropical peoples as food. Tubers from the King Fern or para (Ptisana salicina) are a traditional
food in New Zealand and the South Pacific. Fern tubers were used for food 30,000 years ago in Europe.[7][8]
Fern tubers were used by the Guanches to make gofio in the Canary Islands. Licorice fern rhizomes were
chewed by the natives of the Pacific Northwest for their flavor.
Ferns of the genus Azolla are very small, floating plants that do not resemble ferns. Called mosquito
fern, they are used as a biological fertilizer in the rice paddies of southeast Asia, taking advantage of their
ability to fix nitrogen from the air into compounds that can then be used by other plants.
Many ferns are grown in horticulture as landscape plants, for cut foliage and as houseplants,
especially the Boston fern (Nephrolepis exaltata) and other members of the genus Nephrolepis. The Bird's
Nest Fern (Asplenium nidus) is also popular, as is the staghorn ferns (genus Platycerium). Perennial (also
known as hardy) ferns planted in gardens in the northern hemisphere also have a considerable following.
Several ferns are noxious weeds or invasive species, including Japanese climbing fern (Lygodium
japonicum), mosquito fern and sensitive fern (Onoclea sensibilis). Giant water fern (Salvinia molesta) is one
of the world's worst aquatic weeds. The important fossil fuel coal consists of the remains of primitive plants,
including ferns.
Ferns have been studied and found to be useful in the removal of heavy metals, especially arsenic,
from the soil. Other ferns with some economic significance include:
• Dryopteris filix-mas (male fern), used as a vermifuge, and formerly in the US Pharmacopeia;
also, this fern accidentally sprouting in a bottle resulted in Nathaniel Bagshaw Ward's 1829 invention
of the terrarium or Wardian case
• Rumohra adiantiformis (floral fern), extensively used in the florist trade
• Microsorum pteropus (Java fern), one of the most popular freshwater aquarium plants.
• Osmunda regalis (royal fern) and Osmunda cinnamomea (cinnamon fern), the root fiber
being used horticulturally; the fiddleheads of O. cinnamomea are also used as a cooked vegetable
• Matteuccia struthiopteris (ostrich fern), the fiddleheads used as a cooked vegetable in North
America
• Pteridium aquilinum or Pteridium esculentum (bracken), the fiddleheads used as a cooked
vegetable in Japan and are believed to be responsible for the high rate of stomach cancer in Japan.
It is also one of the world's most important agricultural weeds, especially in the British highlands, and
often poisons cattle and horses.
• Diplazium esculentum (vegetable fern), a source of food for some native societies
• Pteris vittata (brake fern), used to absorb arsenic from the soil
• Polypodium glycyrrhiza (licorice fern), roots chewed for their pleasant flavor
• Tree ferns, used as building material in some tropical areas
• Cyathea cooperi (Australian tree fern), an important invasive species in Hawaii
• Ceratopteris richardii, a model plant for teaching and research, often called C-fern
[edit] Cultural connotations
Blätter des Manns Walfarn. by Alois Auer, Vienna: Imperial Printing Office, 1853
Ferns figure in folklore, for example in legends about mythical flowers or seeds.[9] In Slavic folklore,
ferns are believed to bloom once a year, during the Ivan Kupala night. Although alleged to be exceedingly
difficult to find, anyone who sees a "fern flower" is thought to be guaranteed to be happy and rich for the rest
of their life. Similarly, Finnish tradition holds that one who finds the "seed" of a fern in bloom on Midsummer
night will, by possession of it, be guided and be able to travel invisibly to the locations where eternally blazing
Will o' the wisps called aarnivalkea mark the spot of hidden treasure. These spots are protected by a spell
that prevents anyone but the fern-seed holder from ever knowing their locations.[10]
"Pteridomania"' is a term for the Victorian era craze of fern collecting and fern motifs in decorative art
including pottery, glass, metals, textiles, wood, printed paper, and sculpture "appearing on everything from
christening presents to gravestones and memorials." The fashion for growing ferns indoors led to the
development of the Wardian case, a glazed cabinet that would exclude air pollutants and maintain the
necessary humidity.[11]
Barnsley fern created using chaos game, through an Iterated function system (IFS).
The dried form of ferns was also used in other arts, being used as a stencil or directly inked for use in
a design. The botanical work, The Ferns of Great Britain and Ireland , is a notable example of this type of
nature printing. The process, patented by the artist and publisher Henry Bradbury, impressed a specimen on
to a soft lead plate. The first publication to demonstrate this was Alois Auer's The Discovery of the Nature
Printing-Process.
[edit] Misunderstood names

Several non-fern plants are called "ferns" and are sometimes confused with true ferns. These
include:
• "Asparagus fern"—This may apply to one of several species of the monocot genus
Asparagus, which are flowering plants.
• "Sweetfern"—A flowering shrub of the genus Comptonia.
• "Air fern"—A group of animals called hydrozoan that are distantly related to jellyfish and
corals. They are harvested, dried, dyed green, and then sold as a "plant" that can "live on air". While
it may look like a fern, it is merely the skeleton of this colonial animal.
• "Fern bush"—Chamaebatiaria millefolium—a rose family shrub with fern-like leaves.
In addition, the book Where the Red Fern Grows has elicited many questions about the mythical "red
fern" named in the book. There is no such known plant, although there has been speculation that the oblique
grape-fern, Sceptridium dissectum, could be referred to here, because it is known to appear on disturbed
sites and its fronds may redden over the winter.
[edit] Gallery
Fern leaf, probably

Tree fern, probably T
Adiantum lunulatum Blechnum nudum
A tree fern Dicksonia antarctica Dicksonia
unrolling a new frond
U
"Filicinae" from Ernst Leaf of fern with spor
Unidentified tree Tree Fern Spores Rotorua,
Haeckel's Kunstformen der
fern in Oaxaca San Diego, CA
Natur, 1904
Ferns in one of
many natural Coast F
Nature prints in The Fern fronds
Redwood undergrowth forest can
Ferns of Great Britain and A young, newly-
settings Santa Cruz, CA. Franklin,
Ireland used fronds to formed fern frond
produce the plates
[edit] See also

• Fern spike
• Fiddlehead greens
• Pteridomania
[edit] References
1. ^ Wattieza, Stein, W. E., F. Mannolini, L. V. Hernick, E. Landling, and C. M. Berry. 2007.
"Giant cladoxylopsid trees resolve the enigma of the Earth's earliest forest stumps at Gilboa", Nature
(19 April 2007) 446:904–907.
2. ^ a b c d Smith, A.R.; Pryer, K.M.; Schuettpelz, E.; Korall, P.; Schneider, H.; Wolf, P.G. (2006).
"A classification for extant ferns". Taxon 55 (3): 705–731. doi:10.2307/25065646.
http://www.pryerlab.net/publication/fichier749.pdf. Retrieved 2008-02-12.
3. ^ Chapman, Arthur D. (2009). Numbers of Living Species in Australia and the World . Report
for the Australian Biological Resources Study. Canberra, Australia. September 2009.
http://www.environment.gov.au/biodiversity/abrs/publications/other/species-numbers/index.html
4. ^ Schuettpelz, Eric. "Fern Phylogeny Inferred from 400 Leptosporangiate Species and Three
Plastid Genes," contained in "The Evolution and Diversification of Epiphytic Ferns." Doctoral
dissertation, Duke University. 2007.
http://dukespace.lib.duke.edu/dspace/bitstream/10161/181/1/D_Schuettpelz_Eric_a_052007.pdf
5. ^ Walker, Matt (19 February 2010). "A mouse that eats ferns like a dinosaur". BBC Earth
News. http://news.bbc.co.uk/earth/hi/earth_news/newsid_8523000/8523825.stm. Retrieved 20
February 2010.
6. ^ a b c d Eric Schuettpelz (2007). "table 1". The evolution and diversification of epiphytic ferns.
Duke University PhD thesis.
http://dukespace.lib.duke.edu/dspace/bitstream/10161/181/1/D_Schuettpelz_Eric_a_052007.pdf
7. ^ "Stone Age humans liked their burgers in a bun", Sonia Van Gilder Cooke, New Scientist,
23 Oct. 2010, p. 18.
8. ^ "Thirty thousand-year-old evidence of plant food processing" by Anna Revedin et al.,
PNAS, published online Oct. 18, 2010.
9. ^ May, Lenore Wile (1978). "The economic uses and associated folklore of ferns and fern
allies". The Botanical Review 44 (4): 491–528. doi:10.1007/BF02860848
10.^ http://www.saunalahti.fi/~marian1/gourmet/season5a.htm
11.^ * Boyd, Peter D. A. (2002-01-02). Pteridomania - the Victorian passion for ferns. Revised:
web version. Antique Collecting 28, 6, 9–12.. http://www.peterboyd.com/pteridomania.htm. Retrieved
2007-10-02.
• Pryer, Kathleen M., Harald Schneider, Alan R. Smith, Raymond Cranfill, Paul G. Wolf, Jeffrey
S. Hunt and Sedonia D. Sipes. 2001. Horsetails and ferns are a monophyletic group and the closest
living relatives to seed plants. Nature 409: 618–622 (abstract here).
• Pryer, Kathleen M., Eric Schuettpelz, Paul G. Wolf, Harald Schneider, Alan R. Smith and
Raymond Cranfill. 2004. Phylogeny and evolution of ferns (monilophytes) with a focus on the early
leptosporangiate divergences. American Journal of Botany 91:1582–1598 (online abstract here).
• Moran, Robbin C. (2004). A Natural History of Ferns. Portland, OR: Timber Press. ISBN 0-
88192-667-1.
• Lord, Thomas R. (2006). Ferns and Fern Allies of Pennsylvania. Indiana, PA: Pinelands
Press. [1]

Wikispecies has information related to: Pteridophyta
Wikimedia Commons has media related to: Pteridophyta
• Tree of Life Web Project: Filicopsida

• A classification of the ferns and their allies
• A fern book bibliography
• Register of fossil Pteridophyta
• L. Watson and M.J. Dallwitz (2004 onwards). The Ferns (Filicopsida) of the British Isles.
• Ferns and Pteridomania in Victorian Scotland
• Non-seed plant images at bioimages.vanderbilt.edu
• "American Fern Society"
• "British Pteridological Society"
• Checklist of Ferns and Lycophytes of the World
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W000
Animal echolocation
A depiction of the ultrasound signals emitted by a bat, and the echo from a nearby object.
Echolocation, also called biosonar, is the biological sonar used by several animals, most notably
microchiropteran bats and odontocetes (toothed whales and dolphins), but has also been demonstrated in
simpler form in other groups such as shrews, one genus of megachiropteran bats (Rousettus) and two cave
dwelling bird groups, the so called cave swiftlets in the genus Aerodramus (formerly Collocalia) and the
unrelated Oilbird Steatornis caripensis. The term echolocation was coined by Donald Griffin, whose work with
Robert Galambos was the first to conclusively demonstrate its existence in bats in 1938.[1][2]. However, long
before that, the Italian 18th century scientist Lazzaro Spallanzani had, by means of a series of elaborate
experiments concluded that bats navigated by hearing and not vision[3]. Echolocation in odontocetes was not
properly described before two decades later, by Schevill and McBride[4].
Echolocating animals emit calls out to the environment and listen to the echoes of those calls that
return from various objects in the environment. They use these echoes to locate, range, and identify the
objects. Echolocation is used for navigation and for foraging (or hunting) in various environments.
Contents
[hide]
• 1 Basic principle
• 2 Bats
• 2.1 Calls and ecology
• 2.2 Acoustic features
• 2.2.1 FM Signal Advantages
• 2.2.2 CF signal advantages
• 2.2.3 Acoustic environments of FM and CF
signals
• 2.3 Neural mechanisms in the brain
• 2.4 Inner ear and primary sensory neurons
• 2.5 Inferior colliculus
• 2.6 Auditory cortex
• 3 Toothed whales
• 4 Oilbirds and swiftlets
• 5 Shrews and tenrecs
• 6 See also
• 7 References
[edit] Basic principle
Echolocation is the same as active sonar, using sounds made by the animal itself. Ranging is done
by measuring the time delay between the animal's own sound emission and any echoes that return from the
environment. The relative intensity of sound received at each ear as well as the time delay between arrival at
the two ears provide information about the horizontal angle (azimuth) from which the reflected sound waves
arrive.[5] Unlike some man-made sonars that relies on many extremely narrow beams and many receivers to
localize a target (multibeam sonar), animal echolocation has only one transmitter and two receivers (the
ears). Echolocating animals have two ears positioned slightly apart. The echoes returning to the two ears
arrive at different times and at different loudness levels, depending on the position of the object generating
the echoes. The time and loudness differences are used by the animals to perceive distance and direction.
With echolocation, the bat or other animal can see not only where it is going but also how big another animal
is, what kind of animal it is, and other features.
[edit] Bats
Spectrogram of Pipistrellus Bat vocalizations. Detail is shown as the pulses transition to a faster
repetition rate. The bat appears to use a hybrid pulse which combines a sharp falling frequency chirp with an
extended constant frequency tail. Such a waveform may offer combined benefits of range estimation as well
as Doppler shift detection. Spectrogram generated with Fatpigdog's PC based Real Time FFT Spectrum
Analyzer.
Pipistrellus Pulses
Recording of Pipistrellus
bat approaching its prey.
Problems listening to this file? See media help.

Microbats use echolocation to navigate and forage, often in total darkness. They generally emerge
from their roosts in caves, attics, or trees at dusk and hunt for insects into the night. Their use of echolocation
allows them to occupy a niche where there are often many insects (that come out at night since there are
fewer predators then) and where there is less competition for food, and where there are fewer other species
that may prey on the bats themselves.
Microbats generate ultrasound via the larynx and emit the sound through the open mouth or, much
more rarely, the nose. The latter is most pronounced in the horseshoe bats (Rhinolophus spp.). Microbat
calls (help·info) range in frequency from 14,000 to well over 100,000 Hz, mostly beyond the range of the
human ear (typical human hearing range is considered to be from 20 Hz to 20,000 Hz). Bats may estimate
the elevation of targets by interpreting the interference patterns caused by the echoes reflecting from the
tragus, a flap of skin in the external ear[6]. There are two hypotheses about the evolution of echolocation in
bats. The first suggests that laryngeal echolocation evolved twice in Chiroptera, once in Yangochiroptera and
once in the rhinolophoids.[7][8] The second proposes that laryngeal echolocation had a single origin in
Chiroptera, was subsequently lost in the family Pteropodidae (all megabats), and later evolved as a system
of tongue-clicking in the genus Rousettus.[9]
Individual bat species echolocate within specific frequency ranges that suit their environment and
prey types. This has sometimes been used by researchers to identify bats flying in an area simply by
recording their calls with ultrasonic recorders known as 'bat detectors'. However echolocation calls are not
always species specific and some bats overlap in the type of calls they use so recordings of echolocation
calls cannot be used to identify all bats. In recent years researchers in several countries have developed 'bat
call libraries' that contain recordings of local bat species that have been identified known as 'reference calls'
to assist with identification.
Since the 1970s there has been an ongoing controversy among researchers as to whether bats use
a form of processing known from radar termed coherent cross-correlation. Coherence means that the phase
of the echolocation signals is used by the bats, while cross-correlation just implies that the outgoing signal is
compared with the returning echoes in a running process. Today most - but not all - researchers believe that
they use cross-correlation, but in an incoherent form, termed a filter bank receiver.
When searching for prey they produce sounds at a low rate (10-20/sec). During the search phase the
sound emission is coupled to respiration, which is again coupled to the wingbeat. This coupling appears to
dramatically conserve energy as there is little to no additional energetic cost of echolocation to flying bats
(Speakman and Racey 1991). After detecting a potential prey item, microbats increase the rate of pulses,
ending with the terminal buzz, at rates as high as 200/sec. During approach to a detected target, the duration
of the sounds is gradually decreased, as is the energy of the sound.
[edit] Calls and ecology

Bats belonging to the suborder Microchiroptera (microbats) occupy a diverse set of ecological
conditions - they can be found living in environments as different as Europe and Madagascar, and hunting for
food sources as different as insects, frogs, nectar, fruit, and blood. Additionally, the characteristics of an
echolocation call are adapted to the particular environment, hunting behavior, and food source of the
particular bat. However, this adaptation of echolocation calls to ecological factors is constrained by the
phylogenetic relationship of the bats, leading to a process known as descent with modification, and resulting
in the diversity seen in the Microchiropteran suborder today. (Jones and Teeling 2006; Grinnell 1995; Zupanc
2004; Fenton 1995; Neuweiler 2003; Simmons and Stein 1980)
[edit] Acoustic features

Describing the diversity of bat echolocation calls requires examination of the frequency and temporal
features of the calls. It is the variations in these aspects that produce echolocation calls suited for different
acoustic environments and hunting behaviors. (Fenton 2005; Jones and Teeling 2006; Zupanc 2004;
Simmons and Stein 1980; Hiryu et al. 2007)
• Frequency Modulation and Constant Frequency: Echolocation calls can be composed of two
different types of frequency structures: frequency modulated (FM) sweeps, and constant frequency
(CF) tones. A particular call can consist of one, the other, or both structures. An FM sweep is a
broadband signal – that is, it contains a downward sweep through a range of frequencies. A CF tone
is a narrowband signal: the sound stays constant at one frequency throughout its duration.
• Intensity: Echolocation calls have been measured at intensities anywhere between 60 and
110 decibels. Certain microbat species can modify their call intensity mid-call, lowering the intensity
as they approach objects that reflect sound strongly. This prevents the returning echo from deafening
the bat (Hiryu et al. 2007). Additionally, the so-called "whispering bats" have adapted low-amplitude
echolocation so that their prey, moths, which are able to hear echolocation calls, are less able to
detect and avoid an oncoming bat (Fullard 1997).
• Harmonic composition: Calls can be composed of one frequency, or multiple frequencies
comprising a harmonic series. In the latter case, the call is usually dominated by a certain harmonic
("dominant" frequencies are those present at higher intensities than other harmonics present in the
call).
• Call duration: A single echolocation call (a call being a single continuous trace on a sound
spectrogram, and a series of calls comprising a sequence or pass) can last anywhere from 0.2 to 100
milliseconds in duration, depending on the stage of prey-catching behavior that the bat is engaged in.
For example, the duration of a call usually decreases when the bat is in the final stages of prey
capture – this enables the bat to call more rapidly without overlap of call and echo. Reducing duration
comes at the cost of having less total sound available for reflecting off objects and being heard by the
bat.
• Pulse interval: The time interval between subsequent echolocation calls (or pulses)
determines two aspects of a bat's perception. First, it establishes how quickly the bat's auditory
scene information is updated. For example, bats increase the repetition rate of their calls (that is,
decrease the pulse interval) as they home in on a target. This allows the bat to get new information
regarding the target's location at a faster rate when it needs it most. Secondly, the pulse interval
determines the maximum range that bats can detect objects. This is because bats can only keep
track of the echoes from one call at a time; as soon as they make another call they stop listening for
echoes from the previously made call (Wilson and Moss 2004). For example, a pulse interval of 100
ms (typical of a bat searching for insects) allows sound to travel in air roughly 34 meters so a bat can
only detect objects as far away as 17 meters (the sound has to travel out and back). With a pulse
interval of 5 ms (typical of a bat in the final moments of a capture attempt), the bat can only detect
objects up to 85 cm away. Therefore the bat constantly has to make a choice between getting new
information updated quickly and detecting objects far away.
[edit] FM Signal Advantages
Echolocation call produced by Pipistrellus pipistrellus, an FM bat. The ultrasonic call has been
"heterodyned" - multiplied by a constant frequency to produce frequency subtraction, and thus an audible
sound - by a bat detector. A key feature of the recording is the increase in the repetition rate of the call as the
bat nears its target - this is called the "terminal buzz".
The major advantage conferred by an FM signal is extremely precise range discrimination, or
localization, of the target. J.A. Simmons demonstrated this effect with a series of elegant experiments that
showed how bats using FM signals could distinguish between two separate targets even when the targets
were less than half a millimeter apart. This amazing ability is due to the broadband sweep of the signal,
which allows for better resolution of the time delay between the call and the returning echo, thereby
improving the cross correlation of the two. Additionally, if harmonic frequencies are added to the FM signal,
then this localization becomes even more precise. (Jones and Teeling 2006; Zupanc 2004; Simmons and
Stein 1980; Grinnell 1995)
One possible disadvantage of the FM signal is a decreased operational range of the call. Because
the energy of the call is spread out among many frequencies, the distance at which the FM-bat can detect
targets is limited (Fenton 1995). This is in part because any echo returning at a particular frequency can only
be evaluated for a brief fraction of a millisecond, as the fast downward sweep of the call does not remain at
any one frequency for long (Grinnell 1995).
[edit] CF signal advantages
The structure of a CF signal is adaptive in that it allows the CF-bat to detect both the velocity of a
target, and the fluttering of a target's wings as Doppler shifted frequencies. A Doppler shift is an alteration in
sound wave frequency, and is produced in two relevant situations: when the bat and its target are moving
relative to each other, and when the target's wings are oscillating back and forth. CF-bats must compensate
for Doppler shifts, lowering the frequency of their call in response to echoes of elevated frequency - this
ensures that the returning echo remains at the frequency to which the ears of the bat are most finely tuned.
The oscillation of a target's wings also produces amplitude shifts, which gives a CF-bat additional help in
distinguishing a flying target from a stationary one. (Schnitzler and Flieger 1983; Zupanc 2004; Simmons and
Stein 1980; Grinnell 1995; Neuweiler 2003; Jones and Teeling 2006)
Additionally, because the signal energy of a CF call is concentrated into a narrow frequency band,
the operational range of the call is much greater than that of an FM signal. This relies on the fact that echoes
returning within the narrow frequency band can be summed over the entire length of the call, which maintains
a constant frequency for up to 100 milliseconds (Grinnell 1995; Fenton 1995)
[edit] Acoustic environments of FM and CF signals

• FM: An FM component is excellent for hunting prey while flying in close, cluttered
environments. Two aspects of the FM signal account for this fact: the precise target localization
conferred by the broadband signal, and the short duration of the call. The first of these is essential
because in a cluttered environment, the bats must be able to resolve their prey from large amounts of
background noise. The 3D localization abilities of the broadband signal enable the bat to do exactly
that, providing it with what Simmons and Stein (1980) call a "clutter rejection strategy." This strategy
is further improved by the use of harmonics, which, as previously stated, enhance the localization
properties of the call. The short duration of the FM call is also best in close, cluttered environments
because it enables the bat to emit many calls extremely rapidly without overlap. This means that the
bat can get an almost continuous stream of information – essential when objects are close, because
they will pass by quickly – without confusing which echo corresponds to which call. (Neuweiler 2003;
Simmons and Stein 1980; Jones and Teeling 2006; Fenton 1995)
• CF: A CF component is often used by bats hunting for prey while flying in open, clutter-free
environments, or by bats that wait on perches for their prey to appear. The success of the former
strategy is due to two aspects of the CF call, both of which confer excellent prey-detection abilities.
First, the greater working range of the call allows bats to detect targets present at great distances – a
common situation in open environments. Second, the length of the call is also suited for targets at
great distances: in this case, there is a decreased chance that the long call will overlap with the
returning echo. The latter strategy is made possible by the fact that the long, narrowband call allows
the bat to detect Doppler shifts, which would be produced by an insect moving either towards or
away from a perched bat. (Neuweiler 2003; Simmons and Stein 1980; Jones and Teeling 2006;
Fenton 1995)
[edit] Neural mechanisms in the brain

Because bats use echolocation to orient themselves and to locate objects, their auditory systems are
adapted for this purpose, highly specialized for sensing and interpreting the stereotyped echolocation calls
characteristic of their own species. This specialization is evident from the inner ear up to the highest levels of
information processing in the auditory cortex.
[edit] Inner ear and primary sensory neurons
Both CF and FM bats have specialized inner ears which allow them to hear sounds in the ultrasonic
range, far outside the range of human hearing. Although in most other aspects, the bat's auditory organs are
similar to those of most other mammals, certain bats (horseshoe bats, Rhinolophus spp. and the moustached
bat, Pteronotus parnelii) with a constant frequency (CF) component to their call (known as high duty cycle
bats) do have a few additional adaptations for detecting the predominant frequency (and harmonics) of the
CF vocalization. These include a narrow frequency "tuning" of the inner ear organs, with an especially large
area responding to the frequency of the bat's returning echoes (Neuweiler 2003).
The basilar membrane within the cochlea contains the first of these specializations for echo
information processing. In bats that use CF signals, the section of membrane that responds to the frequency
of returning echoes is much larger than the region of response for any other frequency. For example, in
Rhinolophus ferrumequinum, the horseshoe bat, there is a disproportionately lengthened and thickened
section of the membrane that responds to sounds around 83 kHz, the constant frequency of the echo
produced by the bat's call. This area of high sensitivity to a specific, narrow range of frequency is known as
an "acoustic fovea" (Schuller and Pollack 1979).
Odontocetes (toothed whales and dolphins) have similar cochlear specializations to those found in
bats. Odontocetes also have the highest neural investment of any cochleae reported to date with ratios of
greater than 1500 ganglion cells/mm of basilar membrane.
Further along the auditory pathway, the movement of the basilar membrane results in the stimulation
of primary auditory neurons. Many of these neurons are specifically "tuned" (respond most strongly) to the
narrow frequency range of returning echoes of CF calls. Because of the large size of the acoustic fovea, the
number of neurons responding to this region, and thus to the echo frequency, is especially high (Carew
2001).
[edit] Inferior colliculus
In the Inferior colliculus, a structure in the bat's midbrain, information from lower in the auditory
processing pathway is integrated and sent on to the auditory cortex. As George Pollak and others showed in
a series of papers in 1977, the interneurons in this region have a very high level of sensitivity to time
differences, since the time delay between a call and the returning echo tells the bat its distance from the
target object. Especially interesting is that while most neurons respond more quickly to stronger stimuli,
collicular neurons maintain their timing accuracy even as signal intensity changes.
These interneurons are specialized for time sensitivity in several ways. First, when activated, they
generally respond with only one or two action potentials. This short duration of response allows their action
potentials to give a very specific indication of the exact moment of the time when the stimulus arrived, and to
respond accurately to stimuli that occur close in time to one another. In addition, the neurons have a very low
threshold of activation – they respond quickly even to weak stimuli. Finally, for FM signals, each interneuron
is tuned to a specific frequency within the sweep, as well as to that same frequency in the following echo.
There is specialization for the CF component of the call at this level as well. The high proportion of neurons
responding to the frequency of the acoustic fovea actually increases at this level (Carew 2001, Pollak 1977,
Zupanc 2004).
[edit] Auditory cortex

The auditory cortex in bats is quite large in comparison with other mammals (Anderson 1995).
Various characteristics of sound are processed by different regions of the cortex, each providing different
information about the location or movement of a target object. Most of the existing studies on information
processing in the auditory cortex of the bat have been done by Nobuo Suga on the mustached bat,
Pteronotus parnellii. This bat's call has both CF tone and FM sweep components.
Suga and his colleagues have shown that the cortex contains a series of "maps" of auditory
information, each of which is organized systematically based on characteristics of sound such as frequency
and amplitude. The neurons in these areas respond only to a specific combination of frequency and timing
(sound-echo delay), and are known as combination-sensitive neurons.
The systematically organized maps in the auditory cortex respond to various aspects of the echo
signal, such as its delay and its velocity. These regions are composed of "combination sensitive" neurons
that require at least two specific stimuli to elicit a response. The neurons vary systematically across the
maps, which are organized by acoustic features of the sound and can be two dimensional. The different
features of the call and its echo are used by the bat to determine important characteristics of their prey. The
maps include:
Sketch of the regions of the auditory cortex in a bat's brain
• FM-FM area: This region of the cortex contains FM-FM combination-sensitive neurons.
These cells respond only to the combination of two FM sweeps: a call and its echo. The neurons in
the FM-FM region are often referred to as "delay-tuned," since each responds to a specific time delay
between the original call and the echo, in order to find the distance from the target object (the range).
Each neuron also shows specificity for one harmonic in the original call and a different harmonic in
the echo. The neurons within the FM-FM area of the cortex of Pteronotus are organized into
columns, in which the delay time is constant vertically but increases across the horizontal plane. The
result is that range is encoded by location on the cortex, and increases systematically across the FM-
FM area (Suga et al. 1975, Suga et al. 1979, Neuweiler 2003, Carew 2001).
• CF-CF area: Another kind of combination-sensitive neuron is the CF-CF neuron. These
respond best to the combination of a CF call containing two given frequencies – a call at 30 kHz
(CF1) and one of its additional harmonics around 60 or 90 kHz (CF2 or CF3) – and the corresponding
echoes. Thus, within the CF-CF region, the changes in echo frequency caused by the Doppler shift
can be compared to the frequency of the original call to calculate the bat's velocity relative to its
target object. As in the FM-FM area, information is encoded by its location within the map-like
organization of the region. The CF-CF area is first split into the distinct CF1-CF2 and CF1-CF3 areas.
Within each area, the CF1 frequency is organized on an axis, perpendicular to the CF2 or CF3
frequency axis. In the resulting grid, each neuron codes for a certain combination of frequencies that
is indicative of a specific velocity (Suga et al. 1975, Suga et al. 1987, Carew 2001).
• DSCF area: This large section of the cortex is a map of the acoustic fovea, organized by
frequency and by amplitude. Neurons in this region respond to CF signals that have been Doppler
shifted (in other words, echoes only) and are within the same narrow frequency range to which the
acoustic fovea responds. For Pteronotus, this is around 61 kHz. This area is organized into columns,
which are arranged radially based on frequency. Within a column, each neuron responds to a
specific combination of frequency and amplitude. Suga's studies have indicated that this brain region
is necessary for frequency discrimination (Suga et al. 1975, Suga et al. 1987, Carew 2001).
[edit] Toothed whales
Diagram illustrating sound generation, propagation and reception in a toothed whale. Outgoing
sounds are red and incoming ones are green
Biosonar is valuable to Toothed whales (suborder odontoceti), including dolphins, porpoises, river
dolphins, killer whales and sperm whales, because they live in an underwater habitat that has favourable
acoustic characteristics and where vision is extremely limited in range due to absorption or turbidity.
Echolocation evolved in these aquatic mammals during the late Eocene (around 30 million years ago) maybe
as an adaptation to diel migrating cephalopods.[10][11] Since its advent, there has been adaptive radiation
especially in the Delphinidae family (dolphins) in which echolocation has become extremely derived.[12]
One specific type of echolocation, narrow-band high frequency (NBHF) clicks, evolved at least four
times in groups of odontocetes, including pygmy sperm whale (Kogiidae) and porpoise (Phocoenidae)
families, Pontoporia blainvillei, the genus Cephalorhynchus, and part of the genus Lagenorhynchus.[13][14]
These high frequency clicks likely evolved as adaptation of predator avoidance, as they inhabit areas that
have many killer whales and the signals are inaudible to killer whales due to the absence of energy below
100 kHz. Another reason for variation in echolocation frequencies is habitat. Shallow waters, where many of
these species live, tend to have more debris; a more directional transmission reduces clutter in reception.[14]
Toothed whales emit a focused beam of high-frequency clicks in the direction that their head is
pointing. Sounds are generated by passing air from the bony nares through the phonic lips.[15] These
sounds are reflected by the dense concave bone of the cranium and an air sac at its base. The focused beam
is modulated by a large fatty organ known as the 'melon'. This acts like an acoustic lens because it is
composed of lipids of differing densities. Most toothed whales use clicks in a series, or click train, for
echolocation, while the sperm whale may produce clicks individually. Toothed whale whistles do not appear
to be used in echolocation. Different rates of click production in a click train give rise to the familiar barks,
squeals and growls of the bottlenose dolphin. A click train with a repetition rate over 600 per second is called
a burst pulse. In bottlenose dolphins, the auditory brain response resolves individual clicks up to 600 per
second, but yields a graded response for higher repetition rates.
It has been suggested that some smaller toothed whales may have their tooth arrangement suited to
aid in echolocation. The placement of teeth in the jaw of a bottlenose dolphin, as an example, are not
symmetrical when seen from a vertical plane, and this asymmetry could possibly be an aid in the dolphin
sensing if echoes from its biosonar are coming from one side or the other.[16][17]. However, this idea lacks
experimental support.
Echoes are received using complex fatty structures around the lower jaw as the primary reception
path, from where they are transmitted to the middle ear via a continuous fat body (Ketten 1992,2000). Lateral
sound may be received though fatty lobes surrounding the ears with a similar density to water. Some
researchers believe that when they approach the object of interest, they protect themselves against the
louder echo by quietening the emitted sound. In bats this is known to happen, but here the hearing sensitivity
is also reduced close to a target.
Before the echolocation abilities of "porpoises" were officially discovered, Jacques Yves Cousteau
suggested that they might exist. In his first book, The Silent World (1953, pp. 206–207), he reported that his
research vessel, the Élie Monier, was heading to the Straits of Gibraltar and noticed a group of porpoises
following them. Cousteau changed course a few degrees off the optimal course to the center of the strait, and
the porpoises followed for a few minutes, then diverged toward mid-channel again. It was obvious that they
knew where the optimal course lay, even if the humans didn't. Cousteau concluded that the cetaceans had
something like sonar, which was a relatively new feature on submarines.
[edit] Oilbirds and swiftlets

Oilbirds and some species of swiftlet are known to use a relatively crude form of echolocation
compared to that of bats and dolphins. These nocturnal birds emit calls while flying and use the calls to
navigate through trees and caves where they live.[18][19]
[edit] Shrews and tenrecs

Main article: Shrews#Echolocation
Terrestrial mammals other than bats known to echolocate include two genera ( Sorex and Blarina) of
shrews and the tenrecs of Madagascar.[20] These include the wandering shrew (Sorex vagrans), the
common or Eurasian shrew (Sorex araneus), and the short-tailed shrew (Blarina brevicauda).[21] The nature
of shrew sounds unlike those of bats are low amplitude, broadband, multi-harmonic and frequency
modulated.[21] They contain no ‘echolocation clicks’ with reverberations and would seem to be used for
simple, close range spatial orientation. In contrast to bats, shrews use echolocation only to investigate their
habitat rather than additionally to pinpoint food.[21]
[edit] See also

• Human echolocation
[edit] References
1. ^ Yoon, Carol Kaesuk. "Donald R. Griffin, 88, Dies; Argued Animals Can Think", The New
York Times, November 14, 2003. Accessed July 16, 2010.
2. ^ D. R. Griffin (1958). Listening in the dark. Yale Univ. Press, New York.
3. ^ S. Dijkgraaf (1949). Spallanzani und die Fledermäuse. Experientia 5:90-92.
4. ^ Schevill, W.E. and McBride, A.F. 1956. Evidence for echolocation by cetaceans. Deep Sea
Research 3:153-154.
5. ^ Jones G. (2005). "Echolocation". Current Biology 15 (13): 484–488.
doi:10.1016/j.cub.2005.06.051. PMID 16005275.
6. ^ Muller, R. (2004). "A numerical study of the role of the tragus in the big brown bat.". JASA
116: 3701–3712. doi:10.1121/1.1815133
7. ^ Teeling et al. 2000. Molecular evidence regarding the origin of echolocation and flight in
bats. Nature 403: 188–192.
8. ^ "Order Chiroptera (Bats)". Animal Diversity Web.
http://animaldiversity.ummz.umich.edu/site/accounts/information/Chiroptera.html. Retrieved 2007-12-
30.
9. ^ Springer et al. 2001. Integrated fossil and molecular data reconstruct bat echolocation.
Proceedings of the National Academy of Sciences 98: 6241–6246.
10.^ Fordyce, R.E., and L.G. Barnes, (1994). "The evolutionary history of whales and
dolphins."Annual Review of Earth and Planetary Sciences 22:419-455.
11.^ Lindberg, D.R., and N.D. Pyenson, (2007). "Things that go bump in the night: evolutionary
interactions between cephalopods and cetaceans in the tertiary." Lethaia 40:335-343.
12.^ McGowen, M.R., M. Spaulding, and J. Gatesy, (2009). "Divergence date estimation and a
comprehensive molecular tree of extant cetaceans." Molecular Phylogenetics and Evolution 53:891-
906.
13.^ Morisaka, T., and R.C. Connor, (2007). "Predation by killer whales ( Orcinus orca) and the
evolution of whistle loss and narrow-band high frequency clicks in odontocetes." Journal of
Evolutionary Biology 20:1439-1458.
14.^ a b Kyhn, L.A., F.H. Jensen, K. Beedholm, J. Tougaard, M. Hansen, and P.T. Madsen,
(2010). "Echolocation in sympatric Peale's dolphins (Lagenorhynchus australis) and Commerson's
dolphins (Cephalorhynchus commersonii) producing narrow-band high-frequency clicks." Journal of
Experimental Biology 213:1940-1949.
15.^ Cranford, T.W., (2000). "In Search of Impulse Sound Sources in Odontocetes." In Hearing
by Whales and Dolphins (Springer Handbook of Auditory Research series), W.W.L. Au, A.N. Popper
and R.R. Fay, Eds. Springer-Verlag, New York.
16.^ Goodson, A.D., and Klinowska, M.A., (1990). "A proposed echolocation receptor for the
Bottlenose Dolphin (Tursiops truncatus): modeling the receive directivity from tooth and lower jaw
geometry." In Sensory Abilities of Cetaceans vol 196 ed J A Thomas and R A Kastelein (New York:
Plenum) pp 255–67 (NATO ASI Series A)
17.^ Dobbins, P. (2007). "Dolphin sonar—modeling a new receiver concept." Bioinspired
Biomimicry 2 (2007) 19–29
18.^ Jon Fjeldså and Niels Krabbe (1990). Birds of the High Andes: a manual to the birds of the
temperate zone of the Andes and Patagonia, South America . Apollo Books. p. 232.
ISBN 9788788757163. http://books.google.com/?
id=NmXSeVrmlgIC&pg=PA232&dq=oilbird+echo+trees+caves+nocturnal.
19.^ Marshall Cavendish Corp. (2000). Exploring Life Science. Marshall Cavendish. p. 547.
id=vC4cwlhjGxsC&pg=PA547&dq=swiftlet+echo+trees+caves+nocturnal.
20.^ Thomas E. Tomasi, "Echolocation by the Short-Tailed Shrew Blarina brevicauda", Journal
of Mammalogy, Vol. 60, No. 4 (Nov., 1979), pp. 751–759.
21.^ a b c Siemers BM, Schauermann G, Turni H, von Merten S. (2009). Why do shrews twitter?
Communication or simple echo-based orientation. Biol Lett. 5(5):593-6. doi:10.1098/rsbl.2009.0378
PMID 19535367
• Hiryu, S. et al. 2007. Echo-intensity compensation in echolocating bats ( Pipistrellus
abramus)during flight measured by a telemetry microphone. J. Acoust. Soc. Am. 121(3): .
• Schnitzler, H.U. and Flieger, E. 1983. Detection of oscillating target movements by
echolocation in the Greater Horseshoe bat. J. Comp. Physiology. 153: 385-391.
• Zupanc, G.K.H. 2004. Behavioral Neurobiology: An Integrative Approach. Oxford University
Press: Oxford, UK.
• Simmons, J.A. and Stein, R.A. 1980. Acoustic Imaging in bat sonar: echolocation signals and
the evolution of echolocation. J. Comp. Physiol. A. 135: 61-84.
• Neuweiler, G. 2003. Evolutionary aspects of bat echolocation. J. Comp. Physiol. A. 189: 245-
256.
• Jones, G. and Teeling, E.C. 2006. The evolution of echolocation in bats. Trends in Ecology
and Evolution. 21(3): 149-156.
• Fenton, M.B. 1995. Natural History and Biosonar Signals. In: Hearing in Bats. Popper, A.N.
and Fay, R.R. (eds.). Springer Verlag. New York. pp. 37–86.
• Grinnell, Alan D. (1995). Hearing in Bats: An Overview. In: Hearing in Bats. Popper, A.N. and
Fay, R.R. (eds.). Springer Verlag. New York. pp. 1–36.
• Reynolds JE III & Rommel SA (1999), Biology of Marine Mammals, Smithsonian Institution
Press, ISBN . Authoritative work on marine mammals with in depth sections on marine mammal
acoustics written by eminent experts in the field.
• Au, Whitlow W. L. (1993). The Sonar of Dolphins. New York: Springer-Verlag. Provides a
variety of findings on signal strength, directionality, discrimination, biology and more.
• Pack, Adam A. & Herman, Louis M. (1995). "Sensory integration in the bottlenosed dolphin:
Immediate recognition of complex shapes across the senses of echolocation and vision", J.
Acoustical Society of America, 98(2), 722-733. Shows evidence for the sensory integration of shape
information between echolocation and vision, and presents the hypothesis of the existence of the
mental representation of an "echoic image".
• Anderson, J.A. (1995) An Introduction to Neural Networks. MIT Press.
• Carew, T. (2001). Behavioral Neurobiology. Sinauer Associates, Inc., USA.
• Hopkins, C. (2007). Echolocation II. BioNB 424 Neuroethology Powerpoint presentation.
Cornell University, Ithaca NY.
• Ketten. D.R. (1992) The Marine mammal ear: Specializations for aquatic audition and
echolocation. In: The Evolutionary Biology of Hearing, D. Webster, R. Fay, and A. Popper (eds.),
Springer-Verlag, pp. 717–750.
• Ketten, D.R. (2000) Cetacean Ears. In: Hearing by Whales and Dolphins. W. Au, R. Fay, and
A. Popper (eds.), SHAR Series for Auditory Research, Springer-Verlag, pp. 43–108.
• Wilson, W. & C. Moss (2004) in Echolocation in Bats and Dolphins, J. Thomas, C. Moss, eds.
pp. 22-.
• Moss C. & Sinha S. (2003). Neurobiology of Echolocation in Bats. Current Opinion in
Neurobiology, 13(6), 751-758.
• Pollak G. et al. (1977). Echo-detecting characteristics of neurons in inferior colliculus of
unanesthetized bats. Science, 196: 675-678.
• Schuller, G. & Pollack, G. (1979). Disproportionate frequency representation in the inferior
colliculus of Doppler-compensating greater horseshoe bats: Evidence of an acoustic fovea. Journal
of Comparative Physiology A. 132: 47-54.
• Speakman J., Racey, P. No cost of echolocation for bats in flight. Nature, 350: 421-423
• Suga, N., Niwa H., Taniguchi I., Margoliash D. (1987). The personalized auditory cortex of
the mustached bat: adaptation for echolocation. Journal of Neurophysiology, 58: 643-654.
• Suga N., O'Neill W.E. (1979). Neural axis representing target range in the auditory cortex of
the mustache bat. Science, 206: 351-353.
• Suga N, Simmons JA and Jen PH. (1975) Peripheral specialization for fine analysis of
doppler-shifted echoes in the auditory system of the "CF-FM" bat Pteronotus parnellii. Journal of
Experimental Biology, 63: 161-192.
• The British Library Sound Archive 150,000 recordings of over 10,000 species, including
many echolocation recordings
• International Bioacoustics Council links to many bioacoustics resources
• Listen to Nature has bat and swiftlet sonar signals
• Bat Ecology & Bioacoustics Lab
• Keep your ears peeled article on physics.org
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W000
Mustang (horse)

This article is about the horse. For other uses, see Mustang (disambiguation).
Mustang
Mustang adopted from the BLM
Distinguishing features: Small, compact, good bone, very hardy
Country of origin: North America
Horse (Equus ferus caballus)

A Mustang is a free-roaming feral horse of the North American west that first descended from horses
brought to the Americas by the Spanish. Mustangs are often referred to as wild horses, but the more correct
term is feral horses.
In 1971, the United States Congress recognized Mustangs as “living symbols of the historic and
pioneer spirit of the West, which continue to contribute to the diversity of life forms within the Nation and
enrich the lives of the American people.” Today, Mustang herds vary in the degree to which they can be
traced to original Iberian horses. Some contain a greater genetic mixture of ranch stock and more recent
breed releases, while others are relatively unchanged from the original Iberian stock, most strongly
represented in the most isolated populations.
Today, the Mustang population is managed and protected by the Bureau of Land Management.
Controversy surrounds the sharing of land and resources by the free ranging Mustangs with the livestock of
the ranching industry, and also with the methods with which the federal government manages the wild
population numbers. Many methods of population management are used, including the adoption by private
individuals of horses taken from the range.
Contents
[hide]
• 1 Etymology and usage
• 2 History
• 3 Ancestry
• 4 Mustangs today
• 5 Land use controversies
• 6 Management and adoption
• 7 See also
• 8 Notes
• 9 References
[edit] Etymology and usage

Mustangs are often referred to as wild horses but, since all free-roaming horses now in the Americas
descended from horses that were once domesticated, the more correct term is feral horses.[1]
The English word "mustang" comes from the Mexican Spanish word mestengo, derived from Spanish
mesteño, meaning "stray livestock animal".[2] The Spanish word in turn may possibly originate from the Latin
expression animalia mixta (mixed beasts), referring to beasts of uncertain ownership, which were distributed
in shepherd councils, known as mestas in medieval Spain.[3] A mestengo was any animal distributed in
those councils, and by extension any feral animal.
[edit] History
Free-roaming Mustangs
Today, the only true wild horse is the Przewalski's Horse, native to Mongolia. However, the horse
family Equidae and the genus Equus evolved in North America. Studies using ancient DNA as well as DNA
of recent individuals shows there once were two closely related horse species in North America, the "wild
horse" (Equus ferus) and the "Stilt-legged Horse;" which is taxonomically assigned to various names.[4][5]
Thus, primitive horses lived in North America in prehistoric times. However, the entire equus genus died out
at the end of the last ice age around 10-12,000 years ago, possibly due to a changing climate or the impact
of newly arrived human hunters.[6] Thus at the beginning of the Columbian Exchange, there were no equids
in the Americas at all. Horses first returned with the Conquistadors, beginning with Columbus, who imported
horses from Spain to the West Indies on his second voyage in 1493.[7] Domesticated horses came to the
mainland with the arrival of Cortés in 1519.[8]
The first Mustangs descended from Iberian horses[9] brought to Mexico and Florida. Most of these
horses were of Andalusian, Arabian and Barb ancestry. Some of these horses escaped or were stolen by
Native Americans, and rapidly spread throughout western North America.
Native Americans quickly adopted the horse as a primary means of transportation. Horses replaced
the dog as a travois puller and greatly improved success in battles, trade, and hunts, particularly bison hunts.
[10]
Starting in the colonial era and continuing with the westward expansion of the 1800s, horses
belonging to explorers, traders and settlers that escaped or were purposely released joined the gene pool of
Spanish-descended herds. It was also common practice for western ranchers to release their horses to
locate forage for themselves in the winter and then recapture them, as well as any additional Mustangs, in
the spring. Some ranchers also attempted to "improve" wild herds by shooting the dominant stallions and
replacing them with pedigreed animals.
By 1900 North America had an estimated two million free-roaming horses.[9] Since 1900, the
Mustang population has been reduced drastically. Mustangs were viewed as a resource that could be
captured and used or sold (especially for military use) or slaughtered for food, especially pet food. The
controversial practice of mustanging was dramatized in the John Huston film The Misfits, and the abuses
linked to certain capture methods, including hunting from airplanes and poisoning, led to the first federal wild
free-roaming horse protection law in 1959.[11] This statute, known as the "Wild Horse Annie Act," prohibited
the use of motor vehicles for hunting wild horses and burros.[12] Protection was increased further by the Wild
Free-Roaming Horse and Burro Act of 1971.[13]
The 1971 Act provided for protection of certain previously established herds of horses and burros.
Today, the Bureau of Land Management is the primary authority that oversees the protection and
management of Mustang herds on public lands,[14] while the United States Forest Service administers
additional wild horse or burro territories.[15]
[edit] Ancestry
Mustangs in Utah
Historically, many of the Native American tribes bred their horses carefully to improve them for their
purposes. Among the most capable horse-breeding people of North America were the Comanche, the
Shoshoni, and the Nez Perce. The last in particular became master horse breeders, and developed one of
the first truly American breeds: the Appaloosa. Most other tribes did not practice extensive amounts of
selective breeding, though they sought out desirable horses through capture, trade and theft, and quickly
traded away or otherwise eliminated those with undesirable traits.[ citation needed]
In some modern mustang herds there is clear evidence of other domesticated horse breeds having
become intermixed with feral herds. Some herds show the signs of the introduction of Thoroughbred or other
light racehorse-types into herds, a process that also led in part to the creation of the American Quarter Horse.
[citation needed] Other herds show signs of the intermixing of heavy draft horse breeds turned loose in an
attempt to create work horses. Other, more isolated herds, retain a strong influence of original Spanish stock.
Some breeders of domestic horses consider the Mustang herds of the west to be inbred and of
inferior quality.[citation needed] However, supporters of the Mustang argue that the animals are merely small
due to their harsh living conditions and that natural selection has eliminated many traits that lead to
weakness or inferiority. Some mustang supporters also maintain that some "inbreeding" actually
concentrates the traits of hardiness and durability, making the mustang a valuable genetic resource.[ citation
needed] Regardless of these debates, the Mustang of the modern west has several different breeding
populations today which are genetically isolated from one another and thus have distinct traits traceable to
particular herds. These herds vary in the degree to which they can be traced to original Iberian horses. Some
contain a greater genetic mixture of ranch stock and more recent breed releases, others are relatively
unchanged from the original Iberian stock.[citation needed]
Two researchers have advanced an argument that Mustangs should be legally classified as "wild"
rather than "feral." They argue that, due to the presence of Equus ferus ferus on the North American
continent till the end of the Pleistocene era, horses were once native animals and should still be considered
as native animals, and therefore defined as "wild,"[16] and not viewed as an exotic species that draws
resources and attention away from true native species.[17]
[edit] Mustangs today
Nevada's State Quarter, featuring the Mustang

Mustang in NW Nevada mountains
Today, free-roaming horses are protected under United States law, but have disappeared from
several states where there were once established populations.[18] A few hundred free-roaming horses
survive in Alberta and British Columbia. The BLM considers roughly 26,000 individuals a manageable
number,[19] but the feral Mustang population in February 2010 was 33,700 horses and 4,700 burros.[19]
More than half of all Mustangs in North America are found in Nevada (which features the horses on its State
Quarter in commemoration of this), with other significant populations in Montana, Wyoming and Oregon.[18]
Another 34,000 horses are in holding facilities.[19]
[edit] Land use controversies
Mustangs at a water source

Controversy surrounds the presence of feral Mustang herds. Supporters argue that Mustangs are
part of the natural heritage of the American West, whose history predates modern land use practices, and
thus the animals have an inherent right of inhabitation.[20] However, other people remain vehemently
opposed to their presence, arguing that the animals degrade rangeland and compete with livestock and wild
species for forage.[21]
The debate as to what degree Mustangs and cattle compete for forage is multifaceted. One group of
opponents, primarily cattle and sheep ranchers and those who depend on the livestock industry, argue
essentially that feral horses degrade rangeland and compete with private livestock for public land forage.[22]
The environmentalist community is split over the position of the Mustang within the North American
ecosystem. This debate centers on the potential classification of Mustangs as either an introduced species
such as cattle, or as a reintroduced native species due to the prehistoric presence of horses in North
America, albeit with a gap of thousands of years between their extinction and reintroduction from European
stock.[23]
Researchers note that most current Mustang herds live in arid areas which cattle cannot fully utilize
due to the lack of water sources. Horses are better adapted by evolution to such climates.[24]; they may
range nine times as far from water sources as cattle, traveling as much as 50 miles a day.[25] This allows
them to utilize areas not grazed by cattle. In addition, horses are "hindgut fermenters," meaning that they
digest nutrients by means of the cecum rather than by a multi-chambered stomach. In practical effect, horses
can obtain adequate nutrition from poorer forage than can cattle, surviving in areas where cattle will starve.
[25]
[edit] Management and adoption

Mustangs at the Palomino Valley Adoption Center
The Bureau of Land Management (BLM) is tasked with protecting, managing, and controlling wild
horses and burros under the authority of the 1971 Wild Free-Roaming Horses and Burros Act to ensure that
healthy herds thrive on healthy rangelands and as multiple-use mission under the 1976 Federal Land Policy
and Management Act. Under the 1971 Act, shooting or poisoning Mustangs in the wild is illegal, and doing so
can be prosecuted as a criminal felony.
Healthy adult Mustangs have few natural predators aside from mountain lions,[26] and to a lesser
extent, grizzly bears and wolves.[27] The mountain lion is well-known for predation on feral horses, and the
larger members of the species may hunt both horses and moose. They are very effective predators that kill
by either leaping onto an animal or chasing it down in a sprint, then grabbing the prey with their front claws
and biting the neck, either at the windpipe or the spine.[28]
Where there is natural balance of predators and prey, Mustang numbers tend to stay in balance.
However, in many areas, natural predators have been eliminated from the ecosystem.[27] Without some form
of population control, Mustang herd sizes can multiply rapidly, doubling as fast as every four years.[12] To
maintain population balance, (or, some argue, to make room for cattle[29]) one of the BLM’s key
responsibilities under the 1971 law is to determine an appropriate management level (AML) of wild horses
and burros in areas of public rangelands dedicated specifically for them.
Control of the population to within AML is achieved through a capture program. There are strict
guidelines for techniques used to round up Mustangs. One method uses a tamed horse, called a "Judas
horse," which has been trained to lead wild horses into a pen or corral. Once the Mustangs are herded into
an area near the holding pen, the Judas horse is released. Its job is then to move to the head of the herd and
lead them into a confined area. Already confused and looking for direction, the wild horses instinctively follow
this animal.[citation needed]
Most horses that are captured are offered for adoption to individuals or groups willing and able to
provide humane, long-term care after payment of an adoption fee that ranges from $25 to $125.[30] In order
to prevent the later sale of mustangs as horse meat, adopted mustangs are still protected under the Act, and
cannot be sold in the first year except when certain very specific criteria are met. As of 2010, nearly 225,000
Mustangs have been adopted.[19]
Because there is a much larger pool of captured horses than of prospective adoptive owners, a
number of efforts have been made to reduce the number of horses in holding facilities. At present, there are
about 34,000 Mustangs in holding facilities and long-term grassland pastures.[19] The BLM has publicly
considered euthanasia as a possible solution to overpopulation.[31] In January 2005, a controversial
amendment was attached to an appropriation bill before the United States Congress by former Senator
Conrad Burns, dubbed the "Burns rider."[32] This modified the adoption program to allow the sale (with the
result usually being slaughter) of captured horses that are "more than 10 years of age", or that were "offered
unsuccessfully for adoption at least three times."[33] In 2009, Secretary of the Interior Ken Salazar proposed
the creation of federal wild horse preserves in the midwest, where non-reproducing animals would be kept.
[34] Another approach to placing excess animals has been advanced by Madeleine Pickens, wife of oil
magnate T. Boone Pickens, who seeks to create a private sanctuary in northern Nevada.[34] There are also
increased efforts to assist with finding appropriate adoption homes. One example is a promotional
competition that gives trainers 100 days to gentle and train 100 mustangs, which are then adopted through
an auction.[35]
[edit] See also
Wikimedia Commons has media related to: Feral horses from America
• Colonial Spanish Horse

• Feral horse
• Kiger Mustang
• Kleppe v. New Mexico
• Spanish Mustang
• Wild horse, including
• Przewalski's horse
• Tarpan
[edit] Notes
1. ^ The American Museum of Natural History The Nature of Horses
2. ^ "Mustang". http://www.etymonline.com/index.php?term=mustang. Retrieved 2009-03-31.
3. ^ Websters Third International Dictionary Unabridged
4. ^ Weinstock, J.; et al. (2005). "Evolution, systematics, and phylogeography of Pleistocene
horses in the New World: a molecular perspective". PLoS Biology 3 (8): e241.
doi:10.1371/journal.pbio.0030241. PMID 15974804. PMC 1159165.
http://biology.plosjournals.org/perlserv/?request=get-
document&doi=10.1371%2Fjournal.pbio.0030241&ct=1. Retrieved 2008-12-19.
5. ^ Orlando, L.; et al. (2008). "Ancient DNA Clarifies the Evolutionary History of American Late
Pleistocene Equids". Journal of Molecular Evolution 66 (5): 533–538. doi:10.1007/s00239-008-9100-
x. PMID 18398561.
6. ^ "Ice Age Horses May Have Been Killed Off by Humans" National Geographic News, May 1,
2006.
7. ^ Bennett, Deb. Conquerors: The Roots of New World Horsemanship. Amigo Publications,
1998, pp. 150 ISBN 0-9658533-0-6
8. ^ Henry, Marguerite and Wesley Dennis. All About Horses. Random House, 1962. ASIN:
B000MAJIB0
9. ^ a b Dobie, The Mustangs
10.^ "Seeds of Change." Corpus Christi Museum, Science and History educational resources.
Accessed June 1, 2007 at http://www.ccmuseumedres.com/tour.php?action=details&record=37
11.^ "Wild Horse Annie Act". Wildhorsepreservation.com.
http://www.wildhorsepreservation.com/resources/annie_act.html. Retrieved 2010-08-09.
12.^ a b Mangum, "The Mustang Dilemma," p. 77
13.^ ""Background Information on HR297"" (PDF).
http://www.house.gov/apps/list/press/ii00_democrats/rahallwhbbkd.pdf. Retrieved 2010-08-09.
14.^ Mangum, "The Mustang Dilemma," p. 75
15.^ "Wild Horse and Burro Territories".
http://www.fs.fed.us/rangelands/ecology/wildhorseburro/territories/index.shtml. Retrieved 2009-01-
29.
16.^ "The Surprising History of America's Wild Horses". Livescience.com. 2008-07-24.
http://www.livescience.com/animals/080724-nhm-wild-horses.html. Retrieved 2010-08-09.
17.^ "Wild Horses". Ngm.nationalgeographic.com.
http://ngm.nationalgeographic.com/2009/02/wild-horses/fuller-text/5. Retrieved 2010-08-09.
18.^ a b "National Summary, FY2007" (PDF).
http://www.wildhorsepreservation.com/pdf/National.pdf. Retrieved 2010-08-09.
19.^ a b c d e Mangum, "The Mustang Dilemma", p.77
20.^ http://www.wildhorsepreservation.org The American Wild Horse Preservation Campaign
21.^ see, e.g. National Academy of Sciences Report, 1982
General Accounting Office Report, 1991
22.^ "Bellisle, Martha. "Legislative battle brews over Nevada's wild horses" ''Associated press''
reprinted at I.G.H.A. / HorseAid's Bureau of Land Management News. Web site accessed May 11,
2007". Igha.org. http://www.igha.org/BLM8.html. Retrieved 2010-08-09.
23.^ "Wild Horses as Native North American Wildlife" Jay F. Kirkpatrick, Ph.D. and Patricia M.
Fazio
24.^ "Wild Horses and the Ecosystem". Wildhorsepreservation.com.
http://www.wildhorsepreservation.com/resources/ecosystem.html. Retrieved 2010-08-09.
25.^ a b Budiansky, Stephen. The Nature of Horses. Free Press, 1997. ISBN 0-684-82768-9
26.^ John W. Turner, Jr. and Michael L. Morrison (2008). "Influence of Predation by Mountain
Lions on Numbers and Survivorship of a Feral Horse Population". The Southwestern Naturalist Vol.
46, No.2 pp. 183-190. http://wf2dnvr2.webfeat.org/. Retrieved 2008-08-29.
27.^ a b "FAQ'S On BLM Wild Horses" Wild Mustang Coalition. Web site accessed December 9,
2010
28.^ French, Brett. "Ferocious appetites: Study finds mountain lions may be eating more than
previously believed." Billings Gazette. December 9, 2010. Accessed December 9, 2010.
29.^ "On BLM's wild horse management practices". Wildhorsepreservation.com.
http://www.wildhorsepreservation.com/resources/study.html. Retrieved 2010-08-09.
30.^ "Adoption". New Mexican Mustang & Burro Association.
http://www.nmmba.org/adoption.html. Retrieved 2010-12-2.
31.^ ""Plan to kill wild horses runs into trouble" ''Associated Press,'' July 7, 2008" (PDF).
http://www.letemrun.com/cnn.pdf. Retrieved 2010-08-09.
32.^ "The Story Behind the Burns Amendment". Wildhorsepreservation.com.
http://www.wildhorsepreservation.com/resources/burns_story.html. Retrieved 2010-08-09.
33.^ "Burns amendment". Wildhorsepreservation.com. 2004-12-06.
http://www.wildhorsepreservation.com/resources/burns_amend.html. Retrieved 2010-08-09.
34.^ a b Mangum, "The Mustang Dilemma", p.78
35.^ http://www.extrememustangmakeover.com The Extreme Mustang Makeover
[edit] References
• Dobie, Frank (1952). The Mustangs (Seventh printing ed.). Boston: Little, Brown and
Company. LC no. 52-6802.
• Mangum, A.J. (December 2010). "The Mustang Dilemma". Western Horseman: 70–80.

• Nimmo, D. G., & Miller, K. K. (2007) Ecological and human dimensions of management of
feral horses in Australia: A review. Wildlife Research, 34, 408-417
• Text of Wild Free-Roaming Horse and Burro Act of 1971
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history the horse in South Asia · Horses in the
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loanwords
W000
Gastropoda

Gastropoda
Gastropod
Temporal range: Late Cambrian–Recent[1]
PreЄ
g
Air-breathing land gastropod Helix pomatia, the Roman snail
Scientific classification [ e ]
Kingdom: Animalia
Phylum: Mollusca
Gastropoda
Class:
Cuvier, 1795[2]
Clades
"Paleozoic uncertain …"

"Basal taxa …"
clade Patellogastropoda
clade Vetigastropoda
clade Cocculiniformia
clade Neritimorpha
clade Caenogastropoda
clade Heterobranchia
The Gastropoda or gastropods are a large taxonomic class within the molluscs, a group of animals
that are more commonly known as snails and slugs. The class includes snails and slugs of all kinds and all
sizes: huge numbers of marine snails and sea slugs, as well as freshwater snails and freshwater limpets, and
the terrestrial (land) snails and slugs. The class Gastropoda contains a vast total of named species, second
only to the insects in overall number. The fossil history of this class goes all the way back to the Late
Cambrian. There are 611 families of gastropods, of which 202 families are extinct, being found only in the
fossil record.[3]
Gastropoda (previously known as univalves and sometimes spelled Gasteropoda) are a major part of
the phylum Mollusca and are the most highly diversified class in the phylum, with 60,000 to 80,000[3][4] living
snail and slug species. The anatomy, behavior, feeding and reproductive adaptations of gastropods vary very
significantly from one clade or group to another. Therefore, it is difficult or impossible to make more than a
few general statements that are valid for all gastropods.
The class Gastropoda has an extraordinary diversification of habitats. Representatives live in
gardens, in woodland, in deserts, and on mountains; in small ditches, great rivers and lakes; in estuaries,
mudflats, the rocky intertidal, the sandy subtidal, in the abyssal depths of the oceans including the
hydrothermal vents, and numerous other ecological niches, including parasitic ones.
Although the name "snail" can be, and often is, applied to all the members of this class, commonly
this word means only those species with an external shell large enough that the soft parts can withdraw
completely into it. Those gastropods without a shell, and those with only a very reduced or internal shell, are
usually known as slugs.
The marine shelled species of gastropod include edible species such as abalone, conches,
periwinkles, whelks, and numerous other sea snails that produce seashells which are coiled in the adult
stage, even though in some cases the coiling may not be very visible, for example in cowries. There are also
a number of families of species such as all the various limpets, where the shell is coiled only in the larval
stage, and is a simple conical structure after that.
Contents
[hide]
• 1 Etymology
• 2 Diversity
• 3 Habitat
• 4 Anatomy
• 4.1 The shell
• 4.2 Body wall
• 4.3 Digestive system
• 4.4 Respiratory system
• 4.5 Circulatory system
• 4.6 Excretory system
• 4.7 Sensory organs and nervous system
• 4.8 Reproductive system
• 5 Life cycle
• 6 Feeding behavior
• 7 Genetics
• 8 Geological history
• 9 Taxonomy
• 10 References
[edit] Etymology
Look up gastropod or univalve in Wiktionary, the free dictionary.
The word "gastropod" is derived from the Ancient Greek words γαστήρ (gastér, stem: gastr-)
"stomach", and πούς (poús, stem: pod-) "foot", hence stomach-foot. This is an anthropomorphic name, based
on the fact that to humans it appears as if snails and slugs crawl on their bellies. In reality, snails and slugs
have their stomach, the rest of their digestive system and all the rest of their viscera in a hump on the
opposite, dorsal side of the body. In most gastropods this visceral hump is covered by, and contained within,
the shell.
In the scientific literature, gastropods were described under the vernacular (French) name
"gasteropodes" by Georges Cuvier in 1795.[2] The name was later Latinized.
The earlier name univalve means "one valve", and contrasts with bivalve ("two valves").
[edit] Diversity
At all taxonomic levels, gastropods are second only to the insects in terms of their diversity.[5]
Gastropods form the class of molluscs with the greatest numbers. However the estimated total
number of gastropod species varies widely, depending on the cited sources. The number of gastropod
species can be deduced from estimates of the number of described species of Mollusca with accepted
names: about 85,000[6] (minimum 50,000,[6] maximum 120,000[6]). But an estimate of the total number of
Mollusca, including undescribed species, is about 200,000 species.[6] The estimate of 85,000 molluscs
includes 24,000 described species of terrestrial gastropods.[6]
Different estimations (from different sources) for aquatic gastropods give about 30,000 species[7] of
marine gastropods and about 5,000 species of freshwater and brackish gastropods.[7] Total number of
recent species of freshwater snails is about 4,000.[8]
The number of prehistoric (fossil) species of gastropods is at least 15,000 species.[9]
[edit] Habitat
Some of the more familiar and better-known gastropods are terrestrial (the land snails and slugs) and
some live in freshwater, but more than two thirds of all named species live in a marine environment.
Gastropods have a worldwide distribution from the near Arctic and Antarctic zones to the tropics.
They have become adapted to almost every kind of existence on earth, having colonized every medium
available except the air.
In habitats where there is not enough calcium carbonate to build a really solid shell, such as on some
acidic soils on land, there are still various species of slugs, and also some snails with a thin translucent shell,
mostly or entirely composed of the protein conchiolin.
Snails such as Sphincterochila boissieri and Xerocrassa seetzeni have adapted to desert conditions,
other snails have adapted to an existence in ditches, near deepwater hydrothermal vents, the pounding surf
of rocky shores, caves, and many other diverse areas.
[edit] Anatomy
The anatomy of a common air-breathing land snail such as Helix aspersa. Note that much of this
anatomy does not apply to gastropods in other clades or groups.
The anatomy of an aquatic snail with a gill, a male prosobranch gastropod. Note that much of this
anatomy does not apply to gastropods in other clades.
Light yellow - body
Brown - shell and operculum
Green - digestive system
Light purple - gills
Yellow - osphradium
Red - heart
Pink -
Dark violet -
1. foot
2. cerebral ganglion
3. pneumostome
4. upper commissura
5. osphradium
6. gills
7. pleural ganglion
8. atrium of heart
9. visceral ganglion
10. ventricle
11. foot
12. operculum
13. brain
14. mouth
15. tentacle (chemosensory, 2 or 4)
16. eye
17. penis (everted, normally internal)
18. esophageal nerve ring
19. pedal ganglion
20. lower commissura
21. vas deferens
22. pallial cavity / mantle cavity / respiratory cavity
23. parietal ganglion
24. anus
25. hepatopancreas
26. gonad
27. rectum
28. nephridium
Snails are distinguished by an anatomical process known as torsion, where the visceral mass of the
animal rotates 180° to one side during development, such that the anus is situated more or less above the
head. This process is unrelated to the coiling of the shell, which is a separate phenomenon. Torsion is
present in all gastropods, but the opisthobranch gastropods are secondarily de-torted to various degrees.[10]
[11]
Torsion occurs in two mechanistic stages. The first is muscular, and the second is mutagenetic. The
effects of torsion are primarily physiological - the organism develops an asymmetrical nature with the majority
of growth occurring on the left side. This leads to the loss of right-paired appendages (e.g. ctenidia (comb-
like respiratory apparatus), gonads, nephridia, etc.). Furthermore, the anus becomes redirected to the same
space as the head. This is speculated to have some evolutionary function, as prior to torsion, when retracting
into the shell, first the posterior end would get pulled in, and then the anterior. Now, the front can be retracted
more easily, perhaps suggesting a defensive purpose.
However, this "rotation hypothesis" is being challenged by the "asymmetry hypothesis" in which the
gastropod mantle cavity originated from one side only of a bilateral set of mantle cavities.[12]
Gastropods typically have a well-defined head with two or four sensory tentacles with eyes, and a
ventral foot, which gives them their name (Greek gaster, stomach, and poda, feet). The foremost division of
the foot is called the propodium. Its function is to push away sediment as the snail crawls. The larval shell of
a gastropod is called a protoconch.
[edit] The shell

Main article: Gastropod shell
The shell of Zonitoides nitidus, a small land snail, has dextral coiling, which is typical (but not
universal) in gastropod shells.
Upper image: dorsal view of the shell, showing the apex
Central image: lateral view showing the spire and aperture of the shell
Lower image: basal view showing the umbilicus
Most shelled gastropods have a one piece shell, typically coiled or spiraled. This coiled shell usually
opens on the right-hand side (as viewed with the shell apex pointing upward). Numerous species have an
operculum, which in many species acts as a trapdoor to close the shell. This is usually made of a horn-like
material, but in some molluscs it is calcareous. In the land slugs, the shell is reduced, internal, or absent, and
the body is streamlined.
[edit] Body wall

Some sea slugs are very brightly colored. This serves either as a warning, when they are poisonous
or contain stinging cells, or to camouflage them on the brightly-colored hydroids, sponges and seaweeds on
which many of the species are found.
Lateral outgrowths on the body of nudibranchs are called cerata. These contain a part of digestive
gland, which is called the diverticula.
[edit] Digestive system

Main articles: Digestive system of gastropods and Radula
The radula of a gastropod is usually adapted to the food that a species eats. The simplest gastropods
are the limpets and abalones, herbivores that use their hard radula to rasp at seaweeds on rocks.
Many marine gastropods are burrowers, and have a siphon that extends out from the mantle edge.
Sometimes the shell has a siphonal canal to accommodate this structure. A siphon enables the animal to
draw water into their mantle cavity and over the gill. They use the siphon primarily to "taste" the water to
detect prey from a distance. Gastropods with siphons tend to be either predators or scavengers.
[edit] Respiratory system

Main articles: Respiratory system of gastropods and Respiratory system#Anatomy of respiratory
system in invertebrates
Almost all marine gastropods breathe with a gill, but many freshwater species, and the majority of
terrestrial species, have a pallial lung. Gastropods with a lung belong to one group with common descent, the
Pulmonata, however, gastropods with gills are paraphyletic. The respiratory protein in almost all gastropods
is hemocyanin, but a pulmonate family Planorbidae have hemoglobin as respiratory protein.
In one large group of sea slugs, the gills are arranged as a rosette of feathery plumes on their backs,
which gives rise to their other name, nudibranchs. Some nudibranchs have smooth or warty backs and have
no visible gill mechanism, such that respiration may likely take place directly through the skin.
[edit] Circulatory system

Main article: Circulatory system of gastropods
Gastropods have open circulatory system and the transport fluid is hemolymph. Hemocyanin is
present in the hemolymph as the respiratory pigment.
[edit] Excretory system
Main article: Excretory system of gastropods
The primary organs of excretion in gastropods are nephridia, which produce either ammonia or uric
acid as a waste product. The nephridium also plays an important role in maintaining water balance in
freshwater and terrestrial species. Additional organs of excretion, at least in some species, include
pericardial glands in the body cavity, and digestive glands opening into the stomach.
[edit] Sensory organs and nervous system
The upper pair of tentacles on the head of Helix pomatia have eye spots, but the main sensory
organs of the snail are sensory receptors for olfaction, situated in the epithelium of the tentacles.
Main articles: Sensory organs of gastropods and Nervous system of gastropods
Sensory organs of gastropods include olfactory organs, eyes, statocysts and mechanoreceptors.[13]
Gastropods have no hearing.[13]
In terrestrial gastropods (land snails and slugs), the olfactory organs, located on the tips of the 4
tentacles, are the most important sensory organ,[13] The chemosensory organs of opisthobranch marine
gastropods are called rhinophores.
The majority of gastropods have simple visual organs, eye spots, that are situated either at the tip of
the tentacles or the base of the tentacles. However "eyes" in gastropods range from these simple ocelli which
cannot process an image being only able to distinguish light and dark, to more complex pit eyes, and even to
lens eyes.[14] In land snails and slugs, vision is not the most important sense, because they are mainly
nocturnal animals.[13]
The nervous system of gastropods includes the peripheral nervous system and the central nervous
system. The central nervous system consist of ganglia connected by nerve cells. It includes paired ganglia:
the cerebral ganglia, pedal ganglia, osphradial ganglia, pleural ganglia, parietal ganglia and the visceral
ganglia. There are sometimes also buccal ganglia.[13]
[edit] Reproductive system

Main article: Reproductive system of gastropods
Courtship is a part of mating behavior in some gastropods including some of the Helicidae. Again, in
some land snails, an unusual feature of the reproductive system of gastropods is the presence and utilization
of love darts.
In many marine gastropods other than the opisthobranchs, there are separate sexes; most land
gastropods however are hermaphrodites.
[edit] Life cycle
A 9-hour-old trochophore of Haliotis asinina

sf - shell field
mating behaviour of Elysia timida
The main aspects of the life cycle of gastropods include:
• Egg laying and the eggs of gastropods
• The Embryonic development of gastropods
• The larvae or larval stadium: some gastropods may be trochophore and/or veliger
• Estivation and hibernation (each of these are present in some gastropods only)
• The growth of gastropods
• Courtship of gastropods and mating of gastropods: fertilisation is internal or external
according to the species. External fertilisation is common in marine gastropods.
[edit] Feeding behavior
Marine gastropods include some that are herbivores, detritus feeders, predatory carnivores,
scavengers, parasites, and also a few ciliary feeders, in which the radula is reduced or absent. In some
species that have evolved into endoparasites, such as Parenteroxenos doglieli, many of the standard
gastropod features are strongly reduced or absent.
A few sea slugs are herbivores and some are carnivores. Many have distinct dietary preferences and
regularly occur in close association with their food species.
Some predatory carnivorous gastropods include, for example: Cone shells, Testacella, Daudebardia,
Ghost slug and others.
[edit] Genetics
Gastropods exhibit an important degree of variation in mt gene organization when compared to other
animals.[15] Main events of gene rearrangement occurred at the origin of Patellogastropoda and
Heterobranchia, whereas fewer changes occurred between the ancestors of Vetigastropoda (only tRNAs D,
C and N) and Caenogastropoda (a large single inversion, and translocations of the tRNAs D and N).[15]
Within Heterobranchia, gene order seems to be relatively conserved and gene rearrangements are mostly
related with transposition of tRNA genes.[15]
[edit] Geological history
Fossil gastropod and attached mytilid bivalves on a Jurassic limestone bedding plane of the Matmor
Formation in southern Israel.
Helix aspersa: a European pulmonate land snail that has been accidentally introduced in many
countries throughout the world.
See also: :fr:Gastropoda (classification phylogénétique) and List of marine gastropod genera in the
fossil record
The first gastropods were exclusively marine, with the earliest representatives of the group appearing
in the Late Cambrian (Chippewaella, Strepsodiscus). Early Cambrian forms like Helcionella and Scenella are
no longer considered gastropods, and the tiny coiled Aldanella of earliest Cambrian time is probably not even
a mollusk. By the Ordovician period the gastropods were a varied group present in a range of aquatic
habitats. Commonly, fossil gastropods from the rocks of the early Palaeozoic era are too poorly preserved for
accurate identification. Still, the Silurian genus Poleumita contains fifteen identified species. Fossil
gastropods were less common during the Palaeozoic era than bivalves.
Most of the gastropods of the Palaeozoic era belong to primitive groups, a few of which still survive
today. By the Carboniferous period many of the shapes we see in living gastropods can be matched in the
fossil record, but despite these similarities in appearance the majority of these older forms are not directly
related to living forms. It was during the Mesozoic era that the ancestors of many of the living gastropods
evolved.
One of the earliest known terrestrial (land-dwelling) gastropods is Maturipupa, which is found in the
Coal Measures of the Carboniferous period in Europe, but relatives of the modern land snails are rare before
the Cretaceous period, when the familiar Helix first appeared.
Cepaea nemoralis: another European pulmonate land snail, which has been introduced to many
other countries
In rocks of the Mesozoic era, gastropods are slightly more common as fossils, their shells are often
well preserved. Their fossils occur in ancient beds deposited in both freshwater and marine environments.
The "Purbeck Marble" of the Jurassic period and the "Sussex Marble" of the early Cretaceous period, which
both occur in southern England, are limestones containing the tightly packed remains of the pond snail
Viviparus.
Rocks of the Cenozoic era yield very large numbers of gastropod fossils, many of these fossils being
closely related to modern living forms. The diversity of the gastropods increased markedly at the beginning of
this era, along with that of the bivalves.
Certain trail-like markings preserved in ancient sedimentary rocks are thought to have been made by
gastropods crawling over the soft mud and sand. Although these trails are of debatable origin, some of them
do resemble the trails made by living gastropods today.
Gastropod fossils may sometimes be confused with ammonites or other shelled cephalopods. An
example of this is Bellerophon from the limestones of the Carboniferous period in Europe, the shell of which
is planispirally coiled and can be mistaken for the shell of a cephalopod.
Gastropods are one of the groups that record the changes in fauna caused by the advance and
retreat of the Ice Sheets during the Pleistocene epoch.
[edit] Taxonomy
A group of fossil Turritella cingulifera from the Pliocene of Cyprus.

The taxonomy of the Gastropoda is under constant revision, and more and more of the old taxonomy
is being abandoned as the results of DNA studies slowly become clearer. Nevertheless a few of the older
terms such as "opisthobranch" and "prosobranch" are still sometimes used in a descriptive way.
The taxonomy of the Gastropoda as shown in various texts can differ in major ways, and on-going
revisions of the higher taxonomic levels are to be expected in the near future.
In the older classification there were four subclasses[16]:
• Opisthobranchia (gills to the right and behind the heart).
• Gymnomorpha (no shell)
• Prosobranchia (gills in front of the heart).
• Pulmonata (with a lung instead of gills)
Main article: Taxonomy of the Gastropoda (Ponder & Lindberg, 1997)
According to newer insights based on DNA sequencing, the taxonomy of the Gastropoda must be
rewritten in terms of strictly monophyletic groups. Integrating these findings into a working taxonomy will
continue to be a challenge in coming years. At present, it is impossible to give a classification of the
Gastropoda that has consistent ranks and also reflects current usage.
Convergent evolution, which appears to exist at especially high frequency in the Gastropoda class,
may account for the observed differences between the phylogenies, which are obtained from morphological
data and more recent gene sequences studies.
Main articles: Taxonomy of the Gastropoda (Bouchet & Rocroi, 2005) and Changes in the taxonomy
of gastropods since 2005
Bouchet & Rocroi (2005)[3][17] made changes in systematics, resulting in a taxonomy that is a step
closer to the evolutionary history of the phylum.
This classification system is based partly on the older systems of classification and partly on new
cladistic research. In the past, the taxonomy of gastropods was largely based on phenetic morphological
characters of the taxa. The recent advances are more based on molecular characters through research of
DNA[18] and RNA. This has made the taxonomical ranks and their hierarchy controversial. The debate about
these issues is not likely to end soon.
In this taxonomy, Bouchet, Rocroi et al. have used unranked clades for taxa above the rank of
superfamily (replacing the ranks suborder, order, superorder and subclass), while using the traditional
Linnaean approach for all taxa below the rank of superfamily. Whenever monophyly has not been tested, or
is known to be paraphyletic or polyphyletic, the term "group" or "informal group" has been used. The
classification of families into subfamilies is often not well resolved, and should be regarded as the best
possible hypothesis.
In 2004 Brian Simison and David R. Lindberg showed possible diphyletic origins of the Gastropoda
based on mitochondrial gene order and amino acid sequence analyses of complete genes.[19]
[edit] References
This article incorporates CC-BY-2.0 text from the reference.[15]
1. ^ 'Latest Early Cambrian', per Landing, E.; Geyer, G.; Bartowski, K. E. (March 2002). "Latest
Early Cambrian Small Shelly Fossils, Trilobites, and Hatch Hill Dysaerobic Interval on the Quebec
Continental Slope". Journal of Paleontology 76 (2): 287–305. doi:10.1666/0022-
3360(2002)076<0287:LECSSF>2.0.CO;2. edit; see section in article for first 'concrete evidence' in
Late Cambrian.
2. ^ a b (French) Cuvier G. (1795). "Second mémoire sur l'organisation et les rapports des
animaux à sang blanc, dans lequel on traite de la structure des Mollusques et de leur division en
ordres, lu à la Société d'histoire naturelle de Paris, le 11 Prairial, an III". Magazin Encyclopédique, ou
Journal des Sciences, des Lettres et des Arts 2: 433-449. page 448.
3. ^ a b c Bouchet P. & Rocroi J.-P. (Ed.); Frýda J., Hausdorf B., Ponder W., Valdes A. & Warén
A. 2005. Classification and nomenclator of gastropod families . Malacologia: International Journal of
Malacology, 47(1-2). ConchBooks: Hackenheim, Germany. ISBN 3-925919-72-4. 397 pp.
http://www.vliz.be/Vmdcdata/imis2/ref.php?refid=78278
4. ^ Britannica online: abundance of the Gastropoda
5. ^ McArthur, A.G.; M.G. Harasewych (2003). "Molecular systematics of the major lineages of
the Gastropoda.". Molecular Systematics and Phylogeography of Mollusks . Washington: Smithsonian
Books. pp. 140–160.
6. ^ a b c d e Chapman, A.D. (2009). Numbers of Living Species in Australia and the World, 2nd
edition. Australian Biological Resources Study, Canberra. Accessed 12 January 2010. ISBN 978 0
642 56860 1 (printed); ISBN 978 0 642 56861 8 (online).
7. ^ a b "gastropod". (2010). In Encyclopædia Britannica. Retrieved March 05, 2010, from
Encyclopædia Britannica Online.
8. ^ Strong E. E., Gargominy O., Ponder W. F. & Bouchet P. (2008). "Global Diversity of
Gastropods (Gastropoda; Mollusca) in Freshwater". Hydrobiologia 595: 149-166.
http://hdl.handle.net/10088/7390 doi:10.1007/s10750-007-9012-6.
9. ^ (Spanish) Nájera J. M. (1996). "Moluscos del suelo como plagas agrícolas y
cuarentenarias". X Congreso Nacional Agronómico / II Congreso de Suelos 1996 51-56. PDF
10.^ Kay, A.; Wells, F. E.; Poder, W. F. (1998). "Class Gastropoda". In Beesley, P. L.; Ross, G.
J. B.; Wells, A.. Mollusca: The Southern Synthesis. Fauna of Australia. CSIRO Publishing. pp. 565–
604. ISBN 0 643 05756 0.
11.^ Brusca, R. C.; Brusca, G. J. (2003). "Phylum Mollusca". Invertebrates. Sinauer Associates,
Inc.. pp. 701–769. ISBN 0-87893-097-3.
12.^ Louise R. Page (2006). "Modern insights on gastropod development: Reevaluation of the
evolution of a novel body plan". Integrative and Comparative Biology 46 (2): 134–143.
doi:10.1093/icb/icj018. http://intl-icb.oxfordjournals.org/cgi/content/full/46/2/134.
13.^ a b c d e Chase R.: Sensory Organs and the Nervous System. in Barker G. M. (ed.): The
biology of terrestrial molluscs. CABI Publishing, Oxon, UK, 2001, ISBN 0-85199-318-4. 1-146, cited
pages: 179-211.
14.^ Götting, Klaus-Jürgen (1994). "Schnecken". In Becker, U., Ganter, S., Just, C. &
Sauermost, R.. Lexikon der Biologie. Heidelberg: Spektrum Akademischer Verlag. ISBN 3-86025-
156-2.
15.^ a b c d Cunha R. L., Grande C. & Zardoya R. (23 August 2009). "Neogastropod phylogenetic
relationships based on entire mitochondrial genomes". BMC Evolutionary Biology 2009, 9: 210.
doi:10.1186/1471-2148-9-210
16.^ Paul Jeffery. Suprageneric classification of class Gastropoda. The Natural History
Museum, London, 2001.
17.^ Poppe G.T. & Tagaro S.P. 2006. The new classification of Gastropods according to
Bouchet & Rocroi, 2005. Visaya, février 2006: 10 pp. http://www.journal-
malaco.fr/bouchet&rocroi_2005_Visaya.pdf
18.^ Elpidio A. Remigio and Paul D.N. Hebert (2003). "Testing the utility of partial COI
sequences for phylogenetic (full text on line)". Molecular Phylogenetics and Evolution 29 (3): 641–
647. doi:10.1016/S1055-7903(03)00140-4. PMID 14615199.
http://www.bolinfonet.org/pdf/MPEVsnailpaper.pdf.
19.^ - Unitas malacologica, Newsletter number 21 december 2004 - a .pdf file

Wikimedia Commons has media related to: Gastropoda
Gastropods portal
• Gastropod reproductive behavior

• Reconstructions of fossil gastropods
• 2004 Linnean taxonomy of gastropods
• Webster S. J. & Fiorito G. (October 2001) "Socially guided behaviour in non-insect
invertebrates". Animal Cognition 4(2): 69–79. doi: 10.1007/s100710100108 - An article about social
learning also in gastropods.
Retrieved from "http://en.wikipedia.org/wiki/Gastropoda"
Categories: Gastropods
W000
Archaea

"Archea" redirects here. For the geologic eon, see Archean. For the spider family, see Archaeidae.
Archaea
Temporal range: Paleoarchean – Recent
Halobacteria sp. strain NRC-1, each cell about 5 μm long
Archaea
Domain:
Woese, Kandler & Wheelis, 1990
Kingdoms and phyla
Crenarchaeota
Euryarchaeota
Korarchaeota
Nanoarchaeota
Thaumarchaeota
The Archaea (/ɑrˈkiːə/ ( listen) ar-KEE-ə) are a group of single-celled microorganisms. A single
individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no
cell nucleus nor any other membrane-bound organelles within their cells. In the past they were viewed as an
unusual group of bacteria and named archaebacteria, but since the Archaea have an independent
evolutionary history and show many differences in their biochemistry from other forms of life, they are now
classified as a separate domain in the three-domain system. In this system the phylogenetically distinct
branches of evolutionary descent are the Archaea, Bacteria and Eukaryota. Archaea are divided into four
recognized phyla, but many more phyla may exist. Of these groups the Crenarchaeota and the
Euryarchaeota are most intensively studied. Classification is still difficult, since the vast majority have never
been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from
the environment. Although archaea have, in the past, been classed with bacteria as prokaryotes (or Kingdom
Monera), this classification is regarded by some as outdated.[1]
Archaea and bacteria are quite similar in size and shape, although a few archaea have very unusual
shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this visual similarity to
bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of
eukaryotes: notably the enzymes involved in transcription and translation. Other aspects of archaean
biochemistry are unique, such as their reliance on ether lipids in their cell membranes. The archaea exploit a
much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as
sugars, to using ammonia, metal ions or even hydrogen gas as nutrients. Salt-tolerant archaea (the
Halobacteria) use sunlight as an energy source and other species of archaea fix carbon; however, unlike
plants and cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and
divide by binary fission, fragmentation, or budding; in contrast to bacteria and eukaryotes, no known species
form spores.
Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs
and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, and
marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of
the most abundant groups of organisms on the planet. Archaea are now recognized as a major part of Earth's
life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal
pathogens or parasites are known, but they are often mutualists or commensals. One example is the
methanogens that inhabit the gut of humans and ruminants, where their vast numbers aid digestion.
Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea
that can endure high temperatures and organic solvents are exploited in biotechnology.
Contents
[hide]
• 1 Classification
• 1.1 New domain
• 1.2 Current classification
• 1.2.1 Species
• 2 Origin and evolution
• 2.1 Archaea and eukaryotes
• 3 Morphology
• 4 Structure, composition development, operation
• 4.1 Membranes
• 4.2 Wall and flagella
• 5 Metabolism
• 6 Genetics
• 7 Reproduction
• 8 Ecology
• 8.1 Habitats
• 8.2 Role in chemical cycling
• 8.3 Interactions with other organisms
• 8.3.1 Mutualism
• 8.3.2 Commensalism
• 9 Significance in technology and industry
[edit] Classification
[edit] New domain
For much of the 20th century, prokaryotes were regarded as a single group of organisms and
classified based on their biochemistry, morphology and metabolism. For example, microbiologists tried to
classify microorganisms based on the structures of their cell walls, their shapes, and the substances they
consume.[2] However, a new approach was proposed in 1965,[3] using the sequences of the genes in these
organisms to work out which prokaryotes are genuinely related to each other. This approach, known as
phylogenetics, is the main method used today.
Archaea were first found in extreme environments, such as volcanic hot springs.
Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George
E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes.[4] These two groups
were originally named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which
Woese and Fox termed Urkingdoms. Woese argued that this group of prokaryotes is a fundamentally
different sort of life. To emphasize this difference, these two domains were later renamed Archaea and
Bacteria.[5] The word archaea comes from the Ancient Greek ἀρχαῖα, meaning "ancient things".[6]
At first, only the methanogens were placed in this new domain, and the archaea were seen as
extremophiles that exist only in habitats such as hot springs and salt lakes. By the end of the 20th century,
microbiologists realized that archaea is a large and diverse group of organisms that are widely distributed in
nature and are common in much less extreme habitats, such as soils and oceans.[7] This new appreciation of
the importance and ubiquity of archaea came from using the polymerase chain reaction to detect prokaryotes
in samples of water or soil from their nucleic acids alone. This allows the detection and identification of
organisms that cannot be cultured in the laboratory, which generally remains difficult.[8][9]
[edit] Current classification

Further information: Biological classification and Systematics
The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field.
Current classification systems aim to organize archaea into groups of organisms that share structural
features and common ancestors.[10] These classifications rely heavily on the use of the sequence of
ribosomal RNA genes to reveal relationships between organisms (molecular phylogenetics).[11] Most of the
culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and
Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species
Nanoarchaeum equitans, which was discovered in 2003, has been given its own phylum, the Nanoarchaeota.
[12] A new phylum Korarchaeota has also been proposed. It contains a small group of unusual thermophilic
species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota.[13]
[14] Other recently detected species of archaea are only distantly related to any of these groups, such as the
Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN), which were discovered in 2006[15] and are
some of the smallest organisms known.[16]
The ARMAN are a new group of archaea recently discovered in acid mine drainage.
[edit] Species
The classification of archaea into species is also controversial. Biology defines a species as a group
of related organisms. The familiar exclusive breeding criterion (organisms that can breed with each other but
not with others), is of no help because archaea reproduce asexually.[17]
Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest
that individuals can be grouped into species-like populations given highly similar genomes and infrequent
gene transfer to/from cells with less-related genomes, as in the genus Ferroplasma.[18] On the other hand,
studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the
criterion's applicability.[19] A second concern is to what extent such species designations have practical
meaning.[20]
Current knowledge on genetic diversity is fragmentary and the total number of archaean species
cannot be estimated with any accuracy.[11] Estimates of the number of phyla range from 18 to 23, of which
only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups
are known from a single rRNA sequence, indicating that the diversity among these organisms remains
obscure.[21] The Bacteria also contain many uncultured microbes with similar implications for
characterization.[22]
[edit] Origin and evolution

Further information: Timeline of evolution
Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do
not have distinctive morphologies and fossil shapes cannot be used to identify them as Archaea.[23] Instead,
chemical fossils of unique lipids are more informative because such compounds do not occur in other
organisms.[24] Some publications suggest that archaean or eukaryotic lipid remains are present in shales
dating from 2.7 billion years ago;[25] such data have since been questioned.[26] Such lipids have also been
detected in Precambrian formations. The oldest such traces come from the Isua district of west Greenland,
which include Earth's oldest sediments, formed 3.8 billion years ago.[27] The archaeal lineage may be the
most ancient that exists on earth.[28]
Phylogenetic tree showing the relationship between the archaea and other forms of life. Eukaryotes
are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al.[29]
Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that
diverged early on from an ancestral colony of organisms.[30][31] A few biologists, however, argue that the
Archaea and Eukaryota arose from a group of bacteria.[32] In any case it is thought that viruses and archaea
began relationships approximately two billion years ago, and that co-evolution may have been occurring
between members of these groups.[33] It is possible that the last common ancestor of the bacteria and
archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments"
in archaeal terms, and organisms that live in cooler environments appeared only later.[34] Since the Archaea
and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote's only
surviving meaning is "not a eukaryote", limiting its value.[35]
[edit] Archaea and eukaryotes

The relationship between archaea and eukaryotes remains problematic. Aside from the similarities in
cell structure and function that are discussed below, many genetic trees group the two.
Complicating factors include claims that the relationship between eukaryotes and the archaeal
phylum Euryarchaeota is closer than the relationship between the Euryarchaeota and the phylum
Crenarchaeota[36] and the presence of archaean-like genes in certain bacteria, such as Thermotoga
maritima, from horizontal gene transfer.[37] The leading hypothesis is that the ancestor of the eukaryotes
diverged early from the Archaea,[38][39] and that eukaryotes arose through fusion of an archaean and
eubacterium, which became the nucleus and cytoplasm; this accounts for various genetic similarities but runs
into difficulties explaining cell structure.[40]
[edit] Morphology
The sizes of prokaryotic cells relative to other cells and biomolecules (logarithmic scale)
Individual archaea range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in various
shapes, commonly as spheres, rods, spirals or plates.[41] Other morphologies in the Crenarchaeota include
irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in
diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum.[42]
Haloquadratum walsbyi are flat, square archaea that live in hypersaline pools.[43] These unusual shapes are
probably maintained both by their cell walls and a prokaryotic cytoskeleton. Proteins related to the
cytoskeleton components of other organisms exist in archaea,[44] and filaments form within their cells,[45]
but in contrast to other organisms, these cellular structures are poorly understood.[46] In Thermoplasma and
Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae.
[47]
Some species form aggregates or filaments of cells up to 200 μm long.[41] These organisms can be
prominent in biofilms.[48] Notably, aggregates of Thermococcus coalescens cells fuse together in culture,
forming single giant cells.[49] Archaea in the genus Pyrodictium produce an elaborate multicell colony
involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect
them into a dense bush-like agglomeration.[50] The function of these cannulae is not settled, but they may
allow communication or nutrient exchange with neighbors.[51] Multi-species colonies exist, such as the
"string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a
novel Euryarchaeota species are spaced along thin filaments that can range up to 15 centimetres (5.9 in)
long; these filaments are made of a particular bacteria species.[52]
[edit] Structure, composition development, operation

Archaea and bacteria have generally similar cell structure, but cell composition and organization set
the archaea apart. Like bacteria, archaea lack interior membranes and organelles.[35] Like bacteria, archaea
cell membranes are usually bounded by a cell wall and they swim using one or more flagella.[53] Structurally,
archaea are most similar to gram-positive bacteria. Most have a single plasma membrane and cell wall, and
lack a periplasmic space; the exception to this general rule is Ignicoccus, which possess a particularly large
periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.[54]
[edit] Membranes
Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-

glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6,
ester linkages; 7, D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes;
10, lipid monolayer of some archaea.
Archaeal membranes are made of molecules that differ strongly from those in other life forms,
showing that archaea are related only distantly to bacteria and eukaryotes.[55] In all organisms cell
membranes are made of molecules known as phospholipids. These molecules possess both a polar part that
dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These
dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the
water and the tails facing away from it. The major structure in cell membranes is a double layer of these
phospholipids, which is called a lipid bilayer.
These phospholipids are unusual in four ways:
• Bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas
archaea have membranes composed of glycerol-ether lipids.[56] The difference is the type of bond
that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right.
In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. Ether bonds are
chemically more resistant than ester bonds. This stability might help archaea to survive extreme
temperatures and very acidic or alkaline environments.[57] Bacteria and eukaryotes do contain some
ether lipids, but in contrast to archaea these lipids are not a major part of their membranes.
• The stereochemistry of the glycerol moiety is the reverse of that found in other organisms.
The glycerol moiety can occur in two forms that are mirror images of one another, called the right-
handed and left-handed forms; in chemistry these are called enantiomers. Just as a right hand does
not fit easily into a left-handed glove, a right-handed glycerol molecule generally cannot be used or
made by enzymes adapted for the left-handed form. This suggests that archaea use entirely different
enzymes for synthesizing phospholipids than do bacteria and eukaryotes. Such enzymes developed
very early in life's history, suggesting an early split from the other two domains.[55]
• Archaeal lipid tails are chemically different from other organisms. Archaeal lipids are based
upon the isoprenoid sidechain and are long chains with multiple side-branches and sometimes even
cyclopropane or cyclohexane rings.[58] This is in contrast to the fatty acids found in other organisms'
membranes, which have straight chains with no branches or rings. Although isoprenoids play an
important role in the biochemistry of many organisms, only the archaea use them to make
phospholipids. These branched chains may help prevent archaean membranes from leaking at high
temperatures.[59]
• In some archaea the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the
tails of two independent phospholipid molecules into a single molecule with two polar heads; this
fusion may make their membranes more rigid and better able to resist harsh environments.[60] For
example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in
its highly acidic habitat.[61]
[edit] Wall and flagella

Further information: Cell wall
Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall.[47] In most archaea the
wall is assembled from surface-layer proteins, which form an S-layer.[62] An S-layer is a rigid array of protein
molecules that cover the outside of the cell (like chain mail).[63] This layer provides both chemical and
physical protection, and can prevent macromolecules from contacting the cell membrane.[64] Unlike
bacteria, archaea lack peptidoglycan in their cell walls.[65] Methanobacteriales do have cell walls containing
pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical
structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-
acetylmuramic acid.[64]
Archaea flagella operate like bacterial flagella—their long stalks are driven by rotatory motors at the
base. These motors are powered by the proton gradient across the membrane. However, archaeal flagella
are notably different in composition and development.[53] The two types of flagella evolved from different
ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system,[66][67] while
archaeal flagella appear to have evolved from bacterial type IV pili.[68] In contrast to the bacterial flagellum,
which is hollow and is assembled by subunits moving up the central pore to the tip of the flagella, archaeal
flagella are synthesized by adding subunits at the base.[69]
[edit] Metabolism
Further information: Microbial metabolism
Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of
energy. These reactions are classified into nutritional groups, depending on energy and carbon sources.
Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs).
These include nitrifiers, methanogens and anaerobic methane oxidisers.[70] In these reactions one
compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One
compound acts as an electron donor and one as an electron acceptor. The energy released generates
adenosine triphosphate (ATP) through chemiosmosis, in the same basic process that happens in the
mitochondrion of eukaryotic cells.[71]
Other groups of archaea use sunlight as a source of energy (they are phototrophs). However,
oxygen–generating photosynthesis does not occur in any of these organisms.[71] Many basic metabolic
pathways are shared between all forms of life; for example, archaea use a modified form of glycolysis (the
Entner–Doudoroff pathway) and either a complete or partial citric acid cycle.[72] These similarities to other
organisms probably reflect both early origins in the history of life and their high level of efficiency.[73]
Nutritional types in archaeal metabolism
Source of
Nutritional type Source of carbon Examples
energy
Organic
Phototrophs Sunlight Halobacteria
compounds
Organic
Inorganic Ferroglobus,
Lithotrophs compounds or carbon
compounds Methanobacteria or Pyrolobus
fixation
Organic
Organic Pyrococcus, Sulfolobus
Organotrophs compounds or carbon
compounds or Methanosarcinales
fixation
Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This form
of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen.[74]
A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen.
Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and
methanofuran.[75] Other organic compounds such as alcohols, acetic acid or formic acid are used as
alternative electron acceptors by methanogens. These reactions are common in gut-dwelling archaea. Acetic
acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These
acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of
microorganisms that produce biogas.[76]
Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in
proton transfer are shown as ball-and-stick models.[77]
Other archaea use CO2 in the atmosphere as a source of carbon, in a process called carbon fixation
(they are autotrophs). This process involves either a highly modified form of the Calvin cycle[78] or a recently
discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle.[79] The
Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA
pathway.[80] Carbon–fixation is powered by inorganic energy sources. No known archaea carry out
photosynthesis.[81] Archaeal energy sources are extremely diverse, and range from the oxidation of
ammonia by the Nitrosopumilales[82][83] to the oxidation of hydrogen sulfide or elemental sulfur by species
of Sulfolobus, using either oxygen or metal ions as electron acceptors.[71]
Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria,
light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions
out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then
converted into ATP by ATP synthase.[41] This process is a form of photophosphorylation. The ability of these
light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a
retinol cofactor buried in the center of the protein.[84]
[edit] Genetics
Further information: Plasmid, Genome
Archaea usually have a single circular chromosome,[85] the size of which may be as great as
5,751,492 base pairs in Methanosarcina acetivorans,[86] the largest known archaean genome. One-tenth of
this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, the smallest archaean genome
known; it is estimated to contain only 537 protein-encoding genes.[87] Smaller independent pieces of DNA,
called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact,
in a process that may be similar to bacterial conjugation.[88][89]
Sulfolobus infected with the DNA virus STSV1.[90] Bar is 1 micrometer.

Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of
virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops.[91] These viruses
have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales.
[92] A single-stranded DNA virus that infects halophilic archaea was identified in 2009.[93] Defenses against
these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of
the viruses.[94][95]
Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins
encoded by any one archaeal genome being unique to the domain, although most of these unique genes
have no known function.[96] Of the remainder of the unique proteins that have an identified function, most
are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common
core of cell function, relating mostly to transcription, translation, and nucleotide metabolism.[97] Other
characteristic archaean features are the organization of genes of related function—such as enzymes that
catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and
their aminoacyl tRNA synthetases.[97]
Transcription and translation in archaea resemble these processes in eukaryotes more than in
bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in
eukaryotes.[85] Although archaea only have one type of RNA polymerase, its structure and function in
transcription seems to be close to that of the eukaryotic RNA polymerase II, with similar protein assemblies
(the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter.[98]
However, other archaean transcription factors are closer to those found in bacteria.[99] Post-transcriptional
modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many
introns in their transfer RNA and ribosomal RNA genes,[100] and introns may occur in a few protein-
encoding genes.[101][102]
[edit] Reproduction
Further information: Asexual reproduction
Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does
not occur, so if a species of archaea exists in more than one form, all have the same genetic material.[41]
Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter
chromosomes separate, the cell divides.[103] Details have only been investigated in the genus Sulfolobus,
but here that cycle has characteristics that are similar to both bacterial and eukaryotic systems. The
chromosomes replicate from multiple starting-points (origins of replication) using DNA polymerases that
resemble the equivalent eukaryotic enzymes.[104] However, the proteins that direct cell division, such as the
protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is
constructed across the center of the cell, are similar to their bacterial equivalents.[103]
Both bacteria and eukaryotes, but not archaea, make spores.[105] Some species of Haloarchaea
undergo phenotypic switching and grow as several different cell types, including thick-walled structures that
are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these
are not reproductive structures and may instead help them reach new habitats.[106]
[edit] Ecology
[edit] Habitats
Archaea exist in a broad range of habitats, and as a major part of global ecosystems,[7] may
contribute up to 20% of earth's biomass.[107] The first-discovered archaeans were extremophiles.[70]
Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black
smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline
water. However, archaea include mesophiles that grow in mild conditions, in marshland, sewage, the oceans,
and soils.[7]
Image of plankton (light green) in the oceans; archaea form a major part of oceanic life.
Extremophile archaea are members of four main physiological groups. These are the halophiles,
thermophiles, alkaliphiles, and acidophiles.[108] These groups are not comprehensive or phylum-specific,
nor are they mutually exclusive, since some archaea belong to several groups. Nonetheless, they are a
useful starting point for classification.
Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt
lakes and outnumber their bacterial counterparts at salinities greater than 20–25%.[70] Thermophiles grow
best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow
optimally at temperatures greater than 80 °C (176 °F).[109] The archaeal Methanopyrus kandleri Strain 116
grows at 122 °C (252 °F), the highest recorded temperature of any organism.[110]
Other archaea exist in very acidic or alkaline conditions.[108] For example, one of the most extreme
archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 molar
sulfuric acid.[111]
This resistance to extreme environments has made archaea the focus of speculation about the
possible properties of extraterrestrial life.[112] Some extremophile habitats are not dissimilar to those on
Mars,[113] leading to the suggestion that viable microbes could be transferred between planets in
meteorites.[114]
Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic
environments but are also present, sometimes in high numbers, at low temperatures as well. For example,
archaea are common in cold oceanic environments such as polar seas.[115] Even more significant are the
large numbers of archaea found throughout the world's oceans in non-extreme habitats among the plankton
community (as part of the picoplankton).[116] Although these archaea can be present in extremely high
numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied
in pure culture.[117] Consequently, our understanding of the role of archaea in ocean ecology is rudimentary,
so their full influence on global biogeochemical cycles remains largely unexplored.[118] Some marine
Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen
cycle,[119] although these oceanic Crenarchaeota may also use other sources of energy.[120] Vast numbers
of archaea are also found in the sediments that cover the sea floor, with these organisms making up the
majority of living cells at depths over 1 meter below the ocean bottom.[121][122]
[edit] Role in chemical cycling

Further information: Biogeochemical cycle
Archaea recycle elements such as carbon, nitrogen and sulfur through their various habitats.
Although these activities are vital for normal ecosystem function, archaea can also contribute to human-made
changes, and even cause pollution.
Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove
nitrogen from ecosystems, such as nitrate-based respiration and denitrification, as well as processes that
introduce nitrogen, such as nitrate assimilation and nitrogen fixation.[123][124] Archaean involvement in
ammonia oxidation reactions was recently discovered. These reactions are particularly important in the
oceans.[125][126] The archaea also appear to be crucial for ammonia oxidation in soils. They produce nitrite,
which other microbes then oxidize to nitrate. Plants and other organisms consume the latter.[127]
In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks,
making it available to other organisms. However, the archaea that do this, such as Sulfolobus, produce
sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to
acid mine drainage and other environmental damage.[128]
In the carbon cycle, methanogen archaea remove hydrogen and are important in the decay of
organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems,
such as sediments, marshes and sewage treatment works.[129] However, methane is one of the most
abundant greenhouse gases in Earth's atmosphere, constituting 18% of the global total.[130] It is 25 times
more potent as a greenhouse gas than carbon dioxide.[131] Methanogens are the primary source of
atmospheric methane, and are responsible for most of the world's yearly methane emissions.[132] As a
consequence, these archaea contribute to global greenhouse gas emissions and global warming.
[edit] Interactions with other organisms

Further information: Biological interaction
Methanogenic archaea form a symbiosis with termites.
The well-characterized interactions between archaea and other organisms are either mutual or
commensal. As of 2007, no clear examples of archaeal pathogens or parasites were known.[133][134]
However, a relationship has been proposed between some species of methanogens and infections in the
mouth,[135][136] and Nanoarchaeum equitans may be a parasite of another species of archaea, since it only
survives and reproduces within the cells of the Crenarchaeon Ignicoccus hospitalis,[137] and appears to offer
no benefit to its host.[138]
[edit] Mutualism
One well-understood example of mutualism is the interaction between protozoa and methanogenic
archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites.[139] In these
anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases
hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens
convert hydrogen to methane, protozoa benefit from more energy.[140]
In anaerobic protozoa such as Plagiopyla frontata, archaea reside inside the protozoa and consume
hydrogen produced in their hydrogenosomes.[141][142] Archaea also associate with larger organisms. For
example, the marine archaean Cenarchaeum symbiosum lives within (is an endosymbiont of) the sponge
Axinella mexicana.[143]
[edit] Commensalism
Archaea can also be commensals, benefiting from an association without helping or harming the
other organism. For example, the methanogen Methanobrevibacter smithii is by far the most common
archaean in the human flora, making up about one in ten of all the prokaryotes in the human gut.[144] In
termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the
gut to aid digestion.[145] Archaean communities also associate with a range of other organisms, such as on
the surface of corals,[146] and in the region of soil that surrounds plant roots (the rhizosphere).[147][148]
[edit] Significance in technology and industry

Further information: Biotechnology
Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and
alkalinity, are a source of enzymes that function under these harsh conditions.[149][150] These enzymes
have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase
from Pyrococcus furiosus, revolutionized molecular biology by allowing the polymerase chain reaction to be
used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and
pullulanases in other species of Pyrococcus that function at over 100 °C (212 °F) allow food processing at
high temperatures, such as the production of low lactose milk and whey.[151] Enzymes from these
thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally
friendly processes in green chemistry that synthesize organic compounds.[150] This stability makes them
easier to use in structural biology. Consequently the counterparts of bacterial or eukaryotic enzymes from
extremophile archaea are often used in structural studies.[152]
In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in
biotechnology is less developed. Methanogenic archaea are a vital part of sewage treatment, since they are
part of the community of microorganisms that carry out anaerobic digestion and produce biogas.[153] In
mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold,
cobalt and copper.[154]
Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been
characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus.[155]
These compounds differ in structure from bacterial antibiotics, so they may have novel modes of action. In
addition, they may allow the creation of new selectable markers for use in archaeal molecular biology.[156]
[edit] See also

• Aerobic methane production
• List of Archaea genera
• List of sequenced archaeal genomes
• The Surprising Archaea (book)
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inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov". Proc Natl Acad Sci USA 93
(13): 6241–6. doi:10.1073/pnas.93.13.6241. PMID 8692799.
144.^ Eckburg PB, Bik EM, Bernstein CN, et al. (June 2005). "Diversity of the human intestinal
microbial flora". Science 308 (5728): 1635–8. doi:10.1126/science.1110591. PMID 15831718.
145.^ Samuel BS, Gordon JI (June 2006). "A humanized gnotobiotic mouse model of host-
archaeal-bacterial mutualism". Proc. Natl. Acad. Sci. U.S.A. 103 (26): 10011–6.
doi:10.1073/pnas.0602187103. PMID 16782812.
146.^ Wegley, L; Yu; Breitbart; Casas; Kline; Rohwer (2004). "Coral-associated Archaea" (PDF).
Marine Ecology Progress Series 273: 89–96. doi:10.3354/meps273089.
http://www.marine.usf.edu/genomics/PDFs%20of%20papers/wegleyetal2004.pdf.
147.^ Chelius MK, Triplett EW (April 2001). "The Diversity of Archaea and Bacteria in
Association with the Roots of Zea mays L". Microb. Ecol. 41 (3): 252–63.
doi:10.1007/s002480000087. PMID 11391463.
148.^ Simon HM, Dodsworth JA, Goodman RM (October 2000). "Crenarchaeota colonize
terrestrial plant roots". Environ. Microbiol. 2 (5): 495–505. doi:10.1046/j.1462-2920.2000.00131.x.
PMID 11233158.
149.^ Breithaupt H (2001). "The hunt for living gold. The search for organisms in extreme
environments yields useful enzymes for industry". EMBO Rep. 2 (11): 968–71. doi:10.1093/embo-
reports/kve238. PMID 11713183.
150.^ a b Egorova K, Antranikian G (2005). "Industrial relevance of thermophilic Archaea". Curr.
Opin. Microbiol. 8 (6): 649–55. doi:10.1016/j.mib.2005.10.015. PMID 16257257.
151.^ Synowiecki J, Grzybowska B, Zdziebło A (2006). "Sources, properties and suitability of
new thermostable enzymes in food processing". Crit Rev Food Sci Nutr 46 (3): 197–205.
doi:10.1080/10408690590957296. PMID 16527752.
152.^ Jenney FE, Adams MW (January 2008). "The impact of extremophiles on structural
genomics (and vice versa)". Extremophiles 12 (1): 39–50. doi:10.1007/s00792-007-0087-9.
PMID 17563834.
153.^ Schiraldi C, Giuliano M, De Rosa M (2002). "Perspectives on biotechnological
applications of archaea" (PDF). Archaea 1 (2): 75–86. doi:10.1155/2002/436561. PMID 15803645.
PMC 2685559. http://archaea.ws/archive/pdf/volume1/issue2/1-75.pdf.
154.^ Norris PR, Burton NP, Foulis NA (2000). "Acidophiles in bioreactor mineral processing".
Extremophiles 4 (2): 71–6. doi:10.1007/s007920050139. PMID 10805560.
155.^ O'Connor EM, Shand RF (January 2002). "Halocins and sulfolobicins: the emerging story
of archaeal protein and peptide antibiotics". J. Ind. Microbiol. Biotechnol. 28 (1): 23–31.
doi:10.1038/sj/jim/7000190. PMID 11938468.
156.^ Shand RF; Leyva KJ (2008). "Archaeal Antimicrobials: An Undiscovered Country". In
Blum P (ed.). Archaea: New Models for Prokaryotic Biology. Caister Academic Press. ISBN 978-1-
904455-27-1.
• Howland, John L. (2000). The Surprising Archaea: Discovering Another Domain of Life.
Oxford: Oxford University Press. ISBN 0-19-511183-4.
• Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed.). Englewood
Cliffs, N.J: Prentice Hall. ISBN 0-13-144329-1.
• Garrett RA, Klenk H (2005). Archaea: Evolution, Physiology and Molecular Biology.
WileyBlackwell. ISBN 1-4051-4404-1.
• Cavicchioli R (2007). Archaea: Molecular and Cellular Biology. American Society for
Microbiology. ISBN 1-55581-391-7.
• Blum P (editor) (2008). Archaea: New Models for Prokaryotic Biology. Caister Academic
Press. ISBN 978-1-904455-27-1.
• Lipps G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends .
Caister Academic Press. ISBN 978-1-904455-35-6.
• Sapp, Jan (2009). The New Foundations of Evolution. On the Tree of Life . New York: Oxford
University Press. ISBN 019538850X.
• Schaechter, M (2009). Archaea (Overview) in The Desk Encyclopedia of Microbiology, 2nd
edition. San Diego and London: Elsevier Academic Press. ISBN 13: 978-0-12-374980-2.

Wikispecies has information related to: Archaea
Wikimedia Commons has media related to: Archaea
Look up Archaea in Wiktionary, the free dictionary.
General
• Introduction to the Archaea, ecology, systematics and morphology
• Oceans of Archaea – E.F. DeLong, ASM News, 2003
Classification
• NCBI taxonomy page on Archaea
• Genera of the domain Archaea – list of Prokaryotic names with Standing in Nomenclature
• Tree of Life illustration showing how Archaea relates to other lifeforms
• Shotgun sequencing finds nanoorganisms – discovery of the ARMAN group of archaea
Genomics
• Browse any completed archaeal genome at UCSC
• Comparative Analysis of Archaeal Genomes (at DOE's IMG system)
[hide]v · d · eArchaea classification

Domain : Archaea - Bacteria - Eukaryota
Crenarchaeota Acidilobales · Desulfurococcales · Sulfolobales · Thermoproteales
Euryarchaeota Archaeoglobi · Halobacteria · Methanobacteria · Methanococci ·

Methanomicrobia · Methanopyri · Thermococci · Thermoplasmata
Thaumarchaeota Cenarchaeales · Nitrosopumilales
Other Korarchaeota · Nanoarchaeota
[hide]v · d · eExtremophiles
Types Acidophile · Alkaliphile · Capnophile ·

Endolith · Halophile · Hypolith · Lipophile ·
Lithoautotroph · Lithophile · Methanogen ·
Metalotolerant · Oligotroph · Osmophile ·
Piezophile · Polyextremophile · Psychrophile ·
Radioresistant · Thermophile/Hyperthermophile ·
Thermoacidophile · Xerophile
Chloroflexus
aurantiacus · Deinococcus
radiodurans · Deinococcus-
Bacteria Thermus · Snottite · Thermus
aquaticus · Thermus
thermophilus · Spirochaeta
Notable americana · GFAJ-1
extremophiles
Pyrococcus furiosus ·
Archaea Strain 121 · Pyrolobus fumarii
Paralvinella sulfincola ·
Animalia Pompeii worm · Tardigrada
Related Abiogenic petroleum origin ·

articles Acidithiobacillales · Acidobacteria · Acidophiles in
acid mine drainage · Archaeoglobaceae · Berkeley
Pit · Blood Falls · Crenarchaeota · Grylloblattidae ·
Halobacteria · Halobacterium · Helaeomyia
petrolei · Hydrothermal vent · Methanopyrus ·
Movile Cave · Radioresistance · Radiotrophic
fungus · Rio Tinto · Taq polymerase ·
Thermostability · Thermotogae
Retrieved from "http://en.wikipedia.org/wiki/Archaea"
Categories: Archaea | Extremophiles | Microbiology

W000
Vertebrate

Vertebrate
Vertebrates
Temporal range: Cambrian-Recent,[1] 525–0 Ma
PreЄ
g
Individual organisms from each major vertebrate group. Clockwise, starting from top left:
Fire Salamander, Saltwater Crocodile, Southern Cassowary, Black-and-rufous Giant Elephant
Shrew, Ocean Sunfish
Kingdom: Animalia
Phylum: Chordata
(unranked): Craniata
Vertebrata
Subphylum:
Cuvier, 1812
Simplified grouping (see text)
• Fishes
• Tetrapods
Vertebrates are members of the subphylum Vertebrata, chordates with backbones and spinal
columns. About 58,000 species of vertebrates have been currently described.[2] Vertebrata is the largest
subphylum of chordates, and contains many familiar groups of large land animals. Vertebrates are the
animals from the groups of jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and
birds. Extant vertebrates range in size from the carp species Paedocypris, at as little as 7.9 mm (0.3 inch), to
the Blue Whale, at up to 33 m (110 ft). Vertebrates make up about 5% of all described animal species; the
rest are invertebrates, which lack backbones.
The vertebrates traditionally include the hagfish, which do not have proper vertebrae, though their
closest living relatives, the lampreys, do have vertebrae.[3] For this reason, the vertebrate subphylum is
sometimes referred to as "Craniata", as all members do possess a cranium.
Contents
[hide]
• 1 Etymology
• 2 Anatomy and morphology
• 3 Evolutionary history
• 4.1 Traditional classification
• 4.2 Phylogenetic relationships
• 5 See also
• 6 References
• 7 Bibliography
[edit] Etymology
The word vertebrate derives from the Latin word vertebratus (Pliny), meaning joint of the spine.[4] It
is closely related to the word vertebra, which refers to any of the bones or segments of the spinal column.[5]
[edit] Anatomy and morphology

All vertebrates are built along the basic chordate body plan: a stiff rod running through the length of
the animal (vertebral column or notochord), with a hollow tube of nervous tissue (the spinal cord) above it
and the gastrointestinal tract below. In all vertebrates the mouth is found at or right below the anterior end of
the animal, while the anus opens to the exterior before the end of the body. The remaining part of the body
continuing aft of the anus forms a tail with vertebrae and spinal cord, but no gut.
The defining characteristic of a vertebrate is the vertebral column, in which the notochord (a stiff rod
of uniform composition) has been replaced by a segmented series of stiffer elements (vertebrae) separated
by mobile joints (intervertebral discs, derived embryonically and evolutionarily from the notochord). However,
a few vertebrates have secondarily lost this anatomy, retaining the notochord into adulthood, as in the
sturgeon and the Latimeria. Jawed vertebrates are typified by paired appendages (fins or legs, which may be
secondarily lost), but this is not part of the definition of vertebrates as a whole.
Fossilized skeleton of Diplodocus, showing an extreme example of the backbone that characterizes
the vertebrates. Exhibited at the Museum für Naturkunde (Museum of Natural Science), Berlin.
[edit] Evolutionary history

Vertebrates originated about 525 million years ago during the Cambrian explosion, which was an
event of massive rise in organism diversity that occurred in the Cambrian period. The earliest known
vertebrate is believed to be the Myllokunmingia.[1] Molecular analysis since 1999 have suggested that the
hagfishes are most closely related to lampreys, and so also are vertebrates. Others consider them a sister
group of vertebrates in the common taxon of Craniata.[3][6] Another early vertebrate is Haikouichthys
ercaicunensis, also from the Chengjiang fauna 524 million years ago. All of these groups lacked a jaw in the
common sense.
The first jawed vertebrates appeared in the Ordovician and became common in the Devonian, often
known as the "Age of Fishes". The two groups of bony fishes, the actinopterygii and sarcopterygii, evolved
and became common. The Devonian also saw the demise of virtually all jawless fishes, save for lampreys
and hagfish, as well as the rise of the first labyrinthodonts, transitional between fish and amphibians. The
Placodermi, a group of fishes that dominated much of the late Silurian and the majority of the Devonian
period, also became extinct at the end of the Devonian.
The reptiles appeared from labyrinthodont stock in the subsequent Carboniferous period. The
anapsid and synapsid reptiles were common during the late Paleozoic, while the diapsids became dominant
during the Mesozoic. The dinosaurs gave rise to the birds in the Jurassic. The demise of the dinosaurs at the
end of the Cretaceous promoted expansion of the mammals, which had developed from the therapsids, a
group of synapsid reptiles, during the Late Triassic Period. The post-dinosaur world have seen great
diversification of bony fishes, frogs, birds and mammals.
Over half of all living vertebrate species (about 32,000 species) are fishes (non-tetrapod craniates), a
diverse set of lineages that inhabit all the world’s aquatic ecosystems, from snow minnows (Cypriniformes) in
Himalayan lakes at elevations over 4,600 meters (15,000 feet) to flatfishes (order Pleuronectiformes) in the
Challenger Deep, the deepest ocean trench at about 11,000 meters (36,000 feet). Fishes of myriad varieties
are the main predators in most of the world’s water bodies, both freshwater and marine. The rest of the
vertebrate species are tetrapods, a single lineage that includes amphibians (frogs, with more than 5,800
species; salamanders, with about 580 species; and caecilians, with about 175 species); mammals (with over
5,400 species); and reptiles and birds (with more than 18,000 species). Tetrapods dominate the megafauna
of most terrestrial environments (including fossorial and arboreal realms) and also include many partially or
fully aquatic groups (e.g., sea snakes, penguins, cetaceans).
There are several ways of classifying animals. Evolutionary systematics relies on anatomy,
physiology and evolutionary history, which is determined through similarities in anatomy and, if possible, the
genetics of organisms. Phylogenetic classification is based solely on phylogeny. Evolutionary systematics
gives an overview; phylogenetic systematics gives detail. The two systems are thus complementary rather
than opposed.[7]
[edit] Traditional classification

Conventional classification has living vertebrates grouped into seven classes based on traditional
interpretations of gross anatomical and physiological traits. This classification is the one most commonly
encountered in school textbooks, overviews, non-specialist, and popular works:[8]
• Subphylum Vertebrata
• Class Agnatha (jawless fish)
• Class Chondrichthyes (cartilaginous fishes)
• Class Osteichthyes (bony fishes)
• Class Amphibia (amphibians)
• Class Reptilia (reptiles)
• Class Aves (birds)
• Class Mammalia (mammals)
While this traditional classification is orderly most of the groups are paraphyletic, i.e. do not contain
all descendants of the class's common ancestor. Descendants of the first reptiles do for instance include the
birds and mammals as well as reptiles. Quite a few scientists working with vertebrates use a classification
based purely on phylogeny, organized by their known evolutionary history and sometimes disregarding the
conventional interpretations of their anatomy and physiology. An example based on Janvier (1981, 1997),
Shu et al. (2003), and Benton (2004)[9] is given here:
• Subphylum Vertebrata
• Superclass Agnatha or Cephalaspidomorphi (lampreys and other jawless fishes,
some ancestral to other vertebrates)
• Infraphylum Gnathostomata (vertebrates with jaws)
• Class †Placodermi (extinct armoured fishes)
• Class Chondrichthyes (cartilaginous fishes)
• Class †Acanthodii (extinct spiny "sharks")
• Superclass Osteichthyes (bony fishes)
• Class Actinopterygii (ray-finned bony fishes)
• Class Sarcopterygii (lobe-finned fishes, some ancestral to tetrapods)
• Superclass Tetrapoda (four-limbed vertebrates)
• Class Amphibia (amphibians, some ancestral to the amniotes)
• Class †Synapsida (extinct mammal-like "reptiles", some ancestral to
mammals, sometimes classed with Reptilia)
• Class Mammalia (mammals)
• Class Reptilia (reptiles, some ancestral to birds)
• Class Aves (birds)
Most of the classes listed are not "complete" taxa: the agnathans have given rise to the jawed
vertebrates; the bony fishes have given rise to the land vertebrates; the traditional "amphibians" have given
rise to the reptiles (traditionally including the mammal-like "reptiles"), which in turn have given rise to the
birds and mammals.
[edit] Phylogenetic relationships

In phylogenetic taxonomy, the relationships between animals are not typically divided into ranks, but
illustrated as a nested "family tree" known as a cladogram. Phylogenetic groups are given definitions based
on their relationship to one another, rather than purely on physical traits such as the presence of a backbone.
This nesting pattern is often combined with traditional taxonomy (as above), in a practice known as
evolutionary taxonomy.
The cladogram presented below is based on studies compiled by Philippe Janvier and others for the
Tree of Life Web Project.[10]
unname
unnamed
unnamed
Gnathostomata
unnamed
Teleostomi
†Ac
ii
Osteichthyes
Actinopterygii
(ray-finned fishes)
Sarcopterygii
?
†Onychodontiformes
Coelacanthimorpha
(coelacanths)
unnamed
†Porolepimorpha
Dipnoi (lungfishes)
unnamed
†Rhizodontimorph
a
unnamed
†Osteolepimorph
a
Terrestrial
vertebrates
[edit] See also
• Invertebrate
• Marine vertebrates
[edit] References
1. ^ a b Shu et al.; Luo, H-L.; Conway Morris, S.; Zhang, X-L.; Hu, S-X.; Chen, L.; Han, J.; Zhu,
M. et al. (November 4, 1999). "Lower Cambrian vertebrates from south China". Nature 402: 42–46.
doi:10.1038/46965.
2. ^ Jonathan E.M. Baillie, et al. (2004). "A Global Species Assessment". World Conservation
Union. http://www.iucn.org/bookstore/HTML-books/Red%20List%202004/completed/table2.1.html.
3. ^ a b Kuraku et al.; Hoshiyama, D; Katoh, K; Suga, H; Miyata, T (December 1999).
"Monophyly of Lampreys and Hagfishes Supported by Nuclear DNA–Coded Genes". Journal of
Molecular Evolution 49 (6): 729. doi:10.1007/PL00006595. PMID 10594174.
4. ^ Douglas Harper, Historian. "vertebrate". Online Etymology Dictionary. Dictionary.com..
http://dictionary.reference.com/browse/vertebrate.
5. ^ Douglas Harper, Historian. "vertebra". Online Etymology Dictionary. Dictionary.com..
http://dictionary.reference.com/browse/vertebra.
6. ^ Nicholls, Henry (10 September 2009). "Mouth to Mouth". Nature 461 (7261): 164–166.
doi:10.1038/461164a. PMID 19741680.
7. ^ Hildebran, M. & Gonslow, G. (2001): Analysis of Vertebrate Structure. 5th edition. John
Wiley & Sons, Inc. New York, page 33: Comment: The problem of naming sister groups
8. ^ Romer, A.S. (1949): The Vertebrate Body. W.B. Saunders, Philadelphia. (2nd ed. 1955; 3rd
ed. 1962; 4th ed. 1970)
9. ^ Benton, Michael J. (2004-11-01). Vertebrate Palaeontology (Third ed.). Blackwell
Publishing. pp. 455 pp.. ISBN 0632056371/978-0632056378.
http://palaeo.gly.bris.ac.uk/benton/vertclass.html.
10.^ Janvier, Philippe. 1997. Vertebrata. Animals with backbones. Version 01 January 1997
(under construction). http://tolweb.org/Vertebrata/14829/1997.01.01 in The Tree of Life Web Project,
http://tolweb.org/
[edit] Bibliography
• Kardong, Kenneth V. (1998). Vertebrates: Comparative Anatomy, Function, Evolution
(second ed.). USA: McGraw-Hill. pp. 747 pp.. ISBN 0-07-115356-X/0-697-28654-1.
http://www.amazon.com/Vertebrates-Comparative-Anatomy-Function-Evolution/dp/0072909560.
• "Vertebrata". Integrated Taxonomic Information System.
http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=331030.
Retrieved 6 August 2007.
Wikispecies has information related to: Vertebrata
• Tree of Life
• Tunicates and not cephalochordates are the closest living relatives of vertebrates
• Vertebrate Pests chapter in United States Environmental Protection Agency and University of
Florida/Institute of Food and Agricultural Sciences National Public Health Pesticide Applicator
Training Manual
[hide]v · d · eExtant phyla of kingdom Animalia by subkingdom
Parazoa Porifera (Calcarea, Demospongiae, Hexactinellida) · Placozoa (Trichoplax)
Mesozoa Orthonectida · Rhombozoa
Eumetazoa Radiata Ctenophora · Cnidaria (Anthozoa, Hydrozoa, Scyphozoa, Cubozoa, Stauroz
Bilateria Protostomia Ecdysozoa Cycloneuralia: Scalidophora (K

Loricifera, Priapulida) · Nematoida (Ne
Nematomorpha)
Panarthropoda: Onychophora
Arthropoda
Platy
Gastrotricha
Gnat
Platyzoa Rotifera · Aca
Gnathostomu
Micrognathoz
Spiralia Cycliophora
Troch
(Sipuncula, N
Mollusca, An
Lophotrochozoa
Lophophorata
Entoprocta, P
Brachiopoda
Deuterostomia Hemichordata · Echinoderma

Ambulacraria
Xenoturbellida
Craniata (Vertebrata, Myxini
Chordata
Cephalochordata · Tunicata
Basal/disputed Acoelomorpha (Acoela, Nemertodermatida) · Chae
[hide]v · d · eExtant Chordata classes by subphylum
Kingdom Animalia · Subkingdom Eumetazoa · (unranked) Bilateria · Superphylum Deuterostomia
Urochordata Ascidiacea (Ascidians) · Thaliacea · Appendicularia (Larvaceans) ·

(Tunicates) Sorberacea
Cephalochordata
(Lancelets) Leptocardii
Myxini (Hagfish) · Hyperoartia (Lampreys) · Chondrichthyes

Craniata (Cartilaginous fish) · Actinopterygii (Ray-finned fish) · Sarcopterygii (Lobe-
finned fish) · Amphibia (Amphibians) · Sauropsida (Reptiles) · Aves (Birds) ·
Mammalia (Mammals)
Retrieved from "http://en.wikipedia.org/wiki/Vertebrate"
Categories: Vertebrates
W000
Amphibian
For other uses, see Amphibian (disambiguation).
Amphibian
Amphibians
Temporal range: Late Devonian–present
PreЄ
g
Strawberry Poison-dart Frog, Oophaga pumilio
Kingdom: Animalia
Phylum: Chordata
Superclass: Tetrapoda
Amphibia
Class:
Linnaeus, 1758
Subclasses and Orders
Order Temnospondyli – extinct

Subclass Lepospondyli – extinct
Subclass Lissamphibia
Order Anura
Order Caudata
Order Gymnophiona
Amphibians (class Amphibia, from Amphi- meaning "on both sides" and -bios meaning "life"), such as
frogs, salamanders, and caecilians, are ectothermic (or cold-blooded) animals that metamorphose from a
juvenile water-breathing form, either to an adult air-breathing form, or to a paedomorph that retains some
juvenile characteristics. Mudpuppies, for example, retain juvenile gills in adulthood. The three modern orders
of amphibians are Anura (frogs and toads), Caudata (salamanders and newts), and Gymnophiona
(caecilians, limbless amphibians that resemble snakes), and in total they numbers approximately 6,500
species.[1] Many amphibians lay their eggs in water. Amphibians are superficially similar to reptiles, but
reptiles are amniotes, along with mammals and birds. The study of amphibians is called batrachology.
Amphibians are ecological indicators,[2] and in recent decades there has been a dramatic decline in
amphibian populations around the globe. Many species are now threatened or extinct.
Amphibians evolved in the Devonian Period and were top predators in the Carboniferous and
Permian Periods, but many lineages were wiped out during the Permian–Triassic extinction. One group, the
metoposaurs, remained important predators during the Triassic, but as the world became drier during the
Early Jurassic they died out, leaving a handful of relict temnospondyls like Koolasuchus and the modern
orders of Lissamphibia.
Contents
[hide]
• 1 Etymology
• 3 Taxonomic history
• 3.1 Respiration
• 3.2 Reproduction
• 4 Conservation
• 5 See also
• 6 References
[edit] Etymology
Amphibian is derived from the Ancient Greek term ἀμφίβιος amphíbios which means both kinds of
life, amphi meaning “both” and bio meaning life. The term was initially used for all kinds of combined natures.
Eventually it was used to refer to animals that live both in the water and on land.[3]

Main article: Labyrinthodontia
See also: List of prehistoric amphibians
The first major groups of amphibians developed in the Devonian Period from fish similar to the
modern coelacanth and lungfish which had evolved multi-jointed leg-like fins that enabled them to crawl
along the sea bottom. These amphibians were as much as one to five meters in length. However,
amphibians never developed the ability to live their entire lives on land, having to return to water to lay their
shell-less eggs.
In the Carboniferous Period, the amphibians moved up in the food chain and began to occupy the
ecological position currently occupied by crocodiles. These amphibians were notable for eating the mega
insects on land and many types of fishes in the water. During the Triassic Period, the better land-adapted
proto-crocodiles began to compete with amphibians, leading to their reduction in size and importance in the
biosphere.
[edit] Taxonomic history

Traditionally, amphibians have included all tetrapod vertebrates that are not amniotes. They are
divided into three subclasses, of which two are only known as extinct subclasses:
• Subclass Labyrinthodontia† (diverse Paleozoic and early Mesozoic group)
• Subclass Lepospondyli† (small Paleozoic group, sometimes included in the
Labyrinthodontia)
• Subclass Lissamphibia (frogs, toads, salamanders, newts, etc.)
Of these only the last subclass includes recent species.
With the phylogenetic classification Labyrinthodontia has been discarded as it is a paraphyletic group
without unique defining features apart from shared primitive characteristics. Classification varies according to
the preferred phylogeny of the author, whether they use a stem-based or node-based classification.
Generally amphibians are defined as the group that includes the common ancestors of all living amphibians
(frogs, salamanders and caecilians) and all their descendants. This may also include extinct groups like the
temnospondyls (traditionally placed in the subclass “Labyrinthodontia”), and the Lepospondyls. This means
that cladistic nomenclature list a large number of basal Devonian and Carboniferous tetrapod groups,
undoubtedly were “amphibians” in biology, that are formally placed in Amphibia in Linnaean taxonomy, but
not in cladistic taxonomy.
All recent amphibians are included in the subclass Lissamphibia, superorder Salientia, which is
usually considered a clade (which means that it is thought that they evolved from a common ancestor apart
from other extinct groups), although it has also been suggested that salamanders arose separately from a
temnospondyl-like ancestor.[4]
Authorities also disagree on whether Salientia is a Superorder that includes the order Anura, or
whether Anura is a sub-order of the order Salientia. Practical considerations seem to favor using the former
arrangement now. The Lissamphibia, superorder Salientia, are traditionally divided into three orders, but an
extinct salamander-like family, the Albanerpetontidae, is now considered part of the Lissamphibia, besides
the superorder Salientia. Furthermore, Salientia includes all three recent orders plus a single Triassic proto-
frog, Triadobatrachus.
Class Amphibia
• Subclass Lissamphibia
• Family Albanerpetontidae — Jurassic to Miocene (extinct)
• Superorder Salientia
• Genus Triadobatrachus — Triassic (extinct)
• Order Anura (frogs and toads): Jurassic to recent — 5,602 recent species in
48 families
• Order Caudata or Urodela (salamanders, newts): Jurassic to recent — 571
recent species in 9 families
• Order Gymnophiona or Apoda (caecilians): Jurassic to recent — 174 recent
species in 3 families
The actual number of species partly also depends on the taxonomic classification followed, the two
most common classifications being the classification of the website AmphibiaWeb, University of California
(Berkeley) and the classification by herpetologist Darrel Frost and The American Museum of Natural History,
available as the online reference database Amphibian Species of the World.[5] The numbers of species cited
above follow Frost.
[edit] Respiration
The lungs in amphibians are primitive compared to that of the amniotes, possessing few internal
septa, large alveoli and therefore a slow diffusion rate of oxygen into the blood. Ventilation is accomplished
by buccal pumping. However, most amphibians are able to exchange gasses with the water or air via their
skin. To enable sufficient cutaneous respiration, the surface of their highly vascularized skin must remain
moist in order for the oxygen to diffuse at a sufficient rate. Because oxygen concentration in the water
increases at both low temperatures and high flow rates, aquatic amphibians in these situations can rely
primarily on cutaneous respiration, as in the Titicaca water frog or hellbender salamanders. In air, where
oxygen is more concentrated, some small species can rely solely on cutaneous gas exchange, most
famously the plethodontid salamanders which have neither lungs nor gills. Many aquatic salamanders and all
tadpoles have gills in their larval stage, with some (such as the axolotl) retaining gills as aquatic adults.
[edit] Reproduction
Caecilian from the San Antonio zoo

For the purpose of reproduction most amphibians require fresh water. A few (e.g. Fejervarya raja)
can inhabit brackish water and even survive (though not thrive) in seawater, but there are no true marine
amphibians. Several hundred frog species in adaptive radiations (e.g., Eleutherodactylus, the Pacific
Platymantines, the Australo-Papuan microhylids, and many other tropical frogs), however, do not need any
water for breeding in the wild. They reproduce via direct development, an ecological and evolutionary
adaptation that has allowed them to be completely independent from free-standing water. Almost all of these
frogs live in wet tropical rainforests and their eggs hatch directly into miniature versions of the adult, passing
through the tadpole stage within the egg. Reproductive success of many amphibians is dependent not only
on the quantity of rainfall, but the seasonal timing.[6]
Several species have also adapted to arid and semi-arid environments, but most of them still need
water to lay their eggs. Symbiosis with single celled algae that lives in the jelly-like layer of the eggs has
evolved several times. The larvae of frogs (tadpoles or polliwogs) breathe with exterior gills at the start, but
soon a pouch is formed that covers the gills and the front legs. Lungs are also formed quite early to assist in
breathing. Newt larvae have large external gills that gradually disappear and the larvae of newts are quite
similar to the adult form from early age on.
Frogs and toads however have a tadpole stage, which is a totally different organism that is a grazing
algae or ongrowth or filtering plankton until a certain size has been reached, where metamorphosis sets in.
This metamorphosis lasts typically only 24 hours and consists of:
• The disappearance of the gill pouch, making the front legs visible.
• The transformation of the jaws into the big jaws of predatory frogs (most tadpoles are
scraping of algae or are filter feeders)
• The transformation of the digestive system: the long spiral gut of the larva is being replaced
by the typical short gut of a predator.
• An adaptation of the nervous system for stereoscopic vision, locomotion and feeding
• A quick growth and movement of the eyes to higher up the skull and the formation of eyelids.
• Formation of skin glands, thickening of the skin and loss of the lateral line system
• An eardrum is developed to lock the middle ear.
The disappearance of the tail is somewhat later (occurs at higher thyroxin levels) and after the tail
has been resorbed the animals are ready to leave the water. The material of the tail is being used for a quick
growth of the legs. The disappearance of the larval structures is a regulated process called apoptosis.
The transformation of newts when leaving the water is reversible except for the loss of the external
gills. When the animals enter the water again for reproduction changes are driven by prolactin, when they
return to the land phase by thyroxin
[edit] Conservation
Main article: Decline in amphibian populations
The Golden Toad of Monteverde, Costa Rica was among the first casualties of amphibian declines.
Formerly abundant, it was last seen in 1989.
Dramatic declines in amphibian populations, including population crashes and mass localized
extinction, have been noted in the past two decades from locations all over the world, and amphibian
declines are thus perceived as one of the most critical threats to global biodiversity. A number of causes are
believed to be involved, including habitat destruction and modification, over-exploitation, pollution, introduced
species, climate change, endocrine-disrupting pollutants, destruction of the ozone layer (ultraviolet radiation
has shown to be especially damaging to the skin, eyes, and eggs of amphibians), and diseases like
chytridiomycosis. However, many of the causes of amphibian declines are still poorly understood, and are a
topic of ongoing discussion. A global strategy to stem the crisis has been released in the form of the
Amphibian Conservation Action Plan (available at http://www.amphibians.org). Developed by over 80 leading
experts in the field, this call to action details what would be required to curtail amphibian declines and
extinctions over the next 5 years - and how much this would cost. The Amphibian Specialist Group of the
World Conservation Union (IUCN) is spearheading efforts to implement a comprehensive global strategy for
amphibian conservation. Amphibian Ark is an organization that was formed to implement the ex-situ
conservation recommendations of this plan, and they have been working with zoos and aquaria around the
world encouraging them to create assurance colonies of threatened amphibians. One such project is the
Panama Amphibian Rescue and Conservation Project that built on existing conservation efforts in Panama to
create a country-wide response to the threat of chytridiomycosis rapidly spreading into eastern Panama[7]
On January 21, 2008, Evolutionarily Distinct and Globally Endangered (EDGE), as given by chief
Helen Meredith, identified nature's most endangered species: "The EDGE amphibians are amongst the most
remarkable and unusual species on the planet and yet an alarming 85% of the top 100 are receiving little or
no conservation attention." The top 10 endangered species (in the List of endangered animal species)
include: the Chinese giant salamander, a distant relative of the newt, the tiny Gardiner's Seychelles, the
limbless Sagalla caecilian, South African ghost frogs, lungless Mexican salamanders, the Malagasy rainbow
frog, Chile's Darwin frog (Rhinoderma rufum) and the Betic Midwife Toad.[8][9][10][11]
[edit] See also

• Vegetal rotation
[edit] References
1. ^ Amphibian diversity and life history.
2. ^ Waddle, J, USE OF AMPHIBIANS AS ECOSYSTEM INDICATOR SPECIES
3. ^ "Amphibious definition". Dictionary.reference.com. http://dictionary.reference.com/search?
q=amphibious&db=luna. Retrieved 2009-04-07.
4. ^ Carroll, 2007
5. ^ Amphibian Species of the World The online database by Darrel Frost and The American
Museum of Natural History
6. ^ C.Michael Hogan. 2010. Abiotic factor. Encyclopedia of Earth. eds Emily Monosson and C.
Cleveland. National Council for Science and the Environment. Washington DC
7. ^ Panama Amphibian Rescue and Conservation Project http://amphibianrescue.org/?
page_id=91
8. ^ Lovell, Jeremy (2008-01-20). "Reuters, Giant newt, tiny frog identified as most at risk".
Reuters.com. http://www.reuters.com/article/latestCrisis/idUSL2038808. Retrieved 2009-04-07.
9. ^ Sample, Ian (2008-01-20). "Drive to save weird and endangered amphibians". The
Guardian (London). http://www.guardian.co.uk/environment/2008/jan/21/conservation. Retrieved
2009-04-07.
10.^ "/environment, images of the species". London: Guardian. 2008-01-18.
http://www.guardian.co.uk/environment/gallery/2008/jan/21/wildlife.conservation?
picture=332110244. Retrieved 2009-04-07.
11.^ "/environment, Gallery: the world's strangest amphibians". London: Guardian. 2008-01-18.
http://www.guardian.co.uk/environment/gallery/2008/jan/21/wildlife.conservation. Retrieved 2009-04-
07.
• Carroll, Robert L. (1988). Vertebrate Paleontology and Evolution. New York: W.H. Freeman
& Co..
• Carroll, Robert L. (2009). The Rise of Amphibians: 365 Million Years of Evolution . Baltimore:
The Johns Hopkins University Press. ISBN 978-0-8018-9140-3.
• Duellman, William E.; Linda Trueb (1994). Biology of Amphibians. Johns Hopkins University
Press. ISBN 978-0801847806.
• Frost, Darrel R.; Taran Grant, Julián Faivovich, Raoul H. Bain, Alexander Haas, Célio F.B.
Haddad, Rafael O. De Sá, Alan Channing, Mark Wilkinson, Stephen C. Donnellan, Christopher J.
Raxworthy, Jonathan A. Campbell, Boris L. Blotto, Paul Moler, Robert C. Drewes, Ronald A.
Nussbaum, John D. Lynch, David M. Green, Ward C. Wheeler (March 2006). "The Amphibian Tree
of Life". Bulletin of the American Museum of Natural History 297: 1–291. doi:10.1206/0003-
0090(2006)297[0001:TATOL]2.0.CO;2. http://hdl.handle.net/2246/5781.
• Pounds, J. Alan; Martín R. Bustamante, Luis A. Coloma, Jamie A. Consuegra, Michael P. L.
Fogden, Pru N. Foster, Enrique La Marca, Karen L. Masters, Andrés Merino-Viteri, Robert
Puschendorf, Santiago R. Ron, G. Arturo Sánchez-Azofeifa, Christopher J. Still and Bruce E. Young
(January 2006). "Widespread amphibian extinctions from epidemic disease driven by global
warming". Nature 439 (7073): 161–167. doi:10.1038/nature04246. PMID 16407945.
http://www.nature.com/nature/journal/v439/n7073/full/nature04246.html.
• San Mauro, Diego; Miguel Vences, Marina Alcobendas, Rafael Zardoya and Axel Meyer
(May 2005). "Initial diversification of living amphibians predated the breakup of Pangaea". American
Naturalist 165 (5): 590–599. doi:10.1086/429523. PMID 15795855.
• San Mauro, Diego (2010). "A multilocus timescale for the origin of extant amphibians".
Molecular Phylogenetics and Evolution 56 (2): 554–561. doi:10.1016/j.ympev.2010.04.019.
PMID 20399871.
• Solomon Berg Martin, Biology
• Stuart, Simon N.; Janice S. Chanson, Neil A. Cox, Bruce E. Young, Ana S. L. Rodrigues,
Debra L. Fischman, Robert W. Waller (December 2004). "Status and trends of amphibian declines
and extinctions worldwide". Science 306 (5702): 1783–1786. doi:10.1126/science.1103538.
PMID 15486254. http://www.sciencemag.org/cgi/content/full/306/5702/1783.
• S.N.Stuart, M.Hoffmann, J.S.Chanson, N.A.Cox, R.J.Berridge, P.Ramani, B.E. Young
(editors), Collective work. (September 2008). Threatened Amphibians of the World. Published by
Lynx Edicions, in association with IUCN-The World Conservation Union, Conservation International
and NatureServe.. ISBN 978-84-96553-41-5. http://www.hbw.com/lynx/en/lynx-edicions/portada-
lynx/MON0017-threatened-amphibians-world.html. 776 pages

Wikispecies has information related to: Amphibia
The Wikibook Dichotomous Key has a page on the topic of

Amphibia
• Save the Frogs!
• Amphibian Specialist Group
• AmphibiaWebEcuador
• Amphibians photos Brazil
• Amphibian Ark
• AmphibiaWeb
• Global Amphibian Assessment
• Amphibians of central Europe
• USGS--Online Guide for the Identification of Amphibians in North America north of Mexico
• General amphibian biology information - Living UnderWorld
• Panama Amphibian Rescue and Conservation Project
• Atlanta Botanical Garden Amphibian Conservation Program
• Amphibian vocalisations on Archival Sound Recordings
• Froglife (British conservation charity)

Cephalochordata Leptocardii
(Lancelets)

Mammalia (Mammals)
[hide]v · d · eExtant amphibian positions by subclass
Kingdom Animalia · Phylum Chordata · Subphylum Craniata · Superclass Tetrapoda
Lissamphibia Anura · Caudata (Urodela) · Gymnophiona (Apoda)
Retrieved from "http://en.wikipedia.org/wiki/Amphibian"
Categories: Amphibians
W000
Sponge
This article is about the aquatic animal. For the porous cleaning tool, see Sponge (material). For
other uses, see Sponge (disambiguation).
Sponge
Fossil range: Ediacaran–Recent
PreЄ
g
Domain: Eukaryota
Kingdom: Animalia
Phylum: Porifera*
Grant in Todd, 1836
Included groups
Calcarea
Hexactinellida
Demospongiae
Sponges are animals of the phylum Porifera (meaning "pore bearer"; pronounced /pɒˈrɪfərə/). Their
bodies consist of jelly-like mesohyl sandwiched between two thin layers of cells. While all animals have
unspecialized cells that can transform into specialized cells, sponges are unique in having some specialized
cells that can transform into other types, often migrating between the main cell layers and the mesohyl in the
process. Sponges do not have nervous, digestive or circulatory systems. Instead, most rely on maintaining a
constant water flow through their bodies to obtain food and oxygen and to remove wastes, and the shapes of
their bodies are adapted to maximize the efficiency of the water flow. All are sessile aquatic animals and,
although there are freshwater species, the great majority are marine (salt water) species, ranging from tidal
zones to depths exceeding 8,800 metres (5.5 mi).
While most of the approximately 5,000–10,000 known species feed on bacteria and other food
particles in the water, some host photosynthesizing micro-organisms as endosymbionts and these alliances
often produce more food and oxygen than they consume. A few species of sponge that live in food-poor
environments have become carnivores that prey mainly on small crustaceans.[1]
Most species use sexual reproduction, releasing sperm cells into the water and meeting ova that in
species are release and others are retained the "mother". The fertilized eggs form larvae which swim off in
search of places to settle. Sponges are known for regenerating from fragments that are broken off, although
this only works if the fragments include the right types of cells. A few species reproduce by budding. When
conditions deteriorate, for example as temperatures drop, many freshwater species and a few marine ones
produce gemmules, "survival pods" of unspecialized cells that remain dormant until conditions improve and
then either form completely new sponges or re-colonize the skeletons of their parents.
The mesohyl functions as an endoskeleton in most sponges, and is the only skeleton in soft sponges
that encrust hard surfaces such as rocks. More commonly the mesohyl is stiffened by mineral spicules, by
spongin fibers or both. Demosponges use spongin, and in many species silica spicules and in some species
calcium carbonate exoskeletons. Demosponges constitute about 90% of all known sponge species, including
all freshwater ones, and have the widest range of habitats. Calcareous sponges, which have calcium
carbonate spicules and in some species calcium carbonate exoskeletons, are restricted to relatively shallow
marine waters where production of calcium carbonate is easiest. The fragile glass sponges, with "scaffolding"
of silica spicules, are restricted to polar regions and the ocean depths where predators are rare. Fossils of all
of these types have been found in rocks dated from 580 million years ago. In addition Archaeocyathids,
whose fossils are common in rocks from 530 to 490 million years ago, are now regarded as a type of sponge.
It is generally thought that the sponge's closest single-celled relatives are choanoflagellates, which
strongly resemble the cells that sponges use to drive their water flow systems and capture most of their food.
It is also generally agreed that sponges do not form a monophyletic group, in other words do not include all
and only the descendants of a common ancestor, because it is thought that Eumetazoa (more complex
animals) are descendants of a sub-group of sponges. However it is uncertain which group of sponges is
closest to Eumetazoa, as both calcareous sponges and a sub-group of demosponges called
Homoscleromorpha have been nominated by different researchers. In addition a study in 2008 suggested
that the earliest animals may have been similar to modern comb jellies.
The few species of demosponge that have entirely soft fibrous skeletons with no hard elements have
been used by humans over thousands of years for several purposes, including as padding and as cleaning
tools. However by the 1950s these had been over-fished so heavily that the industry almost collapsed, and
most sponge-like materials are now synthetic. Sponges and their microscopic endosymbionts are now being
researched as possible sources of medicines for treating a wide range of diseases. Dolphins have been
observed using sponges as tools while foraging.
Contents
[hide]
• 1 Distinguishing features
• 2 Basic structure
• 2.1 Cell types
• 2.2 Glass sponges' syncytia
• 2.3 Water flow and body structures
• 2.4 Skeleton
• 3 Classes
• 4 Vital functions
• 4.1 Movement
• 4.2 Respiration, feeding and excretion
• 4.3 Carnivorous sponges
• 4.4 Endosymbionts
• 4.5 "Immune" system
• 4.6.1 Asexual
• 4.6.2 Sexual
• 4.6.3 Life cycle
• 4.7 Coordination of activities
• 5 Ecology
• 5.1 Habitats
Distinguishing features
Further information: Cnidaria and Ctenophore
Sponges constitute the phylum Porifera, and have been defined as sessile metazoans (multi-celled
animals) that have water intake and outlet openings connected by chambers lined with choanocytes, cells
with whip-like flagella. However, a few carnivorous sponges have lost these water flow systems and the
choanocytes.[2] All known living sponges can remold their bodies, as most types of their cells can move
within their bodies and a few can change from one type to another.[2][3]
Like cnidarians (jellyfish, etc.) and ctenophores (comb jellies), and unlike all other known metazoans,
sponges' bodies consist of a non-living jelly-like mass sandwiched between two main layers of cells.[4][5]
Cnidarians and ctenophores have simple nervous systems, and their cell layers are bound by internal
connections and by being mounted on a basement membrane (thin fibrous mat, also known as "basal
lamina").[5] Sponges have no nervous systems, their middle jelly-like layers have large and varied
populations of cells, and some types of cell in their outer layers may move into the middle layer and change
their functions.[3]
Cnidarians and
Sponges[3][4]
ctenophores[5]
Nervous system No Yes, simple
No , except that Yes: inter-cell

Cells in each layer
Homoscleromorpha have basement connections; basement
bound together
membranes.[6] membranes
Number of
cells in middle "jelly" Many Few
layer
Cells in outer
layers can move
Yes No
inwards and change
functions
Basic structure
Spicule
Cell types Water flow
A sponge's body is hollow and is held in shape by the mesohyl, a
jelly-like substance made mainly of collagen and reinforced by a dense
network of fibers also made of collagen. The inner surface is covered
with choanocytes, cells with cylindrical or conical collars surrounding one
flagellum per choanocyte. The wave-like motion of the whip-like flagella
drives water through the sponge's body. All sponges have ostia,
channels leading to the interior through the mesohyl, and in most
sponges these are controlled by tube-like porocytes that form closable
inlet valves. Pinacocytes, plate-like cells, form a single-layered external
skin over all other parts of the mesohyl that are not covered by
Main cell types of

Porifera[7]
choanocytes, and the pinacocytes also digest food particles that are too large to enter the ostia,[3][4] while
those at the base of the animal are responsible for anchoring it.[4]
Other types of cell live and move within the mesohyl:[3][4]
• Lophocytes are amoeba-like cells that move slowly through the mesohyl and secrete
collagen fibres.
• Collencytes are another type of collagen-producing cell.
• Rhabdiferous cells secrete polysaccharides that also form part of the mesohyl.
• Oocytes and spermatocytes are reproductive cells.
• Sclerocytes secrete the mineralized spicules ("little spines") that form the skeletons of many
sponges and in some species provide some defense against predators.
• In addition to or instead of sclerocytes, demosponges have spongocytes that secrete a form
of collagen that polymerizes into spongin, a thick fibrous material that stiffens the mesohyl.
• Myocytes ("muscle cells") conduct signals and cause parts of the animal to contract.
• "Grey cells" act as sponges' equivalent of an immune system.
• Archaeocytes (or amoebocytes) are amoeba-like cells that are totipotent, in other words each
is capable of transformation into any other type of cell. They also have important roles in feeding and
in clearing debris that block the ostia.
Glass sponges' syncytia
Glass sponges present a distinctive variation on this basic
plan. Their spicules, which are made of silica, form a scaffolding-like
Spicules framework between whose rods the living tissue is suspended like a
syncitium cobweb that contains most of the cell types.[3] This tissue is a
syncytium that in some ways behaves like many cells that share a
Choanosyncitium single external membrane, and in others like a single cell with
and collar bodies multiple nuclei. The mesohyl is absent or minimal. The syncytium's
showing interior cytoplasm, the soupy fluid that fills the interiors of cells, is organised
into "rivers" that transport nuclei, organelles ("organs" within cells)
Water flow and other substances.[9] Instead of choanocytes they have further
syncytia, known as choanosyncytia, which form bell-shaped
chambers which water enters via perforations. The insides of these
chambers are lined with "collar bodies", each consisting of a collar
and flagellum but without a nucleus of its own. The motion of the
flagella sucks water through passages in the "cobweb" and expels it
via the open ends of the bell-shaped chambers.[3]
Some types of cells have a single nucleus and membrane
each, but are connected to other single-nucleus cells and to the main
syncytium by "bridges" made of cytoplasm. The sclerocytes that build
spicules have multiple nuclei, and in glass sponge larvae they are
The glass sponge
connected to other tissues by cytoplasm bridges; such connections
Euplectella[8]
between sclerocytes have not so far been found in adults, but this
may simply reflect the difficulty of investigating such small-scale features. The bridges are controlled by
"plugged junctions" that
apparently permit some
substances to pass while
blocking others.[9]
Water flow and body

structures
Most sponges work
rather like chimneys: they take
in water at the bottom and eject
it from the osculum ("little
mouth") at the top. Since
ambient currents are faster at
the top, the suction effect that
they produce does some of the
work for free. Sponges can
control the water flow by various
combinations of wholly or
partially closing the osculum
Porifera body structures[10]

and ostia (the intake pores) and varying the beat of the flagella, and may shut it down if there is a lot of sand
or silt in the water.[3]
Although the layers of pinacocytes and choanocytes resemble the epithelia of more complex
animals, they are not bound tightly by cell-to-cell connections or a basal lamina (thin fibrous sheet
underneath). The flexibility of these layers and re-modeling of the mesohyl by lophocytes allow the animals to
adjust their shapes throughout their lives to take maximum advantage of local water currents.[3]
The simplest body structure in sponges is a tube or vase shape known as "asconoid", but this
severely limits the size of the animal. If it is simply scaled up, the ratio of its volume to surface area
increases, because surface increases as the square of length or width while volume increases proportionally
to the cube. The amount of tissue that needs food and oxygen is determined by the volume, but the pumping
capacity that supplies food and oxygen depends on the area covered by choanocytes. Asconoid sponges
seldom exceed 1 millimetre (0.039 in) in diameter.[3]
Some sponges overcome this limitation by adopting the "syconoid" structure, in which the body wall
is pleated. The inner pockets of the pleats are lined with choanocytes, which connect to the outer pockets of
the pleats by ostia. This increase in the number of choanocytes and hence in pumping capacity enables
syconoid sponges to grow up to a few centimeters in diameter. The "leuconid" pattern boosts pumping
capacity further by filling the interior almost completely with mesohyl that contains a network of chambers
lined with choanocytes and connected to each other and to the water intakes and outlet by tubes. Leuconid
sponges grow to over 1 metre (3.3 ft) in diameter, and the fact that growth in any direction increases the
number of choanocyte chambers enables them to take a wider range of forms, for example "encrusting"
sponges whose shapes follow those of the surfaces to which they attach. All freshwater and most shallow-
water marine sponges have leuconid bodies. The networks of water passages in glass sponges are similar to
the leuconid structure.[3] In all three types of structure the cross-section area of the choanocyte-lined regions
is much greater than that of the intake and outlet channels. This makes the flow slower near the choanocytes
and thus makes it easier for them to trap food particles.[3] For example in Leuconia, a small leuconoid
sponge about 10 centimetres (3.9 in) tall
and 1 centimetre (0.39 in) in diameter,
water enters each of more than 80,000
intake canals at 6 cm per minute.
However, because Leuconia has more
than 2 million flagellated chambers and other cells in
whose combined diameter is much
greater than that of the canals, water flow
through chambers slows to 3.6 cm per
hour, making it easy for choanocytes to
capture food. All the water is expelled
through a single osculum at about 8.5 cm
per second, fast enough to carry waste
products some distance away.[11] Seabed / rock
Water flow
Skeleton
In zoology a skeleton is any fairly
rigid structure of an animal, irrespective
of whether it has joints and irrespective of
whether it is biomineralized. The mesohyl
functions as an endoskeleton in most
sponges, and is the only skeleton in soft
Sponge with calcium carbonate skeleton[3]

sponges that encrust hard surfaces such as rocks. More commonly the mesohyl is stiffened by mineral
spicules, by spongin fibers or both. Spicules may be made of silica or calcium carbonate, and vary in shape
from simple rods to three-dimensional "stars" with up to six rays. Spicules are produced by sclerocyte cells,
[3] and may be separate, connected by joints, or fused.[2]
Some sponges also secrete exoskeletons that lie completely outside their organic components. For
example sclerosponges ("hard sponges") have massive calcium carbonate exoskeletons over which the
organic matter forms a thin layer with choanocyte chambers in pits in the mineral. These exoskeletons are
secreted by the pinacocytes that form the animals' skins.[3]
Classes
Sponges are divided into classes mainly according to the composition of their skeletons:[4]
Type of Spicules[ Spongin Massive Body
cells[4] 4] fibers[4] exoskeleton[12] form[4]
Single
Calcite Common. Asconoid,
nucleus, single
Calcarea May be individual Never Made of calcite if syconoid or
external
or large masses present. leuconoid
membrane
Mostly Silica
Glass sponges syncytia in all May be individual Never Never Leuconoid
species or fused
Demosponges Single Silica In many In some Leuconoid

nucleus, single species.
external species Made of aragonite if
membrane present.[2][12]
Vital functions
Spongia officinalis, "the kitchen sponge", is dark grey when alive
Movement
Although adult sponges are fundamentally sessile animals, some marine and freshwater species can
move across the bottom at speeds of 1–4 millimetres (0.039–0.16 in) per day, as a result of amoeba-like
movements of pinacocytes and other cells. A few species can contract their whole bodies, and many can
close their oscula and ostia.[3]
Respiration, feeding and excretion
Sponges do not have distinct circulatory, respiratory, digestive, and excretory systems – instead the
water flow system supports all these functions. They filter food particles out of the water flowing through
them. Particles larger than 50 micrometers cannot enter the ostia and pinacocytes consume them by
phagocytosis (engulfing and internal digestion). Particles from 0.5 μm to 50 μm are trapped in the ostia,
which taper from the outer to inner ends. These particles are consumed by pinacocytes or by archaeocytes
which partially extrude themselves through the walls of the ostia. Bacteria-sized particles, below
0.5 micrometers, pass through the ostia and are caught and consumed by choanocytes.[3] Since the
smallest particles are by far the most common, choanocytes typically capture 80% of a sponge's food supply.
[12] Archaeocytes transport food packaged in vesicles from cells that directly digest food to those that do not.
At least one species of sponge has internal fibers that function as tracks for use by nutrient-carrying
archaeocytes,[3] and these tracks also move inert objects.[4]
It used to be claimed that glass sponges could live on nutrients dissolved in sea water and were very
averse to silt.[13] However a study in 2007 found no evidence of this and concluded that they extract bacteria
and other micro-organisms from water very efficiently (about 79%) and process suspended sediment grains
to extract such prey.[14] Collar bodies digest food and distribute it wrapped in vesicles that are transported
by dynein "motor" molecules along bundles of microtubules that run throughout the syncytium.[3]
Sponges' cells absorb oxygen by diffusion from the water flow system, into which carbon dioxide and
other soluble waste products such as ammonia also diffuse. Archeocytes remove mineral particles that
threaten to block the ostia, transport them through the mesohyl and generally dump them into the outgoing
water current, although some species incorporate them into their skeletons.[3]
Carnivorous sponges
A few species that live in waters where the supply of food particles is very poor prey on crustaceans
and other small animals. Most belong to the family Cladorhizidae, but a few members of the Guitarridae and
Esperiopsidae are also carnivores.[15] In most cases little is known about how they actually capture prey,
although some species are thought to use either sticky threads or hooked spicules.[15][16] Most carnivorous
sponges live in deep waters, up to 8,840 metres (5.49 mi),[17] and the development of deep-ocean
exploration techniques is expected to lead to the discovery of several more.[3][15] However one species has
been found in Mediterranean caves at depths of 17–23 metres (56–75 ft), alongside the more usual filter
feeding sponges. The cave-dwelling predators capture crustaceans under 1 millimetre (0.039 in) long by
entangling them with fine threads, digest them by enveloping them with further threads over the course of a
few days, and then return to their normal shape; there is no evidence that they use venom.[17]
Most known carnivorous sponges have completely lost the water flow system and choanocytes.
However the genus Chondrocladia uses a highly modified water flow system to inflate balloon-like structures
that are used for capturing prey.[15][18]
Endosymbionts
Freshwater sponges often host green algae as endosymbionts within archaeocytes and other cells,
and benefit from nutrients produced by the algae. Many marine species host other photosynthesizing
organisms, most commonly cyanobacteria but in some cases dinoflagellates. Symbiotic cyanobacteria may
form a third of the total mass of living tissue in some sponges, and some sponges gain 48% to 80% of their
energy supply from these micro-organisms.[3] In 2008 a University of Stuttgart team reported that spicules
made of silica conduct light into the mesohyl, where the photosynthesizing endosymbionts live.[19] Sponges
that host photosynthesizing organisms are most common in waters with relatively poor supplies of food
particles, and often have leafy shapes that maximize the amount of sunlight they collect.[4]
A recently-discovered carnivorous sponge that lives near hydrothermal vents hosts methane-eating
bacteria, and digests some of them.[4]
"Immune" system
Sponges do not have the complex immune systems of most other animals. However they reject
grafts from other species but accept them from other members of their own species. In a few marine species,
gray cells play the leading role in rejection of foreign material. When invaded, they produce a chemical that
stops movement of other cells in the affected area, thus preventing the intruder from using the sponge's
internal transport systems. If the intrusion persists, the grey cells concentrate in the area and release toxins
that kill all cells in the area. The "immune" system can stay in this activated state for up to three weeks.[4]
Reproduction
Asexual
The freshwater sponge Spongilla lacustris

Sponges have three asexual methods of reproduction: after fragmentation; by budding; and by
producing gemmules. Fragments of sponges may be detached by currents or waves, and perhaps by
predators. They use the mobility of their pinacocytes and choanocytes and reshaping of the mesohyl to re-
attach themselves to a suitable surface and then rebuild themselves as small but functional sponges over the
course of several days. The same capabilities enable sponges that have been squeezed through a fine cloth
to regenerate.[3] A sponge fragment can only regenerate if it contains both collencytes to produce mesohyl
and archeocytes to produce all the other cell types.[12] A very few species reproduce by budding.[3]
Gemmules are "survival pods" which a few marine sponges and many freshwater species produce
by the thousands when dying and which some, mainly freshwater species, regularly produce in autumn.
Spongocytes make gemmules by wrapping shells of spongin, often reinforced with spicules, round clusters of
archeocytes that are full of nutrients.[3] Freshwater gemmules may also include phytosynthesizing
symbionts.[20] The gemmules then become dormant, and in this state can survive cold, drying out, lack of
oxygen and extreme variations in salinity.[3] Freshwater gemmules often do not revive until the temperature
drops, stays cold for a few months and then reaches a near-"normal" level.[20] When a gemmule germinates,
the archeocytes round the outside of the cluster transform into pinacocytes, a membrane over a pore in the
shell bursts, the cluster of cells slowly emerges, and most of the remaining archeocytes transform into other
cell types needed to make a functioning sponge. Gemmules from the same species but different individuals
can join forces to form one sponge.[3] Some gemmules are retained within the parent sponge, and in spring it
can be difficult to tell whether an old sponge has revived or been "recolonized" by its own gemmules.[20]
Sexual
Most sponges are hermaphrodites (function as both sexes simultaneously), although sponges have
no gonads (reproductive organs). Sperm are produced by choanocytes or entire choanocyte chambers that
sink into the mesohyl and form spermatic cysts while eggs are formed by transformation of archeocytes, or of
choanocytes in some species. Each egg generally acquires a yolk by consuming "nurse cells". During
spawning, sperm burst out of their cysts and are expelled via the osculum. If they contact another sponge of
the same species, the water flow carries them to choanocytes that engulf them but, instead of digesting them,
metamorphose to an ameboid form and carry the sperm through the mesohyl to eggs, which in most cases
engulf the carrier and its cargo.[3]
A few species release fertilized eggs into the water, but most retain the eggs until they hatch. There
are four types of larvae, but all are balls of cells with an outer layer of cells whose flagellae or cilia enable the
larvae to move. After swimming for a few days the larvae sink and crawl until they find a place to settle. Most
of the cells transform into archeocytes and then into the types appropriate for their locations in a miniature
adult sponge.[3]
Glass sponge embryos start by dividing into separate cells, but once 32 cells have formed they
rapidly transform into larvae that externally are ovoid with a band of cilia round the middle that they use for
movement, but internally have the typical glass sponge structure of spicules with a cobweb-like main
syncitium draped around and between them and choanosyncytia with multiple collar bodies in the center. The
larvae then leave their parents' bodies.[21]
Life cycle
Sponges in temperate regions live for at most a few years, but some tropical species and perhaps
some deep-ocean ones may live for 200 years or more. Some calcified demosponges grow by only
0.2 millimetres (0.0079 in) per year and, if that rate is constant, specimens 1 metre (3.3 ft) wide must be
about 5,000 years old. Some sponges start sexual reproduction when only a few weeks old, while others wait
until they are several years old.[3]
Coordination of activities
Adult sponges lack neurons or any other kind of nervous tissue. However most species have the
ability to perform movements that are coordinated all over their bodies, mainly contractions of the
pinacocytes, squeezing the water channels and thus expelling excess sediment and other substances that
may cause blockages. Some species can contract the osculum independently of the rest of the body.
Sponges may also contract in order to reduce the area that is vulnerable to attack by predators. In cases
where two sponges are fused, for example if there is a large but still unseparated bud, these contraction
waves slowly become coordinated in both of the "Siamese twins". The coordinating mechanism is unknown,
but may involve chemicals similar to neurotransmitters.[22] However glass sponges rapidly transmit electrical
impulses through all parts of the syncytium, and use this to halt the motion of their flagella if the incoming
water contains toxins or excessive sediment.[3] Myocytes are thought to be responsible for closing the
osculum and for transmitting signals between different parts of the body.[4]
Sponges contain genes very similar to those that contain the "recipe" for the post-synaptic density,
an important signal-receiving structure in the neurons of all other animals. However in sponges these genes
are only activated in "flask cells" that appear only in larvae and may provide some sensory capability while
the larvae are swimming. This raises questions about whether flask cells represent the predecessors of true
neurons or are evidence that sponges' ancestors had true neurons but lost them as they adapted to a sessile
lifestyle.[23]
Ecology
Euplectella aspergillum, a glass sponge known as "Venus' Flower Basket"
Habitats
Sponges are worldwide in their distribution, from the polar regions to the tropics.[12] Most live in
quiet, clear waters, because sediment stirred up by waves or currents would block their pores, making it
difficult for them to feed and breathe.[13] The greatest numbers of sponges are usually found on firm
surfaces such as rocks, but some sponges can attach themselves to soft sediment by means of a root-like
base.[24]
Sponges are more abundant but less diverse in temperate waters than in tropical waters, possibly
because organisms that prey on sponges are more abundant in tropical waters.[25] Glass sponges are the
most common in polar waters and in the depths of temperate and tropical seas, as their very porous
construction enables them to extract food from these resource-poor waters with the minimum of effort.
Demosponges and calcareous sponges are abundant and diverse in shallower non-polar waters.[26]
The different classes of sponge live in different ranges of habitat:
Type of
Water type[4] Depth[4]
surface[4]
less than 100 metres (330

Calcarea Marine Hard
ft)
Soft or firm
Glass sponges Marine Deep
sediment
Marine, brackish; Inter-tidal to abyssal;[4] a
Demosponges and about 150 freshwater carnivorous demosponge has been Any
species[3] found at 8,840 metres (5.49 mi)[17]
As primary producers
Sponges with photosynthesizing endosymbionts produce up to three times more oxygen than they
consume, as well as more organic matter than they consume. Such contributions to their habits' resources
are significant along Australia 's Great Barrier Reef but relatively minor in the Caribbean.[12]
Defenses
Holes made by clionaid sponge (producing the trace Entobia) after the death of a modern bivalve
shell of species Mercenaria mercenaria, from North Carolina
Close-up of the sponge boring Entobia in a modern oyster valve. Note the chambers which are
connected by short tunnels.
Many sponges shed spicules, forming a dense carpet several meters deep that keeps away
echinoderms which would otherwise prey on the sponges.[12] They also produce toxins that prevent other
sessile organisms such as bryozoans or sea squirts from growing on or near them, making sponges very
effective competitors for living space.
A few species, such as the Caribbean fire sponge Tedania ignis, cause a severe rash in humans who
handle them.[3] Turtles and some fish feed mainly on sponges. It is often said that sponges produce
chemical defenses against such predators.[3] However an experiment showed that there is no relationship
between the toxicity of chemicals produced by sponges and how they taste to fish, which would diminish the
usefulness of chemical defenses as deterrents. Predation by fish may even help to spread sponges by
detaching fragments.[4]
Glass sponges produce no toxic chemicals, and live in very deep water where predators are rare.[13]
Predation
Sponge flies, also known as spongilla-flies (Neuroptera, Sisyridae), are specialist predators of
freshwater sponges. The female lays her eggs on vegetation overhanging water. The larvae hatch and drop
into the water where they seek out sponges to feed on. They use their elongated mouthparts to pierce the
sponge and suck the fluids within. The larvae of some species cling to the surface of the sponge while others
take refuge in the sponge's internal cavities. The fully grown larvae leave the water and spin a cocoon in
which to pupate.[27]
Bioerosion
The Caribbean chicken-liver sponge Chondrilla nucula secretes toxins that kill coral polyps, allowing
the sponges to grow over the coral skeletons.[3] Others, especially in the family Clionaidae, use corrosive
substances secreted by their archeocytes to tunnel into rocks, corals and the shells of dead molluscs.[3]
Sponges may remove up to 1 metre (3.3 ft) per year from reefs, creating visible notches just below low-tide
level.[12]
Diseases
Caribbean sponges of the genus Aplysina suffer from Aplysina red band syndrome. This causes
Aplysina to develop one or more rust-colored bands, sometimes with adjacent bands of necrotic tissue
(dead). These lesions may completely encircle branches of the sponge. The disease appears to be
contagious (spread by physical contact). The rust-colored bands are caused by a cyanobacterium, but it is
unknown whether this organism actually causes the disease.[28]
Collaboration with other organisms

In addition to hosting photosynthesizing endosymbionts,[3] sponges are noted for their wide range of
collaborations with other organisms. The relatively large encrusting sponge Lissodendoryx colombiensis is
most common on rocky surfaces, but has extended its range into seagrass meadows by letting itself be
surrounded or overgrown by seagrass sponges, which are distasteful to the local starfish and therefore
protect Lissodendoryx against them; in return the seagrass sponges get higher positions away from the sea-
floor sediment.[29]
Shrimps of the genus Synalpheus form colonies in sponges, and each shrimp species inhabits a
different sponge species, making Synalpheus one of the most diverse crustacean genera.[30]
Evolutionary history
Fossil record
Traces of the chemical 24-
isopropylcholestane have been found in rocks formed
1,800 million years ago.[31] This is a stable derivative
of 24-isopropylcholesterol, which is thought to be
produced by demosponges but not by eumetazoans 7
("true animals", i.e. cnidarians and bilaterians). Since
choanoflagellates are thought to be animals' closest 1: Gap
single-celled relatives, a team of scientists examined 2: Central cavity
the biochemistry and genes of one choanoflagellate 3 Internal wall 4: Pore
species. They concluded that this species could not (all walls have pores)
produce 24-isopropylcholesterol but that investigation 5 Septum 6 Outer wall
of a wider range of choanoflagellates would be
7 Holdfast
necessary in order to prove that the fossil 24-
isopropylcholestane could only have been produced
by demosponges.[32]
Silica spicules like those of demosponges
Fossil sponge have been reported from Nevada in rocks dated
Raphidonema around 750 million years ago.[33] Well-preserved
faringdonense from fossil sponges from about 580 million years ago in
Cretaceous rocks in the Ediacaran period have been found in the
England
Archaeocyathid
structure
Doushantuo Formation. These fossils, which include spicules, pinacocytes, porocytes, archeocytes,
sclerocytes and the internal cavity, have been classified as demosponges. Fossils of glass sponges have
been found from around 540 million years ago in rocks in Australia, China and Mongolia.[34] Calcium
carbonate spicules of calcareous sponges have been found in Early Cambrian rocks from about 530 to 523
million years ago in Australia. Other probable demosponges have been found in the Early Cambrian
Chengjiang fauna, from 525 to 520 million years ago.[35] Freshwater sponges appear to be much younger,
as the earliest known fossils date from the Mid-Eocene period about 48 to 40 million years ago.[34] Although
about 90% of modern sponges are demosponges, fossilized remains of this type are less common than
those of other types because their skeletons are composed of relatively soft spongin that does not fossilize
well.[36]
Archaeocyathids, which some classify as a type of coralline sponge, are common in the Cambrian
period from about 530 million years ago, but apparently died out by the end of the Cambrian 490 million
years ago.[35]
Family tree
A choanoflagellate
Choanoflagellates
In the 1990s sponges were widely regarded as a monophyletic group, in other words all of them
descended from a common ancestor that was itself a sponge, and as the "sister-group" to all other
Metazoa
metazoans (multi-celled animals), which themselves form a monophyletic group. On the other hand some
Glass
1990s analyses also revived the idea that animals' nearest evolutionary relatives are choanoflagellates,
sponges
single-celled organisms very similar to sponges' choanocytes – which would imply that most Metazoa evolved
from very sponge-like ancestors and therefore that sponges may not be monophyletic, as the same sponge-
like ancestors may have given rise both to modern sponges and to non-sponge members of Metazoa.[37]
Demosponges
Calcareous
sponges
Eumetazoa
Comb
jellies
Placozoa
Cnidaria
(jellyfish, etc.)
Analyses since 2001 have concluded that Eumetazoa (more complex than sponges) are more
closely related to particular groups of sponges than to the rest of the sponges. Such conclusions imply that
sponges are not monophyletic, because the last common ancestor of all sponges would also be a direct
ancestor of the Eumetazoa, which are not sponges. A study in 2001 based on comparisons of ribosome DNA
concluded that the most fundamental division within sponges was between glass sponges and the rest, and
that Eumetazoa are more closely related to Calcareous sponges, those with calcium carbonate spicules, than
to other types of sponge.[37] In 2007 one analysis based on comparisons of RNA and another based mainly
on comparison of spicules concluded that demosponges and glass sponges are more closely related to each
other than either is to calcareous sponges, which in turn are more closely related to Eumetazoa.[34][39]
Other anatomical and biochemical evidence links the Eumetazoa with Homoscleromorpha, a sub-
group of demosponges. A comparison in 2007 of nuclear DNA, excluding glass sponges and comb jellies,
concluded that: Homoscleromorpha are most closely related to Eumetazoa; calcareous sponges are the next
closest; the other demosponges are evolutionary "aunts" of these groups; and the chancelloriids, bag-like
animals whose fossils are found in Cambrian rocks, may be sponges.[38] The sperm of Homoscleromorpha
share with those of Eumetazoa features that those of other sponges lack. In both Homoscleromorpha and
Eumetazoa layers of cells are bound together by attachment to a carpet-like basal membrane composed
mainly of "type IV" collagen, a form of collagen not found in other sponges – although the spongin fibers that
reinforce the mesohyl of all demosponges is similar to "type IV" collagen.[6]
A comb jelly
The analyses described above concluded that sponges are closest to the ancestors of all Metazoa, in
other words of all multi-celled animals including both sponges and more complex groups. However, another
comparison in 2008 of 150 genes in each of 21 genera, ranging from fungi to humans but including only two
species of sponge, suggested that comb jellies (ctenophora) are the most basal lineage of the Metazoa
included in the sample. If this is correct, either modern comb jellies developed their complex structures
independently of other Metazoa, or sponges' ancestors were more complex and all known sponges are
drastically simplified forms. The study recommended further analyses using a wider range of sponges and
other simple Metazoa such as Placozoa.[40] The results of such an analysis, published in 2009, suggest that
a return to the previous view may be warranted. 'Family trees' constructed using a combination of all
available data - morphological, developmental and molecular - concluded that the sponges are in fact a
monophyletic group, and with the cnidarians form the sister group to the bilaterians.[41]
Archaeocyathids are very common fossils in rocks from the Early Cambrian about 530 to 520 million
years ago but are not found after the Late Cambrian. It has been
suggested that they were produced by: sponges; cnidarians; algae;
foraminiferans; a completely separate phylum of animals,
Archaeocyatha; or even a completely separate kingdom of life, labelled
Archaeata or Inferibionta. Since the 1990s archaeocyathids have been
regarded as a distinctive group of sponges.[42]
It is difficult to fit chancelloriids into classifications of sponges or
more complex animals. An analysis in 1996 concluded that they were
closely related to sponges on the grounds that the detailed structure of
chancellorid sclerites ("armor plates") is similar to that of fibers of
Halkieriid sclerite
structure[43]
spongin, a collagen protein, in modern keratose (horny) demosponges such as Darwinella.[44] However
another analysis in 2002 concluded that chancelloriids are not sponges and may be intermediate between
sponges and more complex animals, among other reasons because their skins were thicker and more tightly-
connected than those of sponges.[45] In 2008 a detailed analysis of chancelloriids' sclerites concluded that
they were very similar to those of halkieriids, mobile bilaterian animals that looked like slugs in chain mail and
whose fossils are found in rocks from the very Early Cambrian to the Mid Cambrian. If this is correct, it would
create a dilemma, as it is extremely unlikely that totally unrelated organisms could have developed such
similar sclerites independently, but the huge difference in the structures of their bodies makes it hard to see
how they could be closely related.[43]
Taxonomy
Levels in the Linnean taxonomy.

For a long time sponges were assigned to a separate subkingdom, Parazoa ("beside the animals"),
separate from the Eumetazoa which formed the rest of the kingdom Animalia.[42] They are now classified as
a phylum within Animalia, and divided into classes mainly according to the composition of their skeletons:[2]
[12]
• Hexactinellida (glass sponges) have silicate spicules, the largest of which have six rays and
may be individual or fused.[2] The main components of their bodies are syncytia in which large
numbers of cell share a single external membrane.[12]
• Calcarea have skeletons made of calcite, a form of calcium carbonate, which may form
separate spicules or large masses. All the cells have a single nucleus and membrane.[12]
• Most Demospongiae have silicate spicules or spongin fibers or both within their soft tissues.
However a few also have massive external skeletons made of aragonite, another form of calcium
carbonate.[2][12] All the cells have a single nucleus and membrane.[12]
• Archeocyatha are known only as fossils from the Cambrian period.[42]
In the 1970s sponges with massive calcium carbonate skeletons were assigned to a separate class,
Sclerospongiae, otherwise known as "coralline sponges".[46] However in the 1980s it was found that these
were all members of either the Calcarea or the Demospongiae.[47]
So far scientific publications have identified about 9,000 poriferan species,[12] of which: about 400
are glass sponges; about 500 are calcareous species; and the rest are demosponges.[3] However some
types of habitat, such as vertical rock and cave walls and galleries in rock and coral boulders, have been
investigated very little, even in shallow seas.[12]
Use
By dolphins
A report in 1997 described use of sponges as a tool by bottlenose dolphins in Shark Bay. A dolphin
will attach a marine sponge to its rostrum, which is presumably then used to protect it when searching for
food in the sandy sea bottom.[48] The behaviour, known as sponging, has only been observed in this bay,
and is almost exclusively shown by females. A study in 2005 concluded that mothers teach the behaviour to
their daughters, and that all the sponge-users are closely related, suggesting that it is a fairly recent
innovation.[49]
By humans
Display of natural sponges for sale on Kalymnos in Greece
Skeleton
Main article: Sponge (tool)
The calcium carbonate or silica spicules of most sponge genera make them too rough for most uses,
but two genera, Hippospongia and Spongia, have soft, entirely fibrous skeletons. Early Europeans used soft
sponges for many purposes, including padding for helmets, portable drinking utensils and municipal water
filters. Until the invention of synthetic sponges, they were used as cleaning tools, applicators for paints and
ceramic glazes and discreet contraceptives. However by the mid-20th century, over-fishing brought both the
animals and the industry close to extinction.[50] See also sponge diving.
Many objects with sponge-like textures are now made of substances not derived from poriferans.
Synthetic sponges include personal and household cleaning tools, breast implants,[51] and contraceptive
sponges.[52] Typical materials used are cellulose foam, polyurethane foam, and less frequently, silicone
foam.
The luffa "sponge", also spelled loofah, which is commonly sold for use in the kitchen or the shower,
is not derived from an animal but from the fibrous "skeleton" of a gourd (Cucurbitaceae).[53]
Antibiotic compounds
Sponges have medicinal potential due to the presence in sponges themselves or their microbial
symbionts of chemicals that may be used to control viruses, bacteria, tumors and fungi.[54][55]
See also
• Aaptos kanuux
• Randolph Kirkpatrick
• Sponge reef
• Sponge Reef Project
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the Deep-Sea Floor. Cambridge University Press. pp. 91–93. ISBN 0521336651.
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27.^ Piper, Ross (2007), Extraordinary Animals: An Encyclopedia of Curious and Unusual
Animals, Greenwood Publishing Group.
28.^ Olson, J. B., Gochfeld, D. J., and Slattery, M. (July 2006). " Aplysina red band syndrome: a
new threat to Caribbean sponges". Diseases of aquatic organisms 71 (2): 163–8.
doi:10.3354/dao071163. PMID 16956064. News report at New disease threatens sponges (Practical
Fishkeeping)
29.^ Wulff, J. L (2008). "Collaboration among sponge species increases sponge diversity and
abundance in a seagrass meadow". Marine Ecology 29: 193–204. doi:10.1111/j.1439-
0485.2008.00224.x.
30.^ Duffy, J. E. (1996). "Species boundaries, specialization, and the radiation of sponge-
dwelling alpheid shrimp". Biological Journal of the Linnean Society 58 (3): 307–324.
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31.^ Nichols, S., and Wörheide, G. (2005). "Sponges: New Views of Old Animals". Integrative
and Comparative Biology 45 (2): 333–334. doi:10.1093/icb/45.2.333.
32.^ Kodner, R. B., Summons, R. E., Pearson, A., King, N., and Knoll, A. H. (July 2008). "Sterols
in a unicellular relative of the metazoans". Proceedings of the National Academy of Sciences 105
(29): 9897–9902. doi:10.1073/pnas.0803975105. PMID 18632573.
33.^ Reitner, J., and Wörheide, G. (2002). "Non-Lithistid Fossil Demospongiae – Origins of their
Palaeobiodiversity and Highlights in History of Preservation". In Hooper, J. N. A., and Van Soest, R.
W. M. (PDF). Systema Porifera: A Guide to the Classification of Sponges . New York: Kluwer
Academic Plenum. http://webdoc.sub.gwdg.de/pub/geo/geobiologie/2005/reitner/2002-porifera.pdf.
34.^ a b c Müller, W. E. G., Li, J., Schröder, H. C., Qiao, L., and Wang, X. (2007). "The unique
skeleton of siliceous sponges (Porifera; Hexactinellida and Demospongiae) that evolved first from the
Urmetazoa during the Proterozoic: a review". Biogeosciences 4: 219–232. doi:10.5194/bg-4-219-
2007.
35.^ a b Li, C-W., Chen, J-Y., and Hua, T-E. (February 1998). "Precambrian Sponges with
Cellular Structures". Science 279 (5352): 879–882. doi:10.1126/science.279.5352.879.
PMID 9452391.
36.^ "Demospongia". University of California Museum of Paleontology.
http://www.ucmp.berkeley.edu/porifera/demospongia.html. Retrieved 2888-11-27.
37.^ a b c Borchiellini, C., Manuel, M., Alivon, E., Boury-Esnault, N., Vacelet J., and Le Parco, Y.
(2001). "Sponge paraphyly and the origin of Metazoa". Journal of Evolutionary Biology 14 (1): 171–
179. doi:10.1046/j.1420-9101.2001.00244.x.
38.^ a b Sperling, E.A.; Pisani, D. and Peterson, K.J. (2007). "Poriferan paraphyly and its
implications for Precambrian paleobiology" (PDF). Journal of the Geological Society of London 286:
355–368. doi:10.1144/SP286.25. http://www.dartmouth.edu/~peterson/Sperling,%20Pisani%20and
%20Peterson.pdf. Retrieved 2008-11-04.
39.^ Medina, M., Collins, A. G., Silberman, J. D., and Sogin, M. L. (August 2001). "Evaluating
hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA".
Proceedings of the National Academy of Sciences 98 (17): 9707–9712. doi:10.1073/pnas.171316998.
PMID 11504944.
40.^ Dunn, C. W., Hejnol, A., et al. (2008). "Broad phylogenomic sampling improves resolution
of the animal tree of life". Nature 452 (7188): 745–9. doi:10.1038/nature06614. PMID 18322464.
41.^ Schierwater, B.; Eitel, M.; Jakob, W.; Osigus, J.; Hadrys, H.; Dellaporta, L.; Kolokotronis,
O.; Desalle, R.; Eitel M, Jakob W, Osigus H-J, Hadrys H, et al. (Jan 2009). "Concatenated Analysis
Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis" (Free full
text). PLoS Biology 7 (1): e20. doi:10.1371/journal.pbio.1000020. ISSN 1544-9173. PMID 19175291.
PMC 2631068. http://dx.plos.org/10.1371/journal.pbio.1000020. edit
42.^ a b c Rowland, S. M. (2001). "Archaeocyatha: A history of phylogenetic interpretation".
Journal of Paleontology 75: 1065–1078. doi:10.1666/0022-3360(2001)075<1065:AAHOPI>2.0.CO;2.
http://findarticles.com/p/articles/mi_qa3790/is_200111/ai_n8958761/pg_1?tag=artBody;col1.
43.^ a b Porter, S. M (2008). "Skeletal microstructure indicates Chancelloriids and Halkieriids are
closely related". Palaeontology 51 (4): 865–879. doi:10.1111/j.1475-4983.2008.00792.x.
44.^ Butterfield, N. J., and C. J. Nicholas (1996). "Burgess Shale-type preservation of both non-
mineralizing and "shelly" Cambrian organisms from the Mackenzie Mountains, northwestern
Canada". Journal of Paleontology 70: 893–899.
45.^ Janussen, D., Steiner, M., and Zhu, M-Y. (July 2002). "New Well-preserved Scleritomes of
Chancelloridae from the Early Cambrian Yuanshan Formation (Chengjiang, China) and the Middle
Cambrian Wheeler Shale (Utah, USA) and paleobiological implications". Journal of Paleontology 76
(4): 596–606. doi:10.1666/0022-3360(2002)076<0596:NWPSOC>2.0.CO;2.
http://jpaleontol.geoscienceworld.org/cgi/content/abstract/76/4/596. Retrieved 2008-08-04. Free full
text without images at Janussen, Dorte (2002). "(as above)". Journal of Paleontology.
46.^ Hartman, W. D., and Goreau, T. F. (1970). "Jamaican coralline sponges: Their morphology,
ecology and fossil relatives". Symposium of the Zoological Society of London 25: 205–243. (cited by
MGG.rsmas.miami.edu).
47.^ J. Vacelet (1985). "Coralline sponges and the evolution of the Porifera". In Conway Morris,
S., George, J. D., Gibson, R., and Platt, H. M.. The Origins and Relationships of Lower Invertebrates .
Oxford University Press. pp. 1–13. ISBN 019857181.
48.^ Smolker, R. A., et al. (1997). "Sponge-carrying by Indian Ocean bottlenose dolphins:
Possible tool-use by a delphinid". Ethology 103: 454–465.
49.^ Krutzen M, Mann J, Heithaus M.R., Connor R. C, Bejder L, Sherwin W.B. (2005). "Cultural
transmission of tool use in bottlenose dolphins". Proceedings of the National Academy of Sciences
102 (25): 8939–8943. doi:10.1073/pnas.0500232102. PMID 15947077. . News report at Dolphin
Moms Teach Daughters to Use Tools, publisher National Geographic).
50.^ McClenachan, L. (2008). "Social conflict, Over-fishing and Disease in the Florida Sponge
Fishery, 1849-1939". In Starkey, D. J. Holm, P., and Barnard, M.. Oceans Past: Management
Insights from the History of Marine Animal Populations. Earthscan. pp. 25–27. ISBN 1844075273.
http://books.google.com/?id=cGEeEfFegvEC&pg=PA26&dq=sponge+fishing. Retrieved 2008-11-12.
51.^ Jacobson, N. (2000). Cleavage. Rutgers University Press. p. 62. ISBN 0813527155.
http://books.google.com/?id=3ZIw_3Px4AEC&pg=PA62&dq=sponge+synthetic. Retrieved 2008-11-
12.
52.^ "Sponges". Cervical Barrier Advancement Society. 2004.
http://www.cervicalbarriers.org/information/sponges.cfm. Retrieved 2006-09-17.
53.^ Porterfield, W. M. (July 1955). "Loofah — The sponge gourd". Economic Botany 9 (3): 211–
223. doi:10.1007/BF02859814.
54.^ Imhoff, J. F., and Stöhr, R. (2003). "Sponge-Associated Bacteria". In Müller, W. E. G..
Sponges (Porifera): Porifera. Springer. pp. 43–44. ISBN 354000968X.
55.^ Teeyapant, R., Woerdenbag, H. J., Kreis, P., Hacker, J., Wray, V., Witte, L., and Proksch P.
(1993). "Antibiotic and cytotoxic activity of brominated compounds from the marine sponge Verongia
aerophoba". Zeitschrift für Naturforschung. C, Journal of biosciences 48: 939–45.
Further reading
• Bergquist, Patricia R. (1978). Sponges. London: Hutchinson. ISBN 0091318203. .
• Hickman, C., Jr.; Roberts, L. & Larson, A. (2003). Animal Diversity (3rd ed.). New York:
McGraw-Hill. ISBN 0072349034. .
• Template:Pll icon Bursztyn.px.pl, Collection Jurassic fossils sponges
External links
Wikimedia Commons has media related to: Sponge
Wikispecies has information related to: Porifera

Porifera
• Water flow and feeding in the phylum Porifera (sponges) - Flash animations of sponge body
structures, water flow and feeding
• Bioerosion website at The College of Wooster
• Carsten's Spongepage, Information on the ecology and the biotechnological potential of
sponges and their associated bacteria.
• History of Tarpon Springs, Florida sponge industry
• Nature's 'fibre optics' experts
• The Sponge Reef Project
• Queensland Museum FAQ about sponges
• Sponge Guide from Queensland Museum, John Hooper
• Sponge Guide for Britain and Ireland, Bernard Picton, Christine Morrow & Rob van Soest
• World Porifera database, the world list of extant sponges, includes a searchable database.
Bilateria Protostomia Cycloneuralia: Scalidophora (K

Ecdysozoa Nematomorpha)
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Spiralia Platyzoa Platy

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Rotifera · Aca
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(Sipuncula, N
Mollusca, An
Lophotrochozoa
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Hemichordata · Echinoderma
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Chordata
Retrieved from "http://en.wikipedia.org/wiki/Sponge"
Categories: Poriferans
W000
Cnidaria
Cnidaria
Temporal range: 580–0 Ma
PreЄ
g Ediacaran–Recent
Pacific sea nettles, Chrysaora fuscescens
Domain: Eukaryota
Kingdom: Animalia
Cnidaria
Phylum:
Hatschek, 1888
Subphylum/Classes[3]
Anthozoa—corals and sea anemones

Medusozoa—jellyfish:[1]
Cubozoa—box jellyfish, sea wasps
Hydrozoa—hydroids, hydra-like animals
Scyphozoa—true jellyfish
Staurozoa—stalked jellyfish
Unranked, may not be
scyphozoans[2]
Myxozoa—parasites
Polypodiozoa—parasites
Cnidaria (pronounced /naɪˈdɛəriə/ with a silent c) is a phylum containing over 9,000 species of
animals found exclusively in aquatic and mostly marine environments. Their distinguishing feature is
cnidocytes, specialized cells that they use mainly for capturing prey. Their bodies consist of mesoglea, a non-
living jelly-like substance, sandwiched between two layers of epithelium that are mostly one cell thick. They
have two basic body forms: swimming medusae and sessile polyps, both of which are radially symmetrical
with mouths surrounded by tentacles that bear cnidocytes. Both forms have a single orifice and body cavity
that are used for digestion and respiration. Many cnidarian species produce colonies that are single
organisms composed of medusa-like or polyp-like zooids, or both. Cnidarians' activities are coordinated by a
decentralized nerve net and simple receptors. Several free-swimming Cubozoa and Scyphozoa possess
balance-sensing statocysts, and some have simple eyes. Not all cnidarians reproduce sexually. Many have
complex lifecycles with asexual polyp stages and sexual medusae, but some omit either the polyp or the
medusa stage.
Cnidarians were for a long time grouped with Ctenophores in the phylum Coelenterata, but
increasing awareness of their differences caused them to be placed in separate phyla. Cnidarians are
classified into four main groups: sessile Anthozoa (sea anemones, corals, and sea pens (sea anemones are
not sessile but only move 3-4 inces an hour); swimming Scyphozoa (jellyfish); Cubozoa (box jellies); and
Hydrozoa, a diverse group that includes all the freshwater cnidarians as well as many marine forms, and has
both sessile members such as Hydra and colonial swimmers such as the Portuguese Man o' War. Staurozoa
have recently been recognised as a class in their own right rather than a sub-group of Scyphozoa, and there
is debate about whether Myxozoa and Polypodiozoa are cnidarians or closer to bilaterians (more complex
animals).
Most cnidarians prey on organisms ranging in size from plankton to animals several times larger than
themselves, but many obtain much of their nutrition from endosymbiotic algae, and a few are parasites. Many
are preyed upon by other animals including starfish, sea slugs, fish and turtles. Coral reefs, whose polyps are
rich in endosymbiotic algae, support some of the world's most productive ecosystems, and protect vegetation
in tidal zones and on shorelines from strong currents and tides. While corals are almost entirely restricted to
warm, shallow marine waters, other cnidarians live in the depths, in polar seas and in freshwater.
Fossil cnidarians have been found in rocks formed about 580 million years ago, and other fossils
show that corals may have been present shortly before 490 million years ago and diversified a few million
years later. Fossils of cnidarians that do not build mineralized structures are very rare. Scientists currently
think that cnidarians, ctenophores and bilaterians are more closely related to calcareous sponges than these
are to other sponges, and that anthozoans are the evolutionary "aunts" or "sisters" of other cnidarians, and
the most closely related to bilaterians. Recent analyses have concluded that cnidarians, although considered
more "primitive" than bilaterians, have a wider range of genes.
Jellyfish stings killed several hundred people in the 20th century, and cubozoans are particularly
dangerous. On the other hand, some large jellyfish are considered a delicacy in eastern and southern Asia.
Coral reefs have long been economically important as providers of fishing grounds, protectors of shore
buildings against currents and tides, and more recently as centers of tourism. However, they are vulnerable
to over-fishing, mining for construction materials, pollution, and damage caused by tourism.
Contents
[hide]
• 2 Ecology
• 3 History
• 5 Description
• 5.1 Main cell layers
• 5.2 Cnidocytes
• 5.3 Basic body forms
• 5.4 Colonial forms
• 5.5 Skeletons
• 5.6 Locomotion
• 5.7 Nervous system and senses
• 5.8 Feeding and excretion
• 5.9 Respiration
• 5.10 Regeneration
• 6 Reproduction
• 6.1 Sexual
• 6.2 Asexual
• 7.1 Fossil record
Cnidarians were for a long time grouped with Ctenophores in the phylum Coelenterata, but
increasing awareness of their differences caused them to be placed in separate phyla. Cnidarians are
classified into four main groups: sessile Anthozoa (sea anemones, corals, sea pens); swimming Scyphozoa
(jellyfish); Cubozoa (box jellies); and Hydrozoa, a diverse group that includes all the freshwater cnidarians as
well as many marine forms, and has both sessile members such as Hydra and colonial swimmers such as
the Portuguese Man o' War. Staurozoa have recently been recognised as a class in their own right rather
than a sub-group of Scyphozoa, and there is debate about whether Myxozoa and Polypodiozoa are
cnidarians or closer to bilaterians.
Modern cnidarians are generally classified into four classes:[4]
Hydrozoa Scyphozoa Cubozoa Anthozoa
Number of
2,700 200 20 6,000
species
Sea
Hydra, Box
Examples Jellyfish anemones, corals,
siphonophores jellies
sea pens
Cells found in
No Yes Yes Yes
mesoglea
Nematocysts
No Yes Yes Yes
in exodermis
Yes, except for

Medusa In some
Stauromedusae if they Yes No
phase in life cycle species
are scyphozoans
Number of
(not
medusae produced Many Many One
applicable)
per polyp
Stauromedusae, small sessile cnidarians with stalks and no medusa stage, have traditionally been
classified as members of the Scyphozoa, but recent research suggests they should be regarded as a
separate class, Staurozoa.[5]
The Myxozoa, microscopic parasites, were first classified as protozoans,[6] but recently as heavily
modified cnidarians, and more closely related to Hydrozoa and Scyphozoa than to Anthozoa.[7] However
other recent research suggests that Polypodium hydriforme, a parasite within the egg cells of sturgeon, is
closely related to the Myxozoa and that both Polypodium and the Myxozoa are intermediate between
cnidarians and bilaterian animals.[8]
Some researchers classify the extinct conulariids as cnidarians, while others propose that they form
a completely separate phylum.[9]
[edit] Ecology
Coral reefs support rich ecosystems

Many cnidarians are limited to shallow waters because they depend on endosymbiotic algae for
much of their nutrients. The life cycles of most have polyp stages, which are limited to locations that offer
stable substrates. Nevertheless major cnidarian groups contain species that have escaped these limitations.
Hydrozoans have a worldwide range: some, such as Hydra, live in freshwater; Obelia appears in the coastal
waters of all the oceans; and Liriope can form large shoals near the surface in mid-ocean. Among
anthozoans, a few scleractinian corals, sea pens and sea fans live in deep, cold waters, and some sea
anemones inhabit polar seabeds while others live near hydrothermal vents over 10 kilometres (6.2 mi) below
sea-level. Reef-building corals are limited to tropical seas between 30°N and 30°S with a maximum depth of
46 metres (151 ft), temperatures between 20°C and 28°C, high salinity and low carbon dioxide levels.
Stauromedusae, although usually classified as jellyfish, are stalked, sessile animals that live in cool to Arctic
waters.[10] Cnidarians range in size from Hydra, 5–20 millimetres (0.20–0.79 in) long,[11] to the Lion's mane
jellyfish, which may exceed 2 metres (6.6 ft) in diameter and 75 metres (246 ft) in length.[12]
Prey of cnidarians ranges from plankton to animals several times larger than themselves.[10][13]
Some cnidarians are parasites, mainly on jellyfish but a few are major pests of fish.[10] Others obtain most of
their nourishment from endosymbiotic algae or dissolved nutrients.[4] Predators of cnidarians include: sea
slugs, which can incorporate nematocysts into their own bodies for self-defense;[14] starfish, notably the
crown of thorns starfish, which can devastate corals;[10] butterfly fish and parrot fish, which eat corals;[15]
and marine turtles, which eat jellyfish.[12] Some sea anemones and jellyfish have a symbiotic relationship
with some fish; for example clown fish live among the tentacles of sea anemones, and each partner protects
the other against predators.[10]
Coral reefs form some of the world's most productive ecosystems. Common coral reef cnidarians
include both Anthozoans (hard corals, octocorals, anemones) and Hydrozoans (fire corals, lace corals) The
endosymbiotic algae of many cnidarian species are very effective primary producers, in other words
converters of inorganic chemicals into organic ones that other organisms can use, and their coral hosts use
these organic chemicals very efficiently. In addition reefs provide complex and varied habitats that support a
wide range of other organisms.[16] "Fringing" reefs just below low-tide level also have a mutually beneficial
relationship with mangrove forests at high-tide level and sea grass meadows in between: the reefs protect
the mangroves and seagrass from strong currents and waves that would damage them or erode the
sediments in which they are rooted, while the mangroves and seagrass protect the coral from large influxes
of silt, fresh water and pollutants. This additional level of variety in the environment is beneficial to many
types of coral reef animals, which for example may feed in the sea grass and use the reefs for protection or
breeding.[17]
[edit] History
Fossil cnidarians have been found in rocks formed about 580 million years ago, and other fossils
show that corals may have been present shortly before 490 million years ago and diversified a few million
years later. Fossils of cnidarians that do not build mineralized structures are very rare. Scientists currently
think that cnidarians, ctenophores and bilaterians are more closely related to calcareous sponges than these
are to other sponges, and that anthozoans are the evolutionary "aunts" or "sisters" of other cnidarians, and
the most closely related to bilaterians. Recent analyses have concluded that cnidarians, although considered
more "primitive" than bilaterians, have a wider range of genes.
[edit] Distinguishing features

Further information: Sponge, Ctenophore, and Bilateria
Cnidarians form an animal phylum that is more complex than sponges, about as complex as
ctenophores (comb jellies), and less complex than bilaterians, which include almost all other animals.
However, both cnidarians and ctenophores are more complex than sponges as they have: cells bound by
inter-cell connections and carpet-like basement membranes; muscles; nervous systems; and some have
sensory organs. Cnidarians are distinguished from all other animals by having cnidocytes that fire like
harpoons and are used mainly to capture prey but also as anchors in some species.[4]
Like sponges and ctenophores, cnidarians have two main layers of cells that sandwich a middle layer
of jelly-like material, which is called the mesoglea in cnidarians; more complex animals have three main cell
layers and no intermediate jelly-like layer. Hence, cnidarians and ctenophores have traditionally been
labelled diploblastic, along with sponges.[4][18] However, both cnidarians and ctenophores have a type of
muscle that, in more complex animals, arises from the middle cell layer.[19] As a result some recent text
books classify ctenophores as triploblastic,[20] and it has been suggested that cnidarians evolved from
triploblastic ancestors.[19]
Ctenophores[
Sponges[21][22] Cnidarians[4][18] Bilateria[4]
4][20]
Cnidocytes No Yes No
Colloblasts No Yes No
Digestive
and circulatory No Yes
organs
Number of Two[4] or
Two, with jelly-like layer between them Three
main cell layers Three[19][20]
Cells in No, except that

each layer bound Homoscleromorpha have Yes: inter-cell connections; basement membranes
together basement membranes.[23]
Sensory
No Yes
organs
Number of
(Not
cells in middle Many Few
applicable)
"jelly" layer
Cells in
outer layers can (Not
Yes No
move inwards and applicable)
change functions
Nervous Simple to
No Yes, simple
system complex
Mostly Mostly Mostly

Muscles None
epitheliomuscular myoepithelial myocytes
[edit] Description
[edit] Main cell layers
Cnidaria are diploblastic animals, in other words they have two main cell layers, while more complex
animals are triploblasts having three main layers. The two main cell layers of cnidarians form epithelia that
are mostly one cell thick, and are attached to a fibrous basement membrane, which they secrete. They also
secrete the jelly-like mesoglea that separates the layers. The layer that faces outwards, known as the
ectoderm ("outside skin"), generally contains the following types of cells:[4]
• Epitheliomuscular cells whose bodies form part of the epithelium but whose bases extend to
form muscle fibers in parallel rows.[24] The fibers of the outward-facing cell layer generally run at
right angles to the fibers of the inward-facing one. In Anthozoa (anemones, corals, etc.) and
Scyphozoa (jellyfish), the mesoglea also contains some muscle cells.[18]
• Cnidocytes, the harpoon-like "nettle cells" that give the phylum Cnidaria its name. These
appear between or sometimes on top of the muscle cells.[4]
• Nerve cells. Sensory cells appear between or sometimes on top of the muscle cells,[4] and
communicate via synapses (gaps across which chemical signals flow) with motor nerve cells, which
lie mostly between the bases of the muscle cells.[18]
• Interstitial cells, which are unspecialized and can replace lost or damaged cells by
transforming into the appropriate types. These are found between the bases of muscle cells.[4]
In addition to epitheliomuscular, nerve and interstitial cells, the inward-facing gastroderm ("stomach
skin") contains gland cells that secrete digestive enzymes. In some species it also contains low
concentrations of cnidocytes, which are used to subdue prey that is still struggling.[4][18]
The mesoglea contains small numbers of amoeba-like cells,[18] and muscle cells in some species.[4]
However the number of middle-layer cells and types are much lower than in sponges.[18]
[edit] Cnidocytes
A hydra's nematocyst, before firing.

"trigger" cilium[18]
Firing sequence of the cnida in a hydra's nematocyst[18]
Operculum (lid)
"Finger" that turns inside out
/ / / Barbs
Venom
Victim's skin
Victim's tissues
These "nettle cells" function as harpoons, since their payloads remain connected to the bodies of the
cells by threads. Three types of cnidocytes are known:[4][18]
• Nematocysts inject venom into prey, and usually have barbs to keep them embedded in the
victims. Most species have nematocysts.[4]
• Spirocysts do not penetrate the victim or inject venom, but entangle it by means of small
sticky hairs on the thread. Only members of the class Anthozoa (sea anemones and corals) have
spirocysts.[18]
• Ptychocysts are not used for prey capture — instead the threads of discharged ptychocysts
are used for building protective tubes in which their owners live. Ptychocysts are found only in the
order Cerianthria, tube anemones.[18]
The main components of a cnidocyte are:[4][18]
• A cilium (fine hair) which projects above the surface and acts as a trigger. Spirocysts do not
have cilia.
• A tough capsule, the cnida, which houses the thread, its payload and a mixture of chemicals
which may include venom or adhesives or both. ("cnida" is derived from the Greek word κνίδη, which
means "nettle"[25])
• A tube-like extension of the wall of the cnida that points into the cnida, like the finger of a
rubber glove pushed inwards. When a cnidocyte fires, the finger pops out. If the cell is a venomous
nematocyte, the "finger"'s tip reveals a set of barbs that anchor it in the prey.
• The thread, which is an extension of the "finger" and coils round it until the cnidocyte fires.
The thread is usually hollow and delivers chemicals from the cnida to the target.
• An operculum (lid) over the end of the cnida. The lid may be a single hinged flap or three
flaps arranged like slices of pie.
• The cell body which produces all the other parts.
It is difficult to study the firing mechanisms of cnidocytes as these structures are small but very
complex. At least four hypotheses have been proposed:[4]
• Rapid contraction of fibers round the cnida may increase its internal pressure.
• The thread may be like a coiled spring that extends rapidly when released.
• In the case of Chironex (the "sea wasp"), chemical changes in the cnida's contents may
cause them to expand rapidly by polymerization.
• Chemical changes in the liquid in the cnida make it a much more concentrated solution, so
that osmotic pressure forces water in very rapidly to dilute it. This mechanism has been observed in
nematocysts of the class Hydrozoa, sometimes producing pressures as high as 140 atmospheres,
similar to that of scuba air tanks, and fully extending the thread in as little as 2 milliseconds
(0.002 second).[18]
Cnidocytes can only fire once, and about 25% of a hydra's nematocysts are lost from its tentacles
when capturing a brine shrimp. Used cnidocytes have to be replaced, which takes about 48 hours. To
minimise wasteful firing, two types of stimulus are generally required to trigger cnidocytes: their cilia detect
contact, and nearby sensory cells "smell" chemicals in the water. This combination prevents them from firing
at distant or non-living objects. Groups of cnidocytes are usually connected by nerves and, if one fires, the
rest of the group requires a weaker minimum stimulus than the cells that fire first.[4][18]
[edit] Basic body forms
Exoderm
Gastroderm (Endoderm) Oral end of actinodiscus polyp, with close-up of the

mouth
Mesoglea Adult cnidarians appear as either swimming medusae or
sessile polyps. Both are radially symmetrical, like a wheel and a
Digestive cavity tube respectively. Since these animals have no heads, their
ends are described as "oral" (nearest the mouth) and "aboral"
(furthest from the mouth). Most have fringes of tentacles
equipped with cnidocytes around their edges, and medusae
generally have an inner ring of tentacles around the mouth. The
mesoglea of polyps is usually thin and often soft, but that of
medusae is usually thick and springy, so that it returns to its
Medusa (left) and polyp (right)[18]

original shape after muscles around the edge have contracted to squeeze water out, enabling medusae to
swim by a sort of jet propulsion.[18]
[edit] Colonial forms
Tree-like polyp colony[18]

Cnidaria produce a variety of colonial forms, each of which is one organism but consists of polyp-like
zooids. The simplest is a connecting tunnel that runs over the substrate (rock or seabed) and from which
single zooids sprout. In some cases the tunnels form visible webs, and in others they are enclosed in a fleshy
mat. More complex forms are also based on connecting tunnels but produce "tree-like" groups of zooids. The
"trees" may be formed either by a central zooid that functions as a "trunk" with later zooids growing to the
sides as "branches", or in a zig-zag shape as a succession of zooids, each of which grows to full size and
then produces a single bud at an angle to itself. In many cases the connecting tunnels and the "stems" are
covered in periderm, a protective layer of chitin.[18] Some colonial forms have other specialized types of
zooid, for example, to pump water through their tunnels.[10]
Siphonophores form complex colonies that consist of: an upside-down polyp that forms a central
stem with a gas-filled float at the top; one or more sets of medusa-like zooids that provide propulsion; leaf-
like bracts that give some protection to other parts; sets of tentacles that bear nematocytes that capture prey;
other tentacles that act as sensors; near the base of each set of tentacles, a polyp-like zooid that acts as a
stomach for the colony; medusa-like zooids that serve as gonads. Although some of these zooids resemble
polyps or medusae in shape, they lack features that are not relevant to their specific functions, for example
the swimming "medusae" have no digestive, sensory or reproductive cells. The best-known siphonophore is
the Portuguese Man o' War (Physalia physalis).[10][26][27]
[edit] Skeletons
In medusae the only supporting structure is the mesoglea. Hydra and most sea anemones close their
mouths when they are not feeding, and the water in the digestive cavity then acts as a hydrostatic skeleton,
rather like a water-filled balloon. Other polyps such as Tubularia use columns of water-filled cells for support.
Sea pens stiffen the mesoglea with calcium carbonate spicules and tough fibrous proteins, rather like
sponges.[18]
In some colonial polyps a chitinous periderm gives support and some protection to the connecting
sections and to the lower parts of individual polyps. Stony corals secrete massive calcium carbonate
exoskeletons. A few polyps collect materials such as sand grains and shell fragments, which they attach to
their outsides. Some colonial sea anemones stiffen the mesoglea with sediment particles.[18]
[edit] Locomotion
Chrysaora quinquecirrha ("sea nettle") swimming

Medusae swim by a form of jet propulsion: muscles, especially inside the rim of the bell, squeeze
water out of the cavity inside the bell, and the springiness of the mesoglea powers the recovery stroke. Since
the tissue layers are very thin, they provide too little power to swim against currents and just enough to
control movement within currents.[18]
Hydras and some sea anemones can move slowly over rocks and sea or stream beds by various
means: creeping like snails, crawling like inchworms, or by somersaulting. A few can swim clumsily by
waggling their bases.[18]
[edit] Nervous system and senses
Cnidaria have no brains or even central nervous systems. Instead they have decentralized nerve
nets consisting of : sensory neurons that generate signals in response to various types of stimulus, such as
odors; motor neurons that tell muscles to contract; all connected by "cobwebs" of intermediate neurons. As
well as forming the "signal cables", intermediate neurons also form ganglia that act as local coordination
centers. The cilia of the cnidocytes detect physical contact. Nerves inform cnidocytes when odors from prey
or attackers are detected and when neighbouring cnidocytes fire. Most of the communications between nerve
cells are via chemical synapses, small gaps across which chemicals flow. As this process is too slow to
ensure that the muscles round the rim of a medusa's bell contract simultaneously in swimming the neurons
which control this communicate by much faster electrical signals across gap junctions.[18]
Medusae and complex swimming colonies such as siphonophores and chondrophores sense tilt and
acceleration by means of statocysts, chambers lined with hairs which detect the movements of internal
mineral grains called statoliths. If the body tilts in the wrong direction, the animal rights itself by increasing the
strength of the swimming movements on the side that is too low. They also have ocelli ("little eyes"), which
can detect the direction from which light is coming. Box jellies have camera eyes, although these probably do
not form images, and their lenses simply produce a clearer indication of the direction from which light is
coming.[4]
[edit] Feeding and excretion

Cnidarians feed in several ways: predation, absorbing dissolved organic chemicals, filtering food
particles out of the water, and obtaining nutrients from symbiotic algae within their cells. Most obtain the
majority of their food from predation but some, including the corals Hetroxenia and Leptogorgia, depend
almost completely on their endosymbionts and on absorbing dissolved nutrients.[4] Cnidaria give their
symbiotic algae carbon dioxide, some nutrients and a place in the sun.[18]
Predatory species use their cnidocytes to poison or entangle prey, and those with venomous
nematocysts may start digestion by injecting digestive enzymes. The "smell" of fluids from wounded prey
makes the tentacles fold inwards and wipe the prey off into the mouth. In medusae the tentacles round the
edge of the bell are often short and most of the prey capture is done by "oral arms", which are extensions of
the edge of the mouth and are often frilled and sometimes branched to increase their surface area. Medusae
often trap prey or suspended food particles by swimming upwards, spreading their tentacles and oral arms
and then sinking. In species for which suspended food particles are important, the tentacles and oral arms
often have rows of cilia whose beating creates currents that flow towards the mouth, and some produce nets
of mucus to trap particles.[4]
Once the food is in the digestive cavity, gland cells in the gastroderm release enzymes that reduce
the prey to slurry, usually within a few hours. This circulates through the digestive cavity and, in colonial
cnidarians, through the connecting tunnels, so that gastroderm cells can absorb the nutrients. Absorption
may take a few hours, and digestion within the cells may take a few days. The circulation of nutrients is
driven by water currents produced by cilia in the gastroderm or by muscular movements or both, so that
nutrients reach all parts of the digestive cavity.[18] Nutrients reach the outer cell layer by diffusion or, for
animals or zooids such as medusae which have thick mesogleas, are transported by mobile cells in the
mesoglea.[4]
Indigestible remains of prey are expelled through the mouth. The main waste product of cells' internal
processes is ammonia, which is removed by the external and internal water currents.[18]
[edit] Respiration
There are no respiratory organs, and both cell layers absorb oxygen from and expel carbon dioxide
into the surrounding water. When the water in the digestive cavity becomes stale it must be replaced, and
nutrients that have not been absorbed will be expelled with it. Some Anthozoa have ciliated grooves on their
tentacles, allowing them to pump water out of and into the digestive cavity without opening the mouth. This
improves respiration after feeding and allows these animals, which use the cavity as a hydrostatic skeleton,
to control the water pressure in the cavity without expelling undigested food.[4]
Cnidaria that carry photosynthetic symbionts may have the opposite problem, an excess of oxygen,
which may prove toxic. The animals produce large quantities of antioxidants to neutralize the excess oxygen.
[4]
[edit] Regeneration
All cnidarians can regenerate, allowing them to recover from injury and to reproduce asexually.
Medusae have limited ability to regenerate, but polyps can do so from small pieces or even collections of
separated cells. This enables corals to recover even after apparently being destroyed by predators.[4]
[edit] Reproduction
[edit] Sexual
In the Cnidaria sexual reproduction often involves a complex life
cycle with both polyp and medusa stages. For example in Scyphozoa
(jellyfish) and Cubozoa (box jellies) a larva swims until it finds a good site,
and then becomes a polyp. This grows normally but then absorbs its
tentacles and splits horizontally into a series of disks that become juvenile
medusae, a process called strobilation. The juveniles swim off and slowly
grow to maturity, while the polyp re-grows and may continue strobilating
periodically. The adults have gonads in the gastroderm, and these release
ova and sperm into the water in the breeding season.[4][18]
Shortened forms of this life cycle are common, for example some
oceanic scyphozoans omit the polyp stage completely, and cubozoan 12
polyps produce only one medusa. Hydrozoa have a variety of life cycles.
Some have no polyp stages and some (e.g. hydra) have no medusae. In 13
some species the medusae remain attached to the polyp and are 14
responsible for sexual reproduction; in extreme cases these reproductive
zooids may not look much like medusae. Anthozoa have no medusa
stage at all and the polyps are responsible for sexual reproduction.[4]
Spawning is generally driven by environmental factors such as
changes in the water temperature, and their release is triggered by
lighting conditions such as sunrise, sunset or the phase of the moon.
Many species of Cnidaria may spawn simultaneously in the same location, so that there are too many ova
and sperm for predators to eat more than a tiny percentage — one famous example is the Great Barrier Reef,
where at least 110 corals and a few non-cnidarian invertebrates produce enough to turn the water cloudy.
These mass spawnings may produce hybrids, some of which can settle and form polyps, but it is not known
how long these can survive. In some species the ova release chemicals that attract sperm of the same
species.[4]
The fertilized eggs develop into larvae by dividing until there are enough cells to form a hollow
sphere (blastula) and then a depression forms at one end (gastrulation) and eventually become the digestive
cavity. However in cnidarians the depression forms at the end further from the yolk (at the animal pole), while
in bilaterians it forms at the other end (vegetal pole).[18] The larvae, called planulae, swim or crawl by means
of cilia.[4] They are cigar-shaped but slightly broader at the "front" end, which is the aboral, vegetal-pole end
and eventually attaches to a substrate if the species has a polyp stage.[18]
Anthozoan larvae either have large yolks or are capable of feeding on plankton, and some already
have endosymbiotic algae that help to feed them. Since the parents are immobile, these feeding capabilities
extend the larvae's range and avoid overcrowding of sites. Scyphozoan and hydrozoan larvae have little yolk
and most lack endosymbiotic algae, and therefore have to settle quickly and metamorphose into polyps.
Instead these species rely on their medusae to extend their ranges.[18]
[edit] Asexual
All known cnidaria can reproduce asexually by various means, in addition to regenerating after being
fragmented. Hydrozoan polyps only bud, while the medusae of some hydrozoans can divide down the
middle. Scyphozoan polyps can both bud and split down the middle. In addition to both of these methods,
Anthozoa can split horizontally just above the base.[4][18]
[edit] Fossil record
The fossil coral Cladocora from Pliocene rocks in Cyprus

The earliest widely accepted animal fossils are rather modern-looking cnidarians, possibly from
around 580 million years ago, although fossils from the Doushantuo Formation can only be dated
approximately.[28] The identification of some of these as embryos of animals has been contested, but other
fossils from these rocks strongly resemble tubes and other mineralized structures made by corals.[29] Their
presence implies that the cnidarian and bilaterian lineages had already diverged.[30] Although the Ediacaran
fossil Charnia used to be classified as a jellyfish or sea pen,[31] more recent study of growth patterns in
Charnia and modern cnidarians has cast doubt on this hypothesis,[32][33] and there are now no bona-fide
cnidarian body fossils in the Ediacaran. Few fossils of cnidarians without mineralized skeletons are known
from more recent rocks, except in lagerstätten that preserved soft-bodied animals.[34]
A few mineralized fossils that resemble corals have been found in rocks from the Cambrian period,
and corals diversified in the Early Ordovician.[34] These corals, which were wiped out in the Permian-
Triassic extinction about 251 million years ago,[34] did not dominate reef construction since sponges and
algae also played a major part.[35] During the Mesozoic era rudist bivalves were the main reef-builders, but
they were wiped out in the Cretaceous-Tertiary extinction 65 million years ago,[36] and since then the main
reef-builders have been scleractinian corals.[34]
[edit] Family tree

Further information: Phylogeny
Metazoa
spon
Eumetazoa
Ctenophora
(comb jellies)
Planulozoa
Cnidaria
Anthozoa
(sea anemones
and corals)
Medusozoa
Hydrozoa
(Hydra, siphonophores,
etc.)
Cubozoa
(box jellies)
Staurozoa
"Scyphozoa
"
(jellyfish, excluding
Staurozoa)
Placozoa
Bilateria
Myxozoa
Other Bilateria
(more complex)
Family tree of Cnidaria and the origins of animals[2][37][38]
It is difficult to reconstruct the early stages in the evolutionary "family tree" of animals using only
morphology (their shapes and structures), because the large differences between Porifera (sponges),
Cnidaria plus Ctenophora (comb jellies), Placozoa and Bilateria (all the more complex animals) make
comparisons difficult. Hence reconstructions now rely largely or entirely on molecular phylogenetics, which
groups organisms according to similarities and differences in their biochemistry, usually in their DNA or RNA.
[39]
It is now generally thought that the Calcarea (sponges with calcium carbonate spicules) are more
closely related to Cnidaria, Ctenophora (comb jellies) and Bilateria (all the more complex animals) than they
are to the other groups of sponges.[37][40][41] In 1866 it was proposed that Cnidaria and Ctenophora were
more closely related to each other than to Bilateria and formed a group called Coelenterata ("hollow guts"),
because Cnidaria and Ctenophora both rely on the flow of water in and out of a single cavity for feeding,
excretion and respiration. In 1881 it was proposed that Ctenophora and Bilateria were more closely related to
each other, since they shared features that Cnidaria lack, for example muscles in the middle layer (mesoglea
in Ctenophora, mesoderm in Bilateria). However more recent analyses indicate that these similarities are
rather vague, and the current view, based on molecular phylogenetics, is that Cnidaria and Bilateria are more
closely related to each other than either is to Ctenophora. This grouping of Cnidaria and Bilateria has been
labelled "Planulozoa" because it suggests that the earliest Bilateria were similar to the planula larvae of
Cnidaria.[2][38]
Within the Cnidaria, the Anthozoa (sea anemones and corals) are regarded as the sister-group of the
rest, which suggests that the earliest cnidarians were sessile polyps with no medusa stage. However it is
unclear how the other groups acquired the medusa stage, since Hydrozoa form medusae by budding from
the side of the polyp while the other Medusozoa do so by splitting them off from the tip of the polyp. The
traditional grouping of Scyphozoa included the Staurozoa, but morphology and molecular phylogenetics
indicate that Staurozoa are more closely related to Cubozoa (box jellies) than to other "Scyphozoa".
Similarities in the double body walls of Staurozoa and the extinct Conulariida suggest that they are closely
related. The position of Anthozoa nearest the beginning of the cnidarian family tree also implies that
Anthozoa are the cnidarians most closely related to Bilateria, and this is supported by the fact that Anthozoa
and Bilateria share some genes that determine the main axes of the body.[2][42]
However in 2005 Katja Seipel and Volker Schmid suggested that cnidarians and ctenophores are
simplified descendants of triploblastic animals, since ctenophores and the medusa stage of some cnidarians
have striated muscle, which in bilaterians arises from the mesoderm. They did not commit themselves on
whether bilaterians evolved from early cnidarians or from the hypothesized triploblastic ancestors of
cnidarians.[19]
In molecular phylogenetics analyses from 2005 onwards, important groups of developmental genes
show the same variety in cnidarians as in chordates.[43] In fact cnidarians, and especially anthozoans (sea
anemones and corals), retain some genes that are present in bacteria, protists, plants and fungi but not in
bilaterians.[44]
[edit] Interaction with humans

Jellyfish stings killed about 1,500 people in the 20th century,[45] and cubozoans are particularly
dangerous. On the other hand, some large jellyfish are considered a delicacy in eastern and southern Asia.
Coral reefs have long been economically important as providers of fishing grounds, protectors of shore
buildings against currents and tides, and more recently as centers of tourism. However, they are vulnerable
to over-fishing, mining for construction materials, pollution, and damage caused by tourism.
Beaches protected from tides and storms by coral reefs are often the best places for housing in
tropical countries. Reefs are an important food source for low-technology fishing, both on the reefs
themselves and in the adjacent seas.[46] However despite their great productivity reefs are vulnerable to
over-fishing, because much of the organic carbon they produce is exhaled as carbon dioxide by organisms at
the middle levels of the food chain and never reaches the larger species that are of interest to fishermen.[16]
Tourism centered on reefs provides much of the income of some tropical islands, attracting photographers,
divers and sports fishermen. However human activities damage reefs in several ways: mining for
construction materials; pollution, including large influxes of fresh water from storm drains; commercial fishing,
including the use of dynamite to stun fish and the capture of young fish for aquariums; and tourist damage
caused by boat anchors and the cumulative effect of walking on the reefs.[46] Coral, mainly from the Pacific
Ocean has long been used in jewellery, and demand rose sharply in the 1980s.[47]
Some large jellyfish species have been used in Chinese cuisine at least
since 200 AD, and are now fished in the seas around most of South East Asia.
Japan is the largest single consumer of edible jellyfish, importing at first only from
China but now from all of South East Asia as prices rose in the 1970s. This fishing
industry is restricted to daylight hours and calm conditions in two short seasons, from
March to May and August to November.[48] The commercial value of jellyfish food
products depends on the skill with which they are prepared, and "Jellyfish Masters"
guard their trade secrets carefully. Jellyfish is very low in cholesterol and sugars, but
cheap preparation can introduce undesirable amounts of heavy metals.[49]
The "sea wasp" Chironex fleckeri has been described as the world's most
venomous animal and is held responsible for 67 deaths, although it is difficult to
identify the animal as it is almost transparent. Most stingings by C. fleckeri cause
only mild symptoms.[50] Seven other box jellies can cause a set of symptoms called
Irukandji syndrome,[51] which takes about 30 minutes to develop,[52] and from a few
hours to two weeks to disappear.[53] Hospital treatment is usually required, and
there have been a few deaths.[51]
The
dangerous "sea wasp"
Chironex fleckeri
[edit] Notes
1. ^ Classes in Medusozoa based on "The Taxonomicon - Taxon: Subphylum Medusozoa".
Universal Taxonomic Services. http://www.taxonomy.nl/Taxonomicon/TaxonTree.aspx?id=11582.
2. ^ a b c d Collins, A.G. (2002). "Phylogeny of Medusozoa and the Evolution of Cnidarian Life
Cycles" (PDF). Journal of Evolutionary Biology 15 (3): 418–432. doi:10.1046/j.1420-
9101.2002.00403.x. http://cima.uprm.edu/~n_schizas/CMOB_8676/Collins2002.pdf. Retrieved 2008-
11-27.
3. ^ Subphyla Anthozoa and Medusozoa based on "The Taxonomicon - Taxon: Phylum
Cnidaria". Universal Taxonomic Services. http://www.taxonomy.nl/Taxonomicon/TaxonTree.aspx?
id=11551. Retrieved 2007-07-10.
4. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af Hinde, R.T., (1998). "The Cnidaria
and Ctenophora". In Anderson, D.T.,. Invertebrate Zoology. Oxford University Press. pp. 28–57.
ISBN 0195513681.
5. ^ Collins, A.G., Cartwright, P., McFadden, C.S., and Schierwater, B. (2005). "Phylogenetic
Context and Basal Metazoan Model Systems". Integrative and Comparative Biology 45 (4): 585–594.
doi:10.1093/icb/45.4.585.
6. ^ Štolc, A. (1899). "Actinomyxidies, nouveau groupe de Mesozoaires parent des
Myxosporidies". Bull. Int. L'Acad. Sci. Bohème 12: 1–12.
7. ^ E. Jímenez-Guri; Philippe, H; Okamura, B; Holland, PW (July 2007). " Buddenbrockia is a
cnidarian worm". Science 317 (116): 116–118. doi:10.1126/science.1142024. PMID 17615357.
8. ^ Zrzavý, J. and Hypša, V. (2003). "Myxozoa, Polypodium, and the origin of the Bilateria: The
phylogenetic position of "Endocnidozoa" in light of the rediscovery of Buddenbrockia". Cladistics 19
(2): 164–169. doi:10.1111/j.1096-0031.2003.tb00305.x.
9. ^ "The Conulariida". University of California Museum of Paleontology.
http://www.ucmp.berkeley.edu/cnidaria/conulariida.html. Retrieved 2008-11-27.
10.^ a b c d e f g Shostak, S. (2006). "Cnidaria (Coelenterates)". Encyclopedia of Life Sciences.
John Wiley & Sons. doi:10.1038/npg.els.0004117.
11.^ Blaise, C., and Férard, J-F. (2005). Small-scale Freshwater Toxicity Investigations: Toxicity
Test Methods. Springer. p. 398. ISBN 140203119X. http://books.google.com/?
id=Ibew5SLx2oMC&dq=hydra+size+length. Retrieved 2008-11-21.
12.^ a b Safina, C. (2007). Voyage of the Turtle: In Pursuit of the Earth's Last Dinosaur .
Macmillan. p. 154. ISBN 0805083189. http://books.google.com/?
id=dQD883dAv6YC&pg=PA154&dq=cnidaria+turtle. Retrieved 2008-11-21.
13.^ Cowen, R. (2000). History of Life (3 ed.). Blackwell. p. 54. ISBN 0632044446.
http://books.google.com/?id=qvyBS4gwPF4C&pg=PA54&dq=cnidaria+prey. Retrieved 2008-11-21.
14.^ Frick, K (2003). "Predator Suites and Flabellinid Nudibranch Nematocyst Complements in
the Gulf of Maine.". In: SF Norton (ed). Diving for Science...2003. Proceedings of the American
Academy of Underwater Sciences (22nd Annual Scientific Diving Symposium). http://archive.rubicon-
foundation.org/4744. Retrieved 2008-07-03.
15.^ Choat, J.H. and Bellwood, D.R. (1998). Paxton, J.R. and Eschmeyer, W.N.. ed.
Encyclopedia of Fishes. San Diego: Academic Press. pp. 209–211. ISBN 0-12-547665-5.
16.^ a b Barnes, R.S.K., and Mann, K.H. (1991). Fundamentals of Aquatic Ecology. Blackwell
Publishing. pp. 217–227. ISBN 0632029838. http://books.google.com/?
id=mOZZlzgdTrwC&pg=PA227&dq=%22Coral+Reef%22+productivity. Retrieved 2008-11-26.
17.^ Hatcher, B.G. Johannes, R.E., and Robertson, A.J. (1989). "Conservation of Shallow-water
Marine Ecosystems". Oceanography and Marine Biology: An Annual Review: Volume 27. Routledge.
p. 320. ISBN 0080377181. http://books.google.com/?id=XpmNqFaDZ7cC&pg=PA320&dq=
%22Coral+Reef%22+mangrove+%22seagrass%22. Retrieved 2008-11-21.
18.^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af ag Ruppert, E.E., Fox, R.S., and
Barnes, R.D. (2004). Invertebrate Zoology (7 ed.). Brooks / Cole. pp. 111–124. ISBN 0030259827.
19.^ a b c d Seipel, K., and Schmid, V. (June 2005). "Evolution of striated muscle: Jellyfish and
the origin of triploblasty". Developmental Biology 282 (1): 14–26. doi:10.1016/j.ydbio.2005.03.032.
PMID 15936326.
20.^ a b c Ruppert, E.E., Fox, R.S., and Barnes, R.D. (2004). Invertebrate Zoology (7 ed.).
Brooks / Cole. pp. 182–195. ISBN 0030259827.
Cole. pp. 76–97. ISBN 0030259827.
22.^ Bergquist, P.R., (1998). "Porifera". In Anderson, D.T.,. Invertebrate Zoology. Oxford
University Press. pp. 10–27. ISBN 0195513681.
23.^ Exposito, J-Y., Cluzel, C., Garrone, R., and Lethias, C. (2002). "Evolution of collagens".
The Anatomical Record Part A: Discoveries in Molecular, Cellular, and Evolutionary Biology 268 (3):
302–316. doi:10.1002/ar.10162. PMID 12382326.
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phosphorites?". Proceedings of the National Academy of Sciences 97 (25): 13684–13689.
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30.^ Chen, J.-Y., Oliveri, P., Gao, F., Dornbos, S.Q., Li, C-W., Bottjer, D.J. and Davidson, E.H.
(August 2002). "Precambrian Animal Life: Probable Developmental and Adult Cnidarian Forms from
Southwest China" (PDF). Developmental Biology 248 (1): 182–196. doi:10.1006/dbio.2002.0714.
PMID 12142030. http://www.uwm.edu/~sdornbos/PDF's/Chen%20et%20al.%202002.pdf. Retrieved
2008-09-03.
31.^ Donovan, Stephen K., Lewis, David N. (2001). "Fossils explained 35. The Ediacaran biota"
(abstract). Geology Today 17 (3): 115–120. doi:10.1046/j.0266-6979.2001.00285.x.
32.^ Antcliffe, J.B.; Brasier, M. D. (2007). "Charnia and sea pens are poles apart". Journal of the
Geological Society 164 (1): 49–51. doi:10.1144/0016-76492006-080.
33.^ Antcliffe, J.B.; Brasier, Martin D. (2007). "Charnia At 50: Developmental Models For
Ediacaran Fronds". Palaeontology 51 (1): 11–26. doi:10.1111/j.1475-4983.2007.00738.x.
34.^ a b c d "Cnidaria: Fossil Record". University of California Museum of Paleontology.
http://www.ucmp.berkeley.edu/cnidaria/cnidariafr.html. Retrieved 2008-11-27.
35.^ Copper, P. (January 1994). "Ancient reef ecosystem expansion and collapse". Coral Reefs
13 (1): 3–11. doi:10.1007/BF00426428.
36.^ "The Rudists". University of California Museum of Paleontology.
http://www.ucmp.berkeley.edu/taxa/inverts/mollusca/rudists.php. Retrieved 2008-11-27.
37.^ a b Borchiellini, C., Manuel, M., Alivon, E., Boury-Esnault, N., Vacelet J., and Le Parco, Y.
(2001). "Sponge paraphyly and the origin of Metazoa". Journal of Evolutionary Biology 14 (1): 171–
179. doi:10.1046/j.1420-9101.2001.00244.x.
38.^ a b Wallberg, A., Thollesson, M., , Farris, J.S., and Jondelius, U. (2004). "The phylogenetic
position of the comb jellies (Ctenophora) and the importance of taxonomic sampling". Cladistics 20:
558–578. doi:10.1111/j.1096-0031.2004.00041.x.
39.^ Halanych, K.M. (December 2004). "The New View of Animal Phylogeny" (PDF). Annual
Review of Ecology, Evolution, and Systematics 35: 229–256.
doi:10.1146/annurev.ecolsys.35.112202.130124.
http://gump.auburn.edu/halanych/lab/Pub.pdfs/Halanych2004.pdf. Retrieved 2008-11-27.
40.^ Medina, M., Collins, A.G., Silberman, J.D., and Sogin, M.L. (August 2001). "Evaluating
hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA".
PMID 11504944.
41.^ Müller, W.E.G., Li, J., Schröder, H.C., Qiao, L., and Wang, X. (2007). "The unique skeleton
of siliceous sponges (Porifera; Hexactinellida and Demospongiae) that evolved first from the
Urmetazoa during the Proterozoic: a review". Biogeosciences 4: 219–232. doi:10.5194/bg-4-219-
2007.
42.^ Marques, A.C., and Collins, A.G. (2004). "Cladistic analysis of Medusozoa and cnidarian
evolution". Invertebrate Biology 123 (1): 23–42. doi:10.1111/j.1744-7410.2004.tb00139.x.
http://www.marinespecies.org/aphia.php?p=sourceget&id=38492. Retrieved 2008-11-27.
43.^ Miller, D.J., Ball, E.E., and Technau, U. (October 2005). "Cnidarians and ancestral genetic
complexity in the animal kingdom". Trends in Genetics 21 (10): 536–539.
doi:10.1016/j.tig.2005.08.002. PMID 16098631.
44.^ Technau, U., Rudd, S., and Maxwell, P (December 2005). "Maintenance of ancestral
complexity and non-metazoan genes in two basal cnidarians". Trends in Genetics 21 (12): 633–639.
doi:10.1016/j.tig.2005.09.007. PMID 16226338.
45.^ Williamson, J.A., Fenner, P.J., Burnett, J.W., and Rifkin, J. (1996). Venomous and
Poisonous Marine Animals: A Medical and Biological Handbook. UNSW Press. pp. 65–68.
id=YsZ3GryFIzEC&pg=PA75&lpg=PA75&dq=mollusc+venom+fatal. Retrieved 2008-10-03.
46.^ a b Clark, J.R. (1998). Coastal Seas: The Conservation Challenge. Blackwell. pp. 8–9.
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%22+productivity. Retrieved 2008-11-28.
47.^ Cronan, D.S., (1991). Marine Minerals in Exclusive Economic Zones . Springer. pp. 63–65.
ISBN 041229270X. http://books.google.com/?id=4g4nhd8USO8C&pg=PA63&dq=coral+jewellery.
48.^ Omori, M. and Nakano, E. (2001). "Jellyfish fisheries in southeast Asia". In Purcell, J.E.,.
Jellyfish Blooms: Ecological and Societal Importance. Springer. pp. 19–26. ISBN 0792369645.
49.^ Hsieh, Y-H.P. Leong, F-M., and Rudloe, J. (2001). "Jellyfish as food". In Purcell, J.E.,.
Jellyfish Blooms: Ecological and Societal Importance. Springer. pp. 11–17. ISBN 0792369645.
50.^ Greenberg, M.I., Hendrickson, R.G., Silverberg, M., Campbell, C., and Morocco, A. (2004).
"Box Jellyfish Envenomation". Greenberg's Text-atlas of Emergency Medicine. Lippincott Williams &
Wilkins. p. 875. ISBN 0781745861.
51.^ a b Little, M., Pereira, P., Carrette, T., and Seymour, J. (2006). "Jellyfish Responsible for
Irukandji Syndrome". QJM (Quarterly Journal of Medicine) 99 (6): 425–427.
doi:10.1093/qjmed/hcl057. PMID 16687419.
52.^ Barnes, J. (1964). "Cause and effect in Irukandji stingings". Medical Journal of Australia 14:
897–904. PMID 14172390.
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Emergency Medicine 42 (6): 763–6. doi:10.1016/S0196-0644(03)00513-4. PMID 14634600.
[edit] Books
• Arai, M.N. (1997). A Functional Biology of Scyphozoa. London: Chapman & Hall [p. 316].
ISBN 0-412-45110-7.
• Ax, P. (1999). Das System der Metazoa I. Ein Lehrbuch der phylogenetischen Systematik.
Gustav Fischer, Stuttgart-Jena: Gustav Fischer. ISBN 3-437-30803-3.
• Barnes, R.S.K., P. Calow, P. J. W. Olive, D. W. Golding & J. I. Spicer (2001). The
invertebrates—a synthesis. Oxford: Blackwell. 3rd edition [chapter 3.4.2, p. 54]. ISBN 0-632-04761-5.
• Brusca, R.C., G.J. Brusca (2003). Invertebrates. Sunderland, Mass.: Sinauer Associates.
2nd edition [chapter 8, p. 219]. ISBN 0-87893-097-3.
• Dalby, A. (2003). Food in the Ancient World: from A to Z. London: Routledge.
• Moore, J.(2001). An Introduction to the Invertebrates. Cambridge: Cambridge University
Press [chapter 4, p. 30]. ISBN 0-521-77914-6.
• Schäfer, W. (1997). Cnidaria, Nesseltiere. In Rieger, W. (ed.) Spezielle Zoologie. Teil 1.
Einzeller und Wirbellose Tiere. Stuttgart-Jena: Gustav Fischer. Spektrum Akademischer Verl.,
Heidelberg, 2004. ISBN 3-8274-1482-2.
• Werner, B. 4. Stamm Cnidaria. In: V. Gruner (ed.) Lehrbuch der speziellen Zoologie. Begr.
von Kaestner. 2 Bde. Stuttgart-Jena: Gustav Fischer, Stuttgart-Jena. 1954, 1980, 1984, Spektrum
Akad. Verl., Heidelberg-Berlin, 1993. 5th edition. ISBN 3-334-60474-8.
[edit] Journal articles
• D. Bridge, B. Schierwater, C. W. Cunningham, R. DeSalle R, L. W. Buss: Mitochondrial DNA
structure and the molecular phylogeny of recent cnidaria classes. in: Proceedings of the Academy of
Natural Sciences of Philadelphia. Philadelphia USA 89.1992, p. 8750. ISSN 0097-3157
• D. Bridge, C. W. Cunningham, R. DeSalle, L. W. Buss: Class-level relationships in the
phylum Cnidaria—Molecular and morphological evidence. in: Molecular biology and evolution. Oxford
University Press, Oxford 12.1995, p. 679. ISSN 0737-4038
• D. G. Fautin: Reproduction of Cnidaria. in: Canadian Journal of Zoology. Ottawa Ont.
80.2002, p. 1735. (PDF, online) ISSN 0008-4301
• G. O. Mackie: What's new in cnidarian biology? in: Canadian Journal of Zoology. Ottawa Ont.
80.2002, p. 1649. (PDF, online) ISSN 0008-4301
• P. Schuchert: Phylogenetic analysis of the Cnidaria. in: Zeitschrift für zoologische Systematik
und Evolutionsforschung. Paray, Hamburg-Berlin 31.1993, p. 161. ISSN 0044-3808
• G. Kass-Simon, A. A. Scappaticci Jr.: The behavioral and developmental physiology of
nematocysts. in: Canadian Journal of Zoology. Ottawa Ont. 80.2002, p. 1772. (PDF, online)
ISSN 0044-3808
• J. Zrzavý (2001). "The interrelationships of metazoan parasites: a review of phylum- and
higher-level hypotheses from recent morphological and molecular phylogenetic analyses" (PDF).
Folia Parasitologica 48 (2): 81–103. PMID 11437135. Archived from the original on 2007-10-25.
http://web.archive.org/web/20071025220832/http://www.paru.cas.cz/folia/pdf/2-01/Zrz.pdf. Retrieved
2009-01-26.
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Categories: Venomous animals | Cnidarians
W000
Ichthyosaur

Ichthyosaur
Ichthyosauria
PreЄ
g Middle Triassic - Late Cretaceous
Mounted fossil of Temnodontosaurus trigonodon, Staatliches Museum für Naturkunde Stuttgart
Kingdom: Animalia
Phylum: Chordata
Class: Reptilia
Superorder: †Ichthyopterygia
(unranked): †Eoichthyosauria
†Ichthyosauria
Order:
Blainville, 1835
Families
Ichthyosauridae
Leptopterygiidae
Mixosauridae
Ophthalmosauridae
Shastasauridae
Stenopterygiidae
Temnodontosauridae
Toretocnemidae
Ichthyosaurs (Greek for "fish lizard" - ιχθυς/ichthys meaning "fish" and σαυρος/sauros meaning
"lizard") were giant marine reptiles that resembled fish and dolphins. Ichthyosaurs thrived during much of the
Mesozoic era; based on fossil evidence, they first appeared approximately 245 million years ago (mya) and
disappeared about 90 million years ago, about 25 million years before the dinosaurs became extinct. During
the middle Triassic Period, ichthyosaurs evolved from as-yet unidentified land reptiles that moved back into
the water, in a development parallel to that of the ancestors of modern-day dolphins and whales. They were
particularly abundant in the Jurassic Period, until they were replaced as the top aquatic predators by
plesiosaurs in the Cretaceous Period. They belong to the order known as Ichthyosauria or Ichthyopterygia
('fish flippers' - a designation introduced by Sir Richard Owen in 1840, although the term is now used more
for the parent clade of the Ichthyosauria).
Contents
[hide]
• 1 Description
• 2 Reproduction
• 3 Feeding
• 4 History of discoveries
• 6 Taxonomy
• 7 Phylogeny
• 8 Geologic formations
• 9 References
[edit] Description
CGI restoration of Ichthyosaurus

Ichthyosaurs averaged 2–4 metres (6.6–13 ft) in length (although a few were smaller, and some
species grew much larger), with a porpoise-like head and a long, toothed snout. Built for speed, like modern
tuna, some ichthyosaurs appear also to have been deep divers, like some modern whales (Motani, 2000). It
has been estimated that ichthyosaurs could swim at speeds up to 40 kilometres per hour (25 mph).[1] Similar
to modern cetaceans such as whales and dolphins, they were air-breathing.
According to weight estimates by Ryosuke Motani[2] a 2.4 meters (8 ft) Stenopterygius weighed
around 163–168 kilograms (360–370 lb) whilst a 4 meters (13 ft) Ophthalmosaurus icenicus weighed 930–950
kilograms (1.03–1.05 short tons).
Although ichthyosaurs looked like fish, they were not. Biologist Stephen Jay Gould said the
ichthyosaur was his favorite example of convergent evolution, where similarities of structure are analogous
not homologous, for this group:
converged so strongly on fishes that it actually evolved a dorsal fin and tail in just the right place
and with just the right hydrological design. These structures are all the more remarkable
because they evolved from nothing — the ancestral terrestrial reptile had no hump on its back or
blade on its tail to serve as a precursor.
Ichthyosaur 'paddle' (Charmouth Heritage Coast Centre).

In fact the earliest reconstructions of ichthyosaurs omitted the dorsal fin, which had no hard skeletal
structure, until finely-preserved specimens recovered in the 1890s from the Holzmaden lagerstätten in
Germany revealed traces of the fin. Unique conditions permitted the preservation of soft tissue impressions.
[3]
Ichthyosaur vertebra from the Sundance Formation (Jurassic) of Natrona County, Wyoming. Note the
characteristic "figure-8" cross-section for this variety. Scale in mm.
Ichthyosaurs had fin-like limbs, which were possibly used for stabilization and directional control,
rather than propulsion, which would have come from the large shark-like tail. The tail was bi-lobed, with the
lower lobe being supported by the caudal vertebral column, which was "kinked" ventrally to follow the
contours of the ventral lobe.
Apart from the obvious similarities to fish, the ichthyosaurs also shared parallel developmental
features with dolphins, lamnid sharks, and tunas. This gave them a broadly similar appearance, possibly
implied similar activity levels (including thermoregulation), and presumably placed them broadly in a similar
ecological niche.
[edit] Reproduction
Adult and juvenile Stenopterygius quadriscissus

They were viviparous (bore live young). Some adult fossils have even been found containing fetuses.
Although they were reptiles and descended from egg-laying ancestors, viviparity is not as unexpected as it
first appears. Air-breathing marine creatures must either come ashore to lay eggs, like turtles and some sea
snakes, or else give birth to live young in surface waters, like whales and dolphins. Given their streamlined
bodies, heavily adapted for fast swimming, it would have been difficult for ichthyosaurs to move far enough
on land to lay eggs.
Crocodiles, most sea turtles and some lizards, control offspring gender by manipulating the
temperature of the eggs' environment. I.e., they do not have of distinct sex chromosomes. Live-bearing
reptiles do not regulate sex through incubation temperature. A recent study examined 94 living species of
reptiles, birds and mammals and found that the genetic control of sex appears to be crucial to live birth and
that genetics likely controlled gender in ichthyosaurs, mosasaurs and other extinct marine reptiles.[4]
[edit] Feeding
Ichthyosaurus acutirostris with ammonoids

For their food, many of the fish-shaped ichthyosaurs relied heavily on ancient cephalopod kin of
squids called belemnites. Some early ichthyosaurs had teeth adapted for crushing shellfish. They also most
likely fed on fish, and a few of the larger species had heavy jaws and teeth that indicated they fed on smaller
reptiles. Ichthyosaurs ranged so widely in size, and survived for so long, that they are likely to have had a
wide range of prey. Typical ichthyosaurs have very large eyes, protected within a bony ring, suggesting that
they may have hunted at night.
[edit] History of discoveries
Diagram of the skeletal anatomy of an Ichthyosaurus communis found by Mary Anning, from an 1824
paper by Conybeare
The nominate genus Ichthyosaurus had first been described in 1699 from fossil fragments
discovered in Wales.
The first fossil vertebrae were published twice in 1708 as tangible mementos of the Universal
Deluge. The first complete ichthyosaur fossil was found in 1811 by Mary Anning in Lyme Regis, along what is
now called the Jurassic Coast. She subsequently discovered three separate species.
In 1905, the Saurian Expedition led by John C. Merriam of the University of California and financed
by Annie Alexander, found 25 specimens in central Nevada, which during the Triassic was under a shallow
ocean. Several of the specimens are now in the collection of the University of California Museum of
Paleontology. Other specimens are embedded in the rock and visible at Berlin–Ichthyosaur State Park in Nye
County. In 1977, the Triassic ichthyosaur Shonisaurus became the State Fossil of Nevada. Nevada is the
only state to possess a complete skeleton, 17 m (55 ft) of this extinct marine reptile. In 1992, Canadian
ichthyologist Dr. Elizabeth Nicholls (Curator of Marine Reptiles at the Royal Tyrrell Museum) uncovered the
largest known specimen, a 23 m-long (75 ft) example.
Grippia longirostris from early Triassic of Spitsbergen

The earliest ichthyosaurs, looking more like finned lizards than the familiar fish or dolphin forms, are
known from the Early and Early-Middle (Olenekian and Anisian) Triassic strata of Canada, China, Japan, and
Spitsbergen in Norway. These primitive forms included the genera Chaohusaurus, Grippia, and
Utatsusaurus.
These very early proto-ichthyosaurs, which are now classified as Ichthyopterygia rather than as
ichthyosaurs proper (Motani 1997, Motani et al. 1998), quickly gave rise to true ichthyosaurs sometime
around the boundary between the Early Triassic and Middle Triassic. These later diversified into a variety of
forms, including the sea serpent like Cymbospondylus, which reached 10 metres, and smaller more typical
forms like Mixosaurus. By the Late Triassic, ichthyosaurs consisted of both classic Shastasauria and more
advanced, "dolphin"-like Euichthyosauria (Californosaurus, Toretocnemus) and Parvipelvia (Hudsonelpidia,
Macgowania). Experts disagree over whether these represent an evolutionary continuum, with the less
specialised shastosaurs a paraphyletic grade that was evolving into the more advanced forms (Maisch and
Matzke 2000), or whether the two were separate clades that evolved from a common ancestor earlier on
(Nicholls and Manabe 2001).
Shonisaurus popularis.
During the Carnian and Norian, shastosaurs reached huge sizes. Shonisaurus popularis, known from
a number of specimens from the Carnian of Nevada, was 15 metres long. Norian shonisaurs are known from
both sides of the Pacific. Himalayasaurus tibetensis and Tibetosaurus (probably a synonym) have been
found in Tibet. These large (10 to 15 metres long) ichthyosaurs probably belong to the same genus as
Shonisaurus (Motani et al., 1999; Lucas, 2001, pp. 117–119). While the gigantic Shonisaurus sikanniensis,
whose remains were found in the Pardonet formation of British Columbia by Elizabeth Nicholls, reached as
much as 21 metres in length - the largest marine reptile known to date.
These giants (along with their smaller cousins) seemed to have disappeared at the end of the Norian.
Rhaetian (latest Triassic) ichthyosaurs are known from England, and these are very similar to those of the
Early Jurassic. Like the dinosaurs, the ichthyosaurs and their contemporaries the plesiosaurs survived the
end-Triassic extinction event, and immediately diversified to fill the vacant ecological niches of the earliest
Jurassic.
Ichthyosaurus sp. fossil
The Early Jurassic, like the Late Triassic, was the heyday of the ichthyosaurs, which are represented
by four families and a variety of species, ranging from one to ten metres in length. Genera include
Eurhinosaurus, Ichthyosaurus, Leptonectes, Stenopterygius, and the large predator Temnodontosaurus,
along with the persistently primitive Suevoleviathan, which was little changed from its Norian ancestors. All
these animals were streamlined, dolphin-like forms, although the more primitive animals were perhaps more
elongated than the advanced and compact Stenopterygius and Ichthyosaurus.
Ichthyosaurs were still common in the Middle Jurassic, but had now decreased in diversity. All
belonged to the single clade Ophthalmosauria. Represented by the 4 metre long Ophthalmosaurus and
related genera, they were very similar to Ichthyosaurus, and had attained a perfect "tear-drop" streamlined
form. The eyes of Ophthalmosaurus were huge, and it is likely that these animals hunted in dim and deep
water (Motani 2000).
Platypterygius kiprijanovi - Albian-Cenomanian of Kursk region (Russia)
Ichthyosaurs seemed to decrease in diversity even further with the Cretaceous. Only three genera
are known, Caypullisaurus, Maiaspondylus, and Platypterygius, although they had a worldwide distribution.
This last ichthyosaur genus became extinct during the Cenomanian-Turonian extinction event early in the
Late Cretaceous (as did the pliosaurs). Interestingly, less hydrodynamically efficient animals like mosasaurs
and long-necked plesiosaurs flourished. It could be that the ichthyosaurian over-specialisation was a
contributing factor to their extinction, possibly being unable to 'keep up' with the fast swimming and highly
evasive new teleost fish, which had become dominant at this time, against which the sit-and-wait ambush
strategies of the mosasaurs proved superior (Lingham-Soliar 1999).
[edit] Taxonomy
• Superorder Ichthyopterygia
• Family Grippidae
• Chaohusaurus
• Grippia
• Family Utatsusauridae
• Utatsusaurus
• Order ICHTHYOSAURIA
• Cymbospondylus
• Family Mixosauridae
• Mixosaurus
• Suborder Merriamosauriformes
• Guanlingsaurus
• (unranked) Merriamosauria
• Infraorder Shastasauria
• Family Shastasauridae
• Himalayasaurus
• Shastasaurus
• Shonisaurus
• Tibetosaurus
• Infraorder Ichthyosauria (=Euichthyosauruia)
• Family Ichthyosauridae
• Ichthyosaurus
• Family Leptopterygiidae
• Eurhinosaurus
• Excalibosaurus
• Leptonectes
• Family Temnodontosauridae
• Temnodontosaurus
• Family Ophthalmosauridae
• Aegirosaurus
• Arthropterygius
• Brachypterygius
• Caypullisaurus
• Nannopterygius
• Ophthalmosaurus
• Platypterygius
• Family Stenopterygiidae
• ?Chacaicosaurus
• Stenopterygius
• Family Toretocnemidae
• Californosaurus
• Qianichthyosaurus
• Toretocnemus
• Family Suevoleviathanidae
• Suevoleviathan
• Infraorder Parvipelvia
• Hudsonelpidia
• Macgowania
[edit] Phylogeny
The following cladogram is based on Motani (1999):[5]
Chaohusaurus
Grippia
Merriamosaur
Euichthyosauria
Parvipelvia
Hu
Suevoleviatha
n
Eurhinosauria
Temnodontosaurus
Thunnosauria
Stenopterygius
Ichthyosaurus
Ophthalmosauridae
Cladogram based on Maisch and Matzke (2000)[6] and Maisch and Matzke (2003)[7] with clade
names following Maisch (2010)[8]:
Ichthyosauria
Grippidia
Chaohusaurus
Grippia
Macgowan
Hudsonelp
Temnodontosaurus
Eurhinosauria
Suevoleviatha
n
Ichthyosaurus
[edit] Geologic formations
The following is a list of geologic formations with ichthyosaur fossils.
Name Age Location Notes
Franciscan Formation • USA
Hosselkus Limestone • USA
• Arge
Los Molles Formation
ntina
Oxford Clay • UK
• Germ
Solnhofen Limestone
any
• Cana
Sulphur Mountain Formation
da
Sundance Formation • USA

[edit] References
1. ^ http://www.genetologisch-onderzoek.nl/index.php/42/beeldende-kunst/
2. ^ http://www.ucmp.berkeley.edu/people/motani/ichthyo/weight.html
3. ^ Martill D.M. 1993. Soupy Substrates: A Medium for the Exceptional Preservation of
Ichthyosaurs of the Posidonia Shale (Lower Jurassic) of Germany. Kaupia - Darmstädter Beiträge
zur Naturgeschichte 2: 77-97
4. ^ Carroll, Sean B. (March 22, 2010). "For Extinct Monsters of the Deep, a Little Respect".
The New York Times. http://www.nytimes.com/2010/03/23/science/23creatures.html?
src=sch&pagewanted=all.
5. ^ Motani, Ryosuke (1999). "Phylogeny of the Ichthyopterygia". Journal of Vertebrate
Paleontology 19: 472–495. http://www.ucmp.berkeley.edu/people/motani/ichthyo/phylogeny.html.
6. ^ Michael W. Maisch and Andreas T. Matzke (2000). "The Ichthyosauria". Stuttgarter
Beiträge zur Naturkunde: Serie B 298: 159. http://www.naturkundemuseum-
bw.de/stuttgart/pdf/b_pdf/B298.pdf.
7. ^ Michael W. Maisch and Andreas T. Matzke (2003). "Observations on Triassic ichthyosaurs.
Part XII. A new Lower Triassic ichthyosaur genus from Spitzbergen". Neues Jahrbuch für Geologie
und Paläontologie Abhandlungen 229: 317–338.
8. ^ Michael W. Maisch (2010). "Phylogeny, systematics, and origin of the Ichthyosauria – the
state of the art". Palaeodiversity 3: 151–214.
http://www.palaeodiversity.org/pdf/03/Palaeodiversity_Bd3_Maisch.pdf.
• Ellis, Richard, (2003) Sea Dragons - Predators of the Prehistoric Oceans. University Press of
Kansas ISBN 0-7006-1269-6
• Stephen Jay Gould, "Bent out of Shape" in Eight Little Piggies.
• Lingham-Soliar, T. (1999): A functional analysis of the skull of Goronyosaurus nigeriensis
(Squamata: Mosasauridae) and Its Bearing on the Predatory Behavior and Evolution of the Enigmatic
Taxon. N. Jb. Geol. Palaeont. Abh. 2134 (3):355-74
• Maisch, M. W. & Matzke, A. T. (2000) The ichthyosauria. Stuttgarter Beitraege zur
Naturkunde. Serie B. Geologie und Palaeontologie . 2000; (298):1-159.
• McGowan, Christopher (1992) Dinosaurs, Spitfires and Sea Dragons, Harvard University
Press, ISBN 0-674-20770-X
• McGowan, Christopher & Motani, Ryosuke, (2003) Ichthyopterygia, Handbook of
Paleoherpetology, Part 8, Verlag Dr. Friedrich Pfeil
• Motani, R. (1997), Temporal and spatial distribution of tooth implantation in ichthyosaurs, in
JM Callaway & EL Nicholls (eds.), Ancient Marine Reptiles. Academic Press. pp. 81–103.
• Motani, R. (2000), Rulers of the Jurassic Seas, Scientific American vol.283, no. 6
• Motani, R., Minoura, N. & Ando, T. (1998), Ichthyosaurian relationships illuminated by new
primitive skeletons from Japan. Nature 393:255-257.
• Motani, R., Manabe, M., and Dong, Z-M, (1999) The status of Himalayasaurus tibetensis
(Ichthyopterygia) pdf, Paludicola2(2):174-181.
• Nicholls, E. L. & Manabe, M. 2001. A new genus of ichthyosaur from the Late Triassic
Pardonet Formation of British Columbia: bridging the Triassic-Jurassic gap. Canadian Journal of
Earth Sciences 38:983-1002.
Wikimedia Commons has media related to: Ichthyosauria
• USMP Berkeley's ichthyosaur introduction

• Ryosuke Motani's detailed Ichthyosaur homepage, with vivid graphics
• Eureptilia: Ichthyosauria - Palaeos
• Ichthyosauria - cladogram (Mikko's Phylogeny Archive)
• Hauff Museum, Germany - exhibiting the finds of Holzmaden
Retrieved from "http://en.wikipedia.org/wiki/Ichthyosaur"
Categories: Ichthyosaurs | Natural history of Nevada

W000
Annelid
Annelida
Temporal range: Early Ordovician–Recent[1]
PreЄ
g
Glycera sp.
Kingdom: Animalia
Superphylum: Lophotrochozoa
Annelida
Phylum:
Lamarck, 1809
Classes and subclasses
Class Polychaeta (paraphyletic?)

Class Clitellata (see below)
Oligochaeta – earthworms, etc.
Branchiobdellida
Hirudinea – leeches
Class Myzostomida
Class Archiannelida (polyphyletic)
The annelids (also called "ringed worms"), formally called Annelida (from French annelés "ringed
ones", ultimately from Latin anellus "little ring"[2]), are a large phylum of segmented worms, with over 17,000
modern species including ragworms, earthworms and leeches. They are found in marine environments from
tidal zones to hydrothermal vents, in freshwater, and in moist terrestrial environments. Although most
textbooks still use the traditional division into polychaetes (almost all marine), oligochaetes (which include
earthworms) and leech-like species, research since 1997 has radically changed this scheme, viewing
leeches as a sub-group of oligochaetes and oligochaetes as a sub-group of polychaetes. In addition, the
Pogonophora, Echiura and Sipuncula, previously regarded as separate phyla, are now regarded as sub-
groups of polychaetes. Annelids are considered members of the Lophotrochozoa, a "super-phylum" of
protostomes that also includes molluscs, brachiopods, flatworms and nemerteans.
The basic annelid form consists of multiple segments, each of which has the same sets of organs
and, in most polychaetes, a pair of parapodia that many species use for locomotion. Septa separate the
segments of many species, but are poorly-defined or absent in some, and Echiura and Sipuncula show no
obvious signs of segmentation. In species with well-developed septa, the blood circulates entirely within
blood vessels, and the vessels in segments near the front ends of these species are often built up with
muscles to act as hearts. The septa of these species also enable them to change the shapes of individual
segments, which facilitates movement by peristalsis ("ripples" that pass along the body) or by undulations
that improve the effectiveness of the parapodia. In species with incomplete septa or none, the blood
circulates through the main body cavity without any kind of pump, and there is a wide range of locomotory
techniques – some burrowing species turn their pharynges inside out to drag themselves through the
sediment.
Although many species can reproduce asexually and use similar mechanisms to regenerate after
severe injuries, sexual reproduction is the normal method in species whose reproduction has been studied.
The minority of living polychaetes whose reproduction and lifecycles are known produce trochophore larvae,
which live as plankton and then sink and metamorphose into miniature adults. Oligochaetes are full
hermaphrodites and produce a ring-like cocoon round their bodies, in which the eggs and hatchlings are
nourished until they are ready to emerge.
Earthworms support terrestrial food chains both as prey and by aerating and enriching soil. The
burrowing of marine polychaetes, which may constitute up to a third of all species in near-shore
environments, encourages the development of ecosystems by enabling water and oxygen to penetrate the
sea floor. In addition to improving soil fertility, annelids serve humans as food and as bait. Scientists observe
annelids to monitor the quality of marine and fresh water. Although blood-letting is no longer in favor with
doctors, some leech species are regarded as endangered species because they have been over-harvested
for this purpose in the last few centuries. Ragworms' jaws are now being studied by engineers as they offer
an exceptional combination of lightness and strength.
Since annelids are soft-bodied, their fossils are rare – mostly jaws and the mineralized tubes that
some of the species secreted. Although some late Ediacaran fossils may represent annelids, the oldest
known fossil that is identified with confidence comes from about 518 million years ago in the early Cambrian
period. Fossils of most modern mobile polychaete groups appeared by the end of the Carboniferous, about
299 million years ago. Scientists disagree about whether some body fossils from the mid Ordovician, about
472 to 461 million years ago, are the remains of oligochaetes, and the earliest certain fossils of the group
appear in the Tertiary period, which began 65 million years ago.
Contents
[hide]
• 1 Classification and diversity
• 3 Description
• 3.1 Segmentation
• 3.2 Body wall, chetae and parapodia
• 3.3 Nervous system and senses
• 3.4 Coelom, locomotion and circulatory system
• 3.5 Respiration
• 3.6 Feeding and excretion
• 3.7 Reproduction and life cycle
• 3.7.1 Asexual reproduction
• 3.7.2 Sexual reproduction
• 4 Ecological significance
• 5 Interaction with humans
• 6.1 Fossil record
• 6.2 Family tree
• 7 References
[edit] Classification and diversity
There are over 17,000 living annelid species,[3] ranging in size from microscopic to the Australian
giant Gippsland earthworm, which can grow up to 3 metres (9.8 ft) long.[4][5] Although research since 1997
has radically changed scientists' views about the evolutionary family tree of the annelids,[6][7] most
textbooks use the traditional classification into the following sub-groups:[4][8]
• Polychaetes (about 12,000 species[3]). As their name suggests, they have multiple chetae
("hairs") per segment. Polychaetes have parapodia that function as
limbs, and nuchal organs ("nuchal" means "on the neck") that are
thought to be chemosensors.[4] Most are marine animals, although
a few species live in fresh water and even fewer on land.[9]
• Clitellates (about 5,000 species[3]). These have few or no
chetae per segment, and no nuchal organs or parapodia. However,
they have a unique reproductive organ, the ring-shaped clitellum
("pack saddle") round their bodies, which produces a cocoon that
stores and nourishes fertilized eggs until they hatch.[8][10] The
clitellates are sub-divided into:[4]
• Oligochaetes ("with few hairs"), which includes
earthworms. Oligochaetes have a sticky pad in the roof of
the mouth.[4] Most are burrowers that feed on wholly or
partly decomposed organic materials.[9]
• Hirudinea, whose name means "leech-shaped" and
whose best known members are leeches.[4] Marine species
are mostly blood-sucking parasites, mainly on fish, while
An earthworm's
clitellum
most freshwater species are predators.[9] They have suckers at both ends of their bodies,
and use these to move rather like inchworms.[11]
The Archiannelida, minute annelids that live in the spaces between grains of sediment, were treated
as a separate class because of their simple body structure, but are now regarded as polychaetes.[8] Some
other groups of animals have been classified in various ways, but are now widely regarded as annelids:
• Pogonophora / Siboglinidae were first discovered in 1914, and their lack of a recognizable
gut made it difficult to classify them. They have been classified as a separate phylum, Pogonophora,
or as two phyla, Pogonophora and Vestimentifera. More recently they have been re-classified as a
family, Siboglinidae, within the polychaetes.[9][12]
• The Echiura have a checkered taxonomic history: in the 19th century they were assigned to
the phylum "Gephyrea", which is now empty as its members have been assigned to other phyla; the
Echiura were next regarded as annelids until the 1940s, when they were classified as a phylum in
their own right; but a molecular phylogenetics analysis in 1997 concluded that Echiurans are
annelids.[3][12][13]
• Myzostomida live on crinoids and other echinoderms, mainly as parasites. In the past they
have been regarded as close relatives of the trematode flatworms or of the tardigrades, but in 1998 it
was suggested that they are a sub-group of polychaetes.[9] However, another analysis in 2002
suggested that myzostomids are more closely related to flatworms or to rotifers and
acanthocephales.[12]

No single feature distinguishes Annelids from other invertebrate phyla, but they have a distinctive
combination of features. Their bodies are long, with segments that are divided externally by shallow ring-like
constrictions called annuli and internally by septa ("partitions") at the same points, although in some species
the septa are incomplete and in a few cases missing. Most of the segments contain the same sets of organs,
although sharing a common gut, circulatory system and nervous system makes them inter-dependent.[4][8]
Their bodies are covered by a cuticle (outer covering) that does not contain cells but is secreted by cells in
the skin underneath, is made of tough but flexible collagen[4] and does not molt[14] – on the other hand
arthropods' cuticles are made of the more rigid α-chitin,[4][15] and molt until the arthropods reach their full
size.[16] Most annelids have closed circulatory systems, where the blood makes its entire circuit via blood
vessels.[14]
Summary of distinguishing features
Recently merged into
Closely-related
Annelida[6]
Annelida[4]
Echiura[1 Sipuncula[ Arth
Nemertea[19]
7] 18] 20]
External Only in a few Yes,

Yes no no
segmentation species in mites
Repetition of In pr
Yes no no Yes
internal organs forms
Septa In most
no no No No
between segments species
Cuticle collagen collagen collagen none α-

material
Generally
no;[14] but some
polychaetes molt
Molting no[23] no[23] no[23] Ye
their jaws, and
leeches molt their
skins[22]
Coelom; but
this is reduced or
2 2 coeloms,
missing in many Coelom only in
Body cavity coeloms, main main and in Hem
leeches and some proboscis
and in proboscis tentacles
small
polychaetes[14]
Open
Circulatory Closed in
outflow, return via Open Closed O
system most species
branched vein
[edit] Description
[edit] Segmentation Prostomium
Most of an annelid's body consists of segments that are practically
identical, having the same sets of internal organs and external chaetae (Greek Peristomium
χαιτα, meaning "hair") and, in some species, appendages. However, the
Mouth
frontmost and rearmost sections are not regarded as true segments as they do
not contain the standard sets of organs and do not develop in the same way as Growth zone
the true segments. The frontmost section, called the prostomium (Greek προ-
meaning "in front of" and στομα meaning "mouth") contains the brain and Pygidium
sense organs, while the rearmost, called the pygidium (Greek πυγιδιον,
meaning "little tail") contains the anus, generally on the underside. The first Anus
section behind the prostomium, called the peristomium (Greek περι- meaning
"around" and στομα meaning "mouth"), is regarded by some zoologists as not
a true segment, but in some polychaetes the peristomium has chetae and
appendages like those of other segments.[4]
The segments develop one at a time from a growth zone just ahead of
the pygidium, so that an annelid's youngest segment is just in front of the
growth zone while the peristomium is the oldest. This pattern is called
teloblastic growth.[4] Some groups of annelids, including all leeches,[11] have
fixed maximum numbers of segments, while others add segments throughout
their lives.[8]
Segments of an
annelid[4][8]
The phylum's name is derived from the Latin word
annelus, meaning "little ring".[3]
[edit] Body wall, chetae and parapodia

Annelids' cuticles are made of collagen fibers, usually
in layers that spiral in alternating directions so that the fibers
cross each other. These are secreted by the one-cell deep
epidermis (outermost skin layer). A few marine annelids that
live in tubes lack cuticles, but their tubes have a similar
structure, and mucus-secreting glands in the epidermis
protect their skins.[4] Under the epidermis is the dermis,
which is made of connective tissue, in other words a 10 Coelom
combination of cells and non-cellular materials such as
collagen. Below this are two layers of muscles, which develop
from the lining of the coelom (body cavity): circular muscles
make a segment longer and slimmer when they contract,
while under them are longitudinal muscles, usually four
distinct strips,[14] whose contractions make the segment
shorter and fatter.[4] Some annelids also have oblique
internal muscles that connect the underside of the body to
each side.[14]
The chetae ("hairs") of annelids project out from the
epidermis to provide traction and other capabilities. The
simplest are unjointed and form paired bundles near the top
Cross-section through a typical

annelid[4][8]
and bottom of each side of each segment. The parapodia ("limbs") of annelids that have them often bear
more complex chetae at their tips – for example jointed, comb-like or hooked.[4] Chetae are made of
moderately flexible β-chitin and are formed by follicles, each of which has a chaetoblast ("hair-forming") cell
at the bottom and muscles that can extend or retract the cheta. The chetoblasts produce chetae by forming
microvilli, fine hair-like extensions that increase the area available for secreting the cheta. When the cheta is
complete, the microvilli withdraw into the chetoblast, leaving parallel tunnels that run almost the full length of
the cheta.[4] Hence annelids' chetae are structurally different from the setae ("bristles") of arthropods, which
are made of the more rigid α-chitin, have a single internal cavity, and are mounted on flexible joints in shallow
pits in the cuticle.[4]
Nearly all polychaetes have parapodia that function as limbs, while other major annelid groups lack
them. Parapodia are unjointed paired extensions of the body wall, and their muscles are derived from the
circular muscles of the body. They are often supported internally by one or more large, thick chetae. The
parapodia of burrowing and tube-dwelling polychaetes are often just ridges whose tips bear hooked chetae.
In active crawlers and swimmers the parapodia are often divided into large upper and lower paddles on a
very short trunk, and the paddles are generally fringed with chetae and sometimes with cirri (fused bundles of
cilia) and gills.[14]
[edit] Nervous system and senses

The brain generally forms a ring round the pharynx (throat), consisting of a pair of ganglia (local
control centers) above and in front of the pharynx, linked by nerve cords either side of the pharynx to another
pair of ganglia just below and behind it.[4] The brains of polychaetes are generally in the prostomium, while
those of clitellates are in the peristomium or sometimes the first segment behind the peristomium.[24] In
some very mobile and active polychaetes the brain is enlarged and more complex, with visible hindbrain,
midbrain and forebrain sections.[14] The rest of the central nervous system is generally "ladder-like",
consisting of a pair of nerve cords that run through the bottom part of the body and have in each segment
paired ganglia linked by a transverse connection. From each segmental ganglion a branching system of local
nerves runs into the body wall and then encircles the body.[4] However, in most polychaetes the two main
nerve cords are fused, and in the tube-dwelling genus Owenia the single nerve chord has no ganglia and is
located in the epidermis.[8][25]
As in arthropods, each muscle fiber (cell) is controlled by more than one neuron, and the speed and
power of the fiber's contractions depends on the combined effects of all its neurons. Vertebrates have a
different system, in which one neuron controls a group of muscle fibers.[4] Most annelids' longitudinal nerve
trunks include giant axons (the output signal lines of nerve cells). Their large diameter decreases their
resistance, which allows them to transmit signals exceptionally fast. This enables these worms to withdraw
rapidly from danger by shortening their bodies. Experiments have shown that cutting the giant axons
prevents this escape response but does not affect normal movement.[4]
The sensors are primarily single cells that detect light, chemicals, pressure waves and contact, and
are present on the head, appendages (if any) and other parts of the body.[4] Nuchal ("on the neck") organs
are paired, ciliated structures found only in polychaetes, and are thought to be chemosensors.[14] Some
polychaetes also have various combinations of ocelli ("little eyes") that detect the direction from which light is
coming and camera eyes or compound eyes that can probably form images.[25] The compound eyes
probably evolved independently of arthropods' eyes.[14] Some tube-worms use ocelli widely spread over
their bodies to detect the shadows of fish, so that they can quickly withraw into their tubes.[25] Some
burrowing and tube-dwelling polychaetes have statocysts (tilt and balance sensors) that tell them which way
is down.[25] A few polychaete genera have on the undersides of their heads palps that are used both in
feeding and as "feelers", and some of these also have antennae that are structurally similar but probably are
used mainly as "feelers".[14]
[edit] Coelom, locomotion and circulatory system
Most annelids have a pair of coeloms (body cavities) in each segment, separated from other
segments by septa and from each other by vertical mesenteries. Each septum forms a sandwich with
connective tissue in the middle and mesothelium (membrane that serves as a lining) from the preceding and
following segments on either side. Each mesentery is similar except that the mesothelium is the lining of
each of the pair of coeloms, and the blood vessels and, in polychaetes, the main nerve cords are embedded
in it.[4] The mesothelium is made of modified epitheliomuscular cells,[4] in other words their bodies form part
of the epithelium but their bases extend to form muscle fibers in the body wall.[26] The mesothelium may
also form radial and circular muscles on the septa, and circular muscles around the blood vessels and gut.
Parts of the mesothelium, especially on the outside of the gut, may also form chloragogen cells that perform
similar functions to the livers of vertebrates: producing and storing glycogen and fat; producing the oxygen-
carrier hemoglobin; breaking down proteins; and turning nitrogenous waste products into ammonia and urea
to be excreted.[4]
Peristalsis moves this "worm" to the right

Many annelids move by peristalsis (waves of contraction and expansion that sweep along the body),
[4] or flex the body while using parapodia to crawl or swim.[27] In these animals the septa enable the circular
and longitudinal muscles to change the shape of individual segments, by making each segment a separate
fluid-filled "balloon".[4] However, the septa are often incomplete in annelids that are semi-sessile or that do
not move by peristalsis or by movements of parapodia – for example some move by whipping movements of
the body, some small marine species move by means of cilia (fine muscle-powered hairs) and some
burrowers turn their pharynges (throats) inside out to penetrate the sea-floor and drag themselves into it.[4]
The fluid in the coeloms contains coelomocyte cells that defend the animals against parasites and
infections. In some species coelomocytes may also contain a respiratory pigment – red hemoglobin in some
species, green chlorocruorin in others[14] – and provide oxygen transport within their segments. Respiratory
pigment is also dissolved in the blood plasma. Species with well-developed septa generally also have blood
vessels running all long their bodies above and below the gut, the upper one carrying blood forwards while
the lower one carries it backwards. Networks of capillaries (fine blood vessels) in the body wall and around
the gut transfer blood between the main blood vessels and to parts of the segment that need oxygen and
nutrients. Both of the major vessels, especially the upper one, can pump blood by contracting. In some
annelids the forward end of the upper blood vessel is enlarged with muscles to form a heart, while in the
forward ends of many earthworms some of the vessels that connect the upper and lower main vessels
function as hearts. Species with poorly-developed or no septa generally have no blood vessels and rely on
the circulation within the coelom for delivering nutrients and oxygen.[4]
However, leeches and their closest relatives have a body structure that is very uniform within the
group but significantly different from that of other annelids, including other members of the Clitellata.[11] In
leeches there are no septa, the connective tissue layer of the body wall is so thick that it occupies much of
the body, and the two coeloms are widely separated and run the length of the body. They function as the
main blood vessels, although they are side-by-side rather than upper and lower. However, they are lined with
mesothelium, like the coeloms and unlike the blood vessels of other annelids. Leeches generally use suckers
at their front and rear ends to move like inchworms. The anus is on the upper surface of the pygidium.[11]
[edit] Respiration
In some annelids, including earthworms, all respiration is via the skin. However, many polychaetes
and some clitellates (the group to which earthworms belong) have gills associated with most segments, often
as extensions of the parapodia in polychaetes. The gills of tube-dwellers and burrowers usually cluster
around whichever end has the stronger water flow.[14]
[edit] Feeding and excretion

Feeding structures in the mouth region vary widely, and have little correlation with the animals' diets.
Many polychaetes have a muscular pharynx that can be everted (turned inside out to extend it). In these
animals the foremost few segments often lack septa so that, when the muscles in these segments contract,
the sharp increase in fluid pressure from all these segments everts the pharynx very quickly. Two families,
the Eunicidae and Phyllodocidae, have evolved jaws, which can be used for seizing prey, biting off pieces of
vegetation, or grasping dead and decaying matter. On the other hand some predatory polychaetes have
neither jaws nor eversible pharynges. Selective deposit feeders generally live in tubes on the sea-floor and
use palps to find food particles in the sediment and then wipe them into their mouths. Filter feeders use
"crowns" of palps covered in cilia that wash food particles towards their mouths. Non-selective deposit
feeders ingest soil or marine sediments via mouths that are generally unspecialized. Some clitellates have
sticky pads in the roofs of their mouths, and some of these can evert the pads to capture prey. Leeches often
have an eversible proboscis, or a muscular pharynx with two or three teeth.[14]
The gut is generally an almost straight tube supported by the mesenteries (vertical partitions within
segments), and ends with the anus on the underside of the pygidium.[4] However, in members of the tube-
dwelling family Siboglinidae the gut is blocked by a swollen lining that houses symbiotic bacteria, which can
make up 15% of the worms' total weight. The bacteria convert inorganic matter – such as hydrogen sulfide
and carbon dioxide from hydrothermal vents, or methane from seeps – to organic matter that feeds
themselves and their hosts, while the worms extend their palps into the gas flows to absorb the gases
needed by the bacteria.[14]
Annelids with blood vessels use metanephridia to remove soluble waste products, while those
without use protonephridia.[4] Both of these systems use a two-stage filtration process, in which fluid and
waste products are first extracted and these are filtered again to re-absorb any re-usable materials while
dumping toxic and spent materials as urine. The difference is that protonephridia combine both filtration
stages in the same organ, while metanephridia perform only the second filtration and rely on other
mechanisms for the first – in annelids special filter cells in the walls of the blood vessels let fluids and other
small molecules pass into the coelomic fluid, where it circulates to the metanephridia.[28] In annelids the
points at which fluid enters the protonephridia or metanephridia are on the forward side of a septum while the
second-stage filter and the nephridiopore (exit opening in the body wall) are in the following segment. As a
result the hindmost segment (before the growth zone and pygidium) has no structure that extracts its wastes,
as there is no following segment to filter and discharge them, while the first segment contains an extraction
structure that passes wastes to the second, but does not contain the structures that re-filter and discharge
urine.[4]
[edit] Reproduction and life cycle
[edit] Asexual reproduction
This sabellid tubeworm is budding

Polychaetes can reproduce asexually, by dividing into two or more pieces or by budding off a new
individual while the parent remains a complete organism.[4][29] Some oligochaetes, such as Aulophorus
furcatus, seem to reproduce entirely asexually, while others reproduce asexually in summer and sexually in
autumn. Asexual reproduction in oligochaetes is always by dividing into two or more pieces, rather than by
budding.[8][30] However, leeches have never been seen reproducing asexually.[8][31]
Most polychaetes and oligochaetes also use similar mechanisms to regenerate after suffering
damage. Two polychaete genera, Chaetopterus and Dodecaceria, can regenerate from a single segment,
and others can regenerate even if their heads are removed.[8][29] Annelids are the most complex animals
that can regenerate after such severe damage.[32] On the other hand leeches cannot regenerate.[31]
[edit] Sexual reproduction
It is thought that annelids were originally animals with
two separate sexes, which released ova and sperm into the
water via their nephridia.[4] The fertilized eggs develop into Apical tuft (cilia)
trochophore larvae, which live as plankton.[34] Later they sink Prototroch (cilia)
to the sea-floor and metamorphose into miniature adults: the
part of the trochophore between the apical tuft and the Stomach
prototroch becomes the prostomium (head); a small area
round the trochophore's anus becomes the pygidium (tail- Mouth
piece); a narrow band immediately in front of that becomes the Metatroch (cilia)
growth zone that produces new segments; and the rest of the
trochophore becomes the peristomium (the segment that Mesoderm
contains the mouth).[4]
Anus
However, the lifecycles of most living polychaetes,
which are almost all marine animals, are unknown, and only /// = cilia
about 25% of the 300+ species whose lifecycles are known
follow this pattern. About 14% use a similar external
fertilization but produce yolk-rich eggs, which reduce the time
the larva needs to spend among the plankton, or eggs from
which miniature adults emerge rather than larvae. The rest
care for the fertilized eggs until they hatch – some by producing
jelly-covered masses of eggs which they tend, some by
attaching the eggs to their bodies and a few species by
keeping the eggs within their bodies until they hatch. These
Trochophore larva[33]
species use a variety of methods for sperm transfer; for example, in some the females collect sperm released
into the water, while in others the males have penes that inject sperm into the female.[34] There is no
guarantee that this is a representative sample of polychaetes' reproductive patterns, and it simply reflects
scientists' current knowledge.[34]
Some polychaetes breed only once in their lives, while others breed almost continuously or through
several breeding seasons. While most polychaetes remain of one sex all their lives, a significant percentage
of species are full hermaphrodites or change sex during their lives. Most polychaetes whose reproduction
has been studied lack permanent gonads, and it is uncertain how they produce ova and sperm. In a few
species the rear of the body splits off and becomes a separate individual that lives just long enough to swim
to a suitable environment, usually near the surface, and spawn.[34]
Most mature clitellates (the group that includes earthworms and leeches) are full hermaphrodites,
although in a few leech species younger adults function as males and become female at maturity. All have
well-developed gonads, and all copulate. Earthworms store their partners' sperm in spermathecae ("sperm
stores") and then the clitellum produces a cocoon that collects ova from the ovaries and then sperm from the
spermathecae. Fertilization and development of earthworm eggs takes place in the cocoon. Leeches' eggs
are fertilized in the ovaries, and then transferred to the cocoon. In all clitellates the cocoon also either
produces yolk when the eggs are fertilized or nutrients while they are developing. All clitellates hatch as
miniature adults rather than larvae.[34]
[edit] Ecological significance

Charles Darwin's book The Formation of Vegetable Mould through the Action of Worms (1881)
presented the first scientific analysis of earthworms' contributions to soil fertility.[35] Some burrow while
others live entirely on the surface, generally in moist leaf litter. The burrowers loosen the soil so that oxygen
and water can penetrate it, and both surface and burrowing worms help to produce soil by mixing organic and
mineral matter, by accelerating the decomposition of organic matter and thus making it more quickly
available to other organisms, and by concentrating minerals and converting them to forms that plants can use
more easily.[36][37] Earthworms are also important prey for birds ranging in size from robins to storks, and
for mammals ranging from shrews to badgers, and in some cases conserving earthworms may be essential
for conserving endangered birds.[38]
Marine annelids may account for over one-third of bottom-dwelling animal species round coral reefs
and in tidal zones.[35] Burrowing species increase the penetration of water and oxygen and water into the
sea-floor sediment, which encourages the growth of populations of bacteria and small animals alongside
their burrows.[39]
Although blood-sucking leeches do little direct harm to their victims, some transmit flagellates that
can be very dangerous to their hosts. Some small tube-dwelling oligochaetes transmit myxosporean
parasites that cause whirling disease in fish.[35]
[edit] Interaction with humans

Earthworms make a significant contribution to soil fertility.[35] The rear end of the Palolo worm, a
marine polychaete that tunnels through coral, detaches in order to spawn at the surface, and the people of
Samoa regard these spawning modules as a delicacy.[35] Anglers sometimes find that worms are more
effective bait than artificial flies, and worms can be kept for several days in a tin lined with damp moss.[40]
Ragworms are commercially important as bait and as food sources for aquaculture, and there have been
proposals to farm them in order to reduce over-fishing of their natural populations.[39] Some marine
polychaetes' predation on molluscs causes serious losses to fishery and aquaculture operations.[35]
Scientists study aquatic annelids to monitor the oxygen content, salinity and pollution levels in fresh
and marine water.[35]
Accounts of the use of leeches for the medically dubious practise of blood-letting have come from
China around 30 AD, India around 200 AD, ancient Rome around 50 AD and later throughout Europe. In the
19th century medical demand for leeches was so high that some areas' stocks were exhausted and other
regions imposed restrictions or bans on exports, and Hirudo medicinalis is treated as an endangered species
by both IUCN and CITES. More recently leeches have been used to assist in microsurgery, and their saliva
has provided anti-inflammatory compounds and several important anticoagulants, one of which also prevents
tumors from spreading.[35]
Ragworms' jaws are strong but much lighter than the hard parts of many other organisms, which are
biomineralized with calcium salts. These advantages have attracted the attention of engineers. Investigations
showed that ragworm jaws are made of unusual proteins that bind strongly to zinc.[41]

Since annelids are soft-bodied, their fossils are rare.[42] Polychaetes' fossil record consists mainly of
the jaws that some species had and the mineralized tubes that some secreted.[43] Some Ediacaran fossils
such as Dickinsonia in some ways resemble polychaetes, but the similarities are too vague for these fossils
to be classified with confidence.[44] The small shelly fossil Cloudina, from 549 to 542 million years ago, has
been classified by some authors as an annelid, but by others as a cnidarian (i.e. in the phylum to which
jellyfish and sea anemones belong).[45] Until 2008 the earliest fossils widely accepted as annelids were the
polychaetes Canadia and Burgessochaeta, both from Canada's Burgess Shale, formed about 505 million
years ago in the early Cambrian.[46] Myoscolex, found in Australia and a little older than the Burgess Shale,
was possibly an annelid. However, it lacks some typical annelid features and has features which are not
usually found in annelids and some of which are associated with other phyla.[46] Then Simon Conway Morris
and John Peel reported Phragmochaeta from Sirius Passet, about 518 million years old, and concluded that
it was the oldest annelid known to date.[44] There has been vigorous debate about whether the Burgess
Shale fossil Wiwaxia was a mollusc or an annelid.[46] Polychaetes diversified in the early Ordovician, about
488 to 474 million years ago. It is not until the early Ordovician that the first annelid jaws are found, thus the
crown-group cannot have appeared before this date and probably appeared somewhat later.[1] By the end of
the Carboniferous, about 299 million years ago, fossils of most of the modern mobile polychaete groups had
appeared.[46] Many fossil tubes look like those made by modern sessile polychaetes, but the first tubes
clearly produced by polychaetes date from the Jurassic, less than 199 million years ago.[46]
The earliest good evidence for oligochaetes occurs in the Tertiary period, which began 65 million
years ago, and it has been suggested that these animals evolved around the same time as flowering plants
in the early Cretaceous, from 130 to 90 million years ago.[47] A trace fossil consisting of a convoluted burrow
partly filled with small fecal pellets may be evidence that earthworms were present in the early Triassic period
from 251 to 245 million years ago.[47][48] Body fossils going back to the mid Ordovician, from 472 to 461
million years ago, have been tentatively classified as oligochaetes, but these identifications are uncertain and
some have been disputed.[47][49]
[edit] Family tree

Annelida
some "Canalipalpata"
Sipuncula, previously a separate

phylum
Clitellata
some
"Oligochaeta"
Hirudines
(leeches)
some
"Oligochaeta"
some
"Oligochaeta"
Aeolosomatidae[
50]
some
"Scolecida" and
"Canalipalpata"
some "Scolecida"
Echiura, previously a separate
phylum
some "Scolecida"
Siblonginidae, previously phylum Pogonophora

Annelid groups and phyla incorporated into Annelida (2007; simplified).[6]

Highlights major changes to traditional classifications.
Traditionally the annelids have been divided into two major groups, the polychaetes and clitellates. In
turn the clitellates were divided into oligochaetes, which include earthworms, and hirudinomorphs, whose
best-known members are leeches.[4] For many years there was no clear arrangement of the approximately
80 polychaete families into higher-level groups.[6] In 1997 Greg Rouse and Kristian Fauchald attempted a
"first heuristic step in terms of bringing polychaete systematics to an acceptable level of rigour", based on
anatomical structures, and divided polychaetes into:[51]
• Scolecida, less than 1,000 burrowing species that look rather like earthworms.[52]
• Palpata, the great majority of polychaetes, divided into:
• Canalipalpata, which are distinguished by having long grooved palps that they use
for feeding, and most of which live in tubes.[52]
• Aciculata, the most active polychaetes, which have parapodia reinforced by internal
spines (aciculae).[52]
Also in 1997 Damhnait McHugh, using molecular phylogenetics to compare similarities and
differences in one gene, presented a very different view, in which: the clitellates were an off-shoot of one
branch of the polychaete family tree; the pogonophorans and echiurans, which for a few decades had been
regarded as a separate phyla, were placed on other branches of the polychaete tree.[53] Subsequent
molecular phylogenetics analyses on a similar scale presented similar conclusions.[54]
In 2007 Torsten Struck and colleagues compared 3 genes in 81 taxa, of which 9 were outgroups,[6]
in other words not considered closely related to annelids but included to give an indication of where the
organisms under study are placed on the larger tree of life.[55] For a cross-check the study used an analysis
of 11 genes (including the original 3) in 10 taxa. This analysis agreed that clitellates, pogonophorans and
echiurans were on various branches of the polychaete family tree. It also concluded that the classification of
polychaetes into Scolecida, Canalipalpata and Aciculata was useless, as the members of these alleged
groups were scattered all over the family tree derived from comparing the 81 taxa. In addition, it also placed
sipunculans, generally regarded at the time as a separate phylum, on another branch of the polychaete tree,
and concluded that leeches were a sub-group of oligochaetes rather than their sister-group among the
clitellates.[6] Rouse accepted the analyses based on molecular phylogenetics,[8] and their main conclusions
are now the scientific consensus, although the details of the annelid family tree remain uncertain.[7]
In addition to re-writing the classification of annelids and 3 previously independent phyla, the
molecular phylogenetics analyses undermine the emphasis that decades of previous writings placed on the
importance of segmentation in the classification of invertebrates. Polychaetes, which these analyses found to
be the parent group, have completely segmented bodies, while polychaetes' echiurans and sipunculan
offshoots are not segmented and pogonophores are segmented only in the rear parts of their bodies. It now
seems that segmentation can appear and disappear much more easily in the course of evolution than was
previously thought.[6][53] The 2007 study also noted that the ladder-like nervous system, which is associated
with segmentation, is less universal than previously thought in both annelids and arthropods.[6]
Annelids are members of the
protostomes, one of the two major
superphyla of bilaterian animals – the
other is the deuterostomes, which Protostomia
includes vertebrates.[54] Within the
protostomes, annelids used to be
grouped with arthropods under the
super-group Articulata ("jointed
animals"), as segmentation is obvious in
most members of both phyla. However, Lophotrochozoa
the genes that drive segmentation in
arthropods do not appear to do the
same in annelids. Arthropods and
annelids both have close relatives that
are unsegmented. It is at least as easy Annelida
to assume that they evolved segmented
bodies independently as it is to assume
that the ancestral protostome or Sipuncula
bilaterian was segmented and that
segmentation disappeared in many
descendant phyla.[54] The current view Mollusca
is that annelids are grouped with
molluscs, brachiopods and several other
phyla that have lophophores (fan-like Phoronida
feeding structures) and/or trochophore and Brachiopoda
Nemertea
Dicyemida
larvae as members of Lophotrochozoa.[56] Bryzoa may be the most basal phylum (the one that first became
distinctive) within the Lophotrochozoa, and the relationships between the other members are not yet known.
[54] Arthropods are now regarded as members of the Ecdysozoa ("animals that molt"), along with some phyla
that are unsegmented.[54][57]
The "Lophotrochozoa" hypothesis is also supported by the fact that many phyla within this group,
including annelids, molluscs, nemerteans and flatworms, follow a similar pattern in the fertilized egg's
development. When their cells divide after the 4-cell stage, descendants of these 4 cells form a spiral pattern.
In these phyla the "fates" of the embryo's cells, in other words the roles their descendants will play in the
adult animal, are the same and can be predicted from a very early stage.[58] Hence this development pattern
is often described as "spiral determinate cleavage".[59]
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• Dales, R. P. 1967. Annelids, 2nd edition. London: Hutchinson University Library.
• "Annelid Fossils" (Web page). The Virtual Fossil Museum. 2006.
http://www.fossilmuseum.net/fossils/Annelid-Fossils.htm. Retrieved May 20, 2006. – Descriptions
and images of annelid fossils from Mazon Creek and the Utah House Range.
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• Polychaete Larva – Guide to the Marine Zooplankton of south eastern Australia , Tasmanian
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Natural selection

For other uses, see Natural Selection (disambiguation).
Part of the Biology series on
Evolution
Mechanisms and processes
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Research and history
Introduction
Evidence
Evolutionary history of life
History
Level of support
Modern synthesis
Objections / Controversy
Social effect
Theory and fact
Evolutionary biology fields
Cladistics
Ecological genetics
Evolutionary anthropology
Evolutionary development
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Molecular evolution
Phylogenetics
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Biology portal ·v · d · e
Natural selection is the process by which traits become more or less common in a population due to
consistent effects upon the survival or reproduction of their bearers. It is a key mechanism of evolution.
The natural genetic variation within a population of organisms may cause some individuals to survive
and reproduce more successfully than others in their current environment. For example, the peppered moth
exists in both light and dark colours in the United Kingdom, but during the industrial revolution many of the
trees on which the moths rested became blackened by soot, giving the dark-colored moths an advantage in
hiding from predators. This gave dark-colored moths a better chance of surviving to produce dark-colored
offspring, and in just a few generations the majority of the moths were dark. Factors which affect reproductive
success are also important, an issue which Charles Darwin developed in his ideas on sexual selection.
Natural selection acts on the phenotype, or the observable characteristics of an organism, but the
genetic (heritable) basis of any phenotype which gives a reproductive advantage will become more common
in a population (see allele frequency). Over time, this process can result in adaptations that specialize
populations for particular ecological niches and may eventually result in the emergence of new species. In
other words, natural selection is an important process (though not the only process) by which evolution takes
place within a population of organisms. As opposed to artificial selection, in which humans favor specific
traits, in natural selection the environment acts as a sieve through which only certain variations can pass.
Natural selection is one of the cornerstones of modern biology. The term was introduced by Darwin
in his influential 1859 book On the Origin of Species,[1] in which natural selection was described as
analogous to artificial selection, a process by which animals and plants with traits considered desirable by
human breeders are systematically favored for reproduction. The concept of natural selection was originally
developed in the absence of a valid theory of heredity; at the time of Darwin's writing, nothing was known of
modern genetics. The union of traditional Darwinian evolution with subsequent discoveries in classical and
molecular genetics is termed the modern evolutionary synthesis. Natural selection remains the primary
explanation for adaptive evolution.
Contents
[hide]
• 1 General principles
• 1.1 Nomenclature and usage
• 1.2 Fitness
• 1.3 Types of selection
• 1.4 Sexual selection
• 1.5 Examples of natural selection
• 2 Evolution by means of natural selection
• 2.1 Speciation
• 3 Historical development
• 3.1 Pre-Darwinian theories
• 3.2 Darwin's theory
• 3.3 Modern evolutionary synthesis
• 4 Impact of the idea
• 4.1 Cell and molecular biology
• 4.2 Social and psychological theory
• 4.3 Information and systems theory
• 5 Genetic basis of natural selection
• 5.1 Genotype and phenotype
• 5.2 Directionality of selection
• 5.3 Selection and genetic variation
[edit] General principles
Darwin's illustrations of beak variation in the finches of the Galápagos Islands, which hold 13 closely
related species that differ most markedly in the shape of their beaks. The beak of each species is suited to its
preferred food, suggesting that beak shapes evolved by natural selection.
Natural variation occurs among the individuals of any population of organisms. Many of these
differences do not affect survival (such as differences in eye color in humans), but some differences may
improve the chances of survival of a particular individual. A rabbit that runs faster than others may be more
likely to escape from predators, and algae that are more efficient at extracting energy from sunlight will grow
faster. Something that increases an animal's survival will often also include its reproductive rate; however,
sometimes there is a trade-off between survival and current reproduction. Ultimately, what matters is total
lifetime reproduction of the animal.
If the traits that give these individuals a reproductive advantage are also heritable, that is, passed
from parent to child, then there will be a slightly higher proportion of fast rabbits or efficient algae in the next
generation. This is known as differential reproduction. Even if the reproductive advantage is very slight, over
many generations any heritable advantage will become dominant in the population. In this way the natural
environment of an organism "selects" for traits that confer a reproductive advantage, causing gradual
changes or evolution of life. This effect was first described and named by Charles Darwin.
The concept of natural selection predates the understanding of genetics, the mechanism of heredity
for all known life forms. In modern terms, selection acts on an organism's phenotype, or observable
characteristics, but it is the organism's genetic make-up or genotype that is inherited. The phenotype is the
result of the genotype and the environment in which the organism lives (see Genotype-phenotype
distinction).
This is the link between natural selection and genetics, as described in the modern evolutionary
synthesis. Although a complete theory of evolution also requires an account of how genetic variation arises in
the first place (such as by mutation and sexual reproduction) and includes other evolutionary mechanisms
(such as genetic drift and gene flow), natural selection appears to be the most important mechanism for
creating complex adaptations in nature.
[edit] Nomenclature and usage

The term natural selection has slightly different definitions in different contexts. It is most often
defined to operate on heritable traits, because these are the traits that directly participate in evolution.
However, natural selection is "blind" in the sense that changes in phenotype (physical and behavioral
characteristics) can give a reproductive advantage regardless of whether or not the trait is heritable (non
heritable traits can be the result of environmental factors or the life experience of the organism).
Following Darwin's primary usage[1] the term is often used to refer to both the evolutionary
consequence of blind selection and to its mechanisms.[2][3] It is sometimes helpful to explicitly distinguish
between selection's mechanisms and its effects; when this distinction is important, scientists define "natural
selection" specifically as "those mechanisms that contribute to the selection of individuals that reproduce",
without regard to whether the basis of the selection is heritable. This is sometimes referred to as "phenotypic
natural selection".[4]
Traits that cause greater reproductive success of an organism are said to be selected for, whereas
those that reduce success are selected against. Selection for a trait may also result in the selection of other
correlated traits that do not themselves directly influence reproductive advantage. This may occur as a result
of pleiotropy or gene linkage.[5]
[edit] Fitness
Main article: Fitness (biology)
The concept of fitness is central to natural selection. Broadly, individuals which are more "fit" have
better potential for survival, as in the well-known phrase "survival of the fittest". However, as with natural
selection above, the precise meaning of the term is much more subtle, and Richard Dawkins manages in his
later books to avoid it entirely. (He devotes a chapter of his book, The Extended Phenotype, to discussing the
various senses in which the term is used). Modern evolutionary theory defines fitness not by how long an
organism lives, but by how successful it is at reproducing. If an organism lives half as long as others of its
species, but has twice as many offspring surviving to adulthood, its genes will become more common in the
adult population of the next generation.
Though natural selection acts on individuals, the effects of chance mean that fitness can only really
be defined "on average" for the individuals within a population. The fitness of a particular genotype
corresponds to the average effect on all individuals with that genotype. Very low-fitness genotypes cause
their bearers to have few or no offspring on average; examples include many human genetic disorders like
cystic fibrosis.
Since fitness is an averaged quantity, it is also possible that a favorable mutation arises in an
individual that does not survive to adulthood for unrelated reasons. Fitness also depends crucially upon the
environment. Conditions like sickle-cell anemia may have low fitness in the general human population, but
because the sickle-cell trait confers immunity from malaria, it has high fitness value in populations which
have high malaria infection rates.
[edit] Types of selection

Natural selection can act on any heritable phenotypic trait, and selective pressure can be produced
by any aspect of the environment, including sexual selection and competition with members of the same or
other species. However, this does not imply that natural selection is always directional and results in adaptive
evolution; natural selection often results in the maintenance of the status quo by eliminating less fit variants.
The unit of selection can be the individual or it can be another level within the hierarchy of biological
organisation, such as genes, cells, and kin groups. There is still debate about whether natural selection acts
at the level of groups or species to produce adaptations that benefit a larger, non-kin group. Likewise, there
is debate as to whether selection at the molecular level prior to gene mutations and fertilization of the zygote
should be ascribed to conventional natural selection because traditionally natural selection is an
environmental and exterior force that acts upon a phenotype typically after birth. Some science journalists
distinguish natural selection from gene selection by informally referencing selection of mutations as "pre-
selection."[6]
Selection at a different level such as the gene can result in an increase in fitness for that gene, while
at the same time reducing the fitness of the individuals carrying that gene, in a process called intragenomic
conflict. Overall, the combined effect of all selection pressures at various levels determines the overall fitness
of an individual, and hence the outcome of natural selection.
The life cycle of a sexually reproducing organism. Various components of natural selection are
indicated for each life stage.[7]
Natural selection occurs at every life stage of an individual. An individual organism must survive until
adulthood before it can reproduce, and selection of those that reach this stage is called viability selection. In
many species, adults must compete with each other for mates via sexual selection, and success in this
competition determines who will parent the next generation. When individuals can reproduce more than
once, a longer survival in the reproductive phase increases the number of offspring, called survival selection.
The fecundity of both females and males (for example, giant sperm in certain species of Drosophila)
[8] can be limited via "fecundity selection". The viability of produced gametes can differ, while intragenomic
conflicts such as meiotic drive between the haploid gametes can result in gametic or "genic selection".
Finally, the union of some combinations of eggs and sperm might be more compatible than others; this is
termed compatibility selection.
[edit] Sexual selection

Main article: Sexual selection
It is useful to distinguish between "ecological selection" and "sexual selection". Ecological selection
covers any mechanism of selection as a result of the environment (including relatives, e.g. kin selection,
competition, and infanticide), while "sexual selection" refers specifically to competition for mates.[9]
Sexual selection can be intrasexual, as in cases of competition among individuals of the same sex in
a population, or intersexual, as in cases where one sex controls reproductive access by choosing among a
population of available mates. Most commonly, intrasexual selection involves male–male competition and
intersexual selection involves female choice of suitable males, due to the generally greater investment of
resources for a female than a male in a single offspring. However, some species exhibit sex-role reversed
behavior in which it is males that are most selective in mate choice; the best-known examples of this pattern
occur in some fishes of the family Syngnathidae, though likely examples have also been found in amphibian
and bird species.[10]
Some features that are confined to one sex only of a particular species can be explained by selection
exercised by the other sex in the choice of a mate, for example, the extravagant plumage of some male birds.
Similarly, aggression between members of the same sex is sometimes associated with very distinctive
features, such as the antlers of stags, which are used in combat with other stags. More generally, intrasexual
selection is often associated with sexual dimorphism, including differences in body size between males and
females of a species.[11]
[edit] Examples of natural selection
Resistance to antibiotics is increased though the survival of individuals which are immune to the
effects of the antibiotic, whose offspring then inherit the resistance, creating a new population of resistant
bacteria.
A well-known example of natural selection in action is the development of antibiotic resistance in
microorganisms. Since the discovery of penicillin in 1928 by Alexander Fleming, antibiotics have been used
to fight bacterial diseases. Natural populations of bacteria contain, among their vast numbers of individual
members, considerable variation in their genetic material, primarily as the result of mutations. When exposed
to antibiotics, most bacteria die quickly, but some may have mutations that make them slightly less
susceptible. If the exposure to antibiotics is short, these individuals will survive the treatment. This selective
elimination of maladapted individuals from a population is natural selection.
These surviving bacteria will then reproduce again, producing the next generation. Due to the
elimination of the maladapted individuals in the past generation, this population contains more bacteria that
have some resistance against the antibiotic. At the same time, new mutations occur, contributing new genetic
variation to the existing genetic variation. Spontaneous mutations are very rare, and advantageous mutations
are even rarer. However, populations of bacteria are large enough that a few individuals will have beneficial
mutations. If a new mutation reduces their susceptibility to an antibiotic, these individuals are more likely to
survive when next confronted with that antibiotic.
Given enough time, and repeated exposure to the antibiotic, a population of antibiotic-resistant
bacteria will emerge. This new changed population of antibiotic-resistant bacteria is optimally adapted to the
context it evolved in. At the same time, it is not necessarily optimally adapted any more to the old antibiotic
free environment. The end result of natural selection is two populations that are both optimally adapted to
their specific environment, while both perform substandard in the other environment.
The widespread use and misuse of antibiotics has resulted in increased microbial resistance to
antibiotics in clinical use, to the point that the methicillin-resistant Staphylococcus aureus (MRSA) has been
described as a "superbug" because of the threat it poses to health and its relative invulnerability to existing
drugs.[12] Response strategies typically include the use of different, stronger antibiotics; however, new
strains of MRSA have recently emerged that are resistant even to these drugs.[13]
This is an example of what is known as an evolutionary arms race, in which bacteria continue to
develop strains that are less susceptible to antibiotics, while medical researchers continue to develop new
antibiotics that can kill them. A similar situation occurs with pesticide resistance in plants and insects. Arms
races are not necessarily induced by man; a well-documented example involves the spread of a gene in the
butterfly Hypolimnas bolina suppressing male-killing activity by Wolbachia bacteria parasites on the island of
Samoa, where the spread of the gene is known to have occurred over a period of just five years [14]
[edit] Evolution by means of natural selection

Main articles: Evolution and Darwinism
A prerequisite for natural selection to result in adaptive evolution, novel traits and speciation, is the
presence of heritable genetic variation that results in fitness differences. Genetic variation is the result of
mutations, recombinations and alterations in the karyotype (the number, shape, size and internal
arrangement of the chromosomes). Any of these changes might have an effect that is highly advantageous or
highly disadvantageous, but large effects are very rare. In the past, most changes in the genetic material
were considered neutral or close to neutral because they occurred in noncoding DNA or resulted in a
synonymous substitution. However, recent research suggests that many mutations in non-coding DNA do
have slight deleterious effects.[15][16] Although both mutation rates and average fitness effects of mutations
are dependent on the organism, estimates from data in humans have found that a majority of mutations are
slightly deleterious.[17]
The exuberant tail of the peacock is thought to be the result of sexual selection by females. This
peacock is an albino; selection against albinos in nature is intense because they are easily spotted by
predators or are unsuccessful in competition for mates.
By the definition of fitness, individuals with greater fitness are more likely to contribute offspring to the
next generation, while individuals with lesser fitness are more likely to die early or fail to reproduce. As a
result, alleles which on average result in greater fitness become more abundant in the next generation, while
alleles which generally reduce fitness become rarer. If the selection forces remain the same for many
generations, beneficial alleles become more and more abundant, until they dominate the population, while
alleles with a lesser fitness disappear. In every generation, new mutations and re-combinations arise
spontaneously, producing a new spectrum of phenotypes. Therefore, each new generation will be enriched
by the increasing abundance of alleles that contribute to those traits that were favored by selection,
enhancing these traits over successive generations.
Some mutations occur in so-called regulatory genes. Changes in these can have large effects on the
phenotype of the individual because they regulate the function of many other genes. Most, but not all,
mutations in regulatory genes result in non-viable zygotes. Examples of nonlethal regulatory mutations occur
in HOX genes in humans, which can result in a cervical rib[18] or polydactyly, an increase in the number of
fingers or toes.[19] When such mutations result in a higher fitness, natural selection will favor these
phenotypes and the novel trait will spread in the population.
X-ray of the left hand of a ten year old boy with polydactyly.
Established traits are not immutable; traits that have high fitness in one environmental context may
be much less fit if environmental conditions change. In the absence of natural selection to preserve such a
trait, it will become more variable and deteriorate over time, possibly resulting in a vestigial manifestation of
the trait, also called evolutionary baggage. In many circumstances, the apparently vestigial structure may
retain a limited functionality, or may be co-opted for other advantageous traits in a phenomenon known as
preadaptation. A famous example of a vestigial structure, the eye of the blind mole rat, is believed to retain
function in photoperiod perception.[20]
[edit] Speciation
Main article: Speciation
Speciation requires selective mating, which result in a reduced gene flow. Selective mating can be
the result of 1. Geographic isolation, 2. Behavioral isolation, or 3. Temporal isolation. For example, a change
in the physical environment (geographic isolation by an extrinsic barrier) would follow number 1, a change in
camouflage for number 2 or a shift in mating times (i.e., one species of deer shifts location and therefore
changes its "rut") for number 3.[citation needed]
Over time, these subgroups might diverge radically to become different species, either because of
differences in selection pressures on the different subgroups, or because different mutations arise
spontaneously in the different populations, or because of founder effects – some potentially beneficial alleles
may, by chance, be present in only one or other of two subgroups when they first become separated. A
lesser-known mechanism of speciation occurs via hybridization, well-documented in plants and occasionally
observed in species-rich groups of animals such as cichlid fishes.[21] Such mechanisms of rapid speciation
can reflect a mechanism of evolutionary change known as punctuated equilibrium, which suggests that
evolutionary change and particularly speciation typically happens quickly after interrupting long periods of
stasis.
Genetic changes within groups result in increasing incompatibility between the genomes of the two
subgroups, thus reducing gene flow between the groups. Gene flow will effectively cease when the distinctive
mutations characterizing each subgroup become fixed. As few as two mutations can result in speciation: if
each mutation has a neutral or positive effect on fitness when they occur separately, but a negative effect
when they occur together, then fixation of these genes in the respective subgroups will lead to two
reproductively isolated populations. According to the biological species concept, these will be two different
species.
[edit] Historical development

Main articles: History of evolutionary thought, Inception of Darwin's theory, and Development of
Darwin's theory
The modern theory of natural selection derives from the work of Charles Darwin in the nineteenth
century.
[edit] Pre-Darwinian theories
Several ancient philosophers expressed the idea that nature produces a huge variety of creatures,
apparently randomly, and that only those creatures survive that manage to provide for themselves and
reproduce successfully; well-known examples include Empedocles[22] and his intellectual successor,
Lucretius,[23] while related ideas were later refined by Aristotle.[24] The struggle for existence was later
described by Al-Jahiz, who argued that environmental factors influence animals to develop new
characteristics to ensure survival.[25][26][27]
Abu Rayhan Biruni described the idea of artificial selection and argued that nature works in much the
same way.[28] Similar ideas were later expressed by Nasir al-Din Tusi[29] and Ibn Khaldun.[30][31] Such
classical arguments were reintroduced in the 18th century by Pierre Louis Maupertuis[32] and others,
including Charles Darwin's grandfather Erasmus Darwin. While these forerunners had an influence on
Darwinism, they later had little influence on the trajectory of evolutionary thought after Charles Darwin.
Until the early 19th century, the prevailing view in Western societies was that differences between
individuals of a species were uninteresting departures from their Platonic idealism (or typus) of created kinds.
However, the theory of uniformitarianism in geology promoted the idea that simple, weak forces could act
continuously over long periods of time to produce radical changes in the Earth's landscape. The success of
this theory raised awareness of the vast scale of geological time and made plausible the idea that tiny,
virtually imperceptible changes in successive generations could produce consequences on the scale of
differences between species.
Early 19th century evolutionists such as Jean Baptiste Lamarck suggested the inheritance of
acquired characteristics as a mechanism for evolutionary change; adaptive traits acquired by an organism
during its lifetime could be inherited by that organism's progeny, eventually causing transmutation of species.
[33] This theory has come to be known as Lamarckism and was an influence on the anti-genetic ideas of the
Stalinist Soviet biologist Trofim Lysenko.[34]
[edit] Darwin's theory

In 1859, Charles Darwin set out his theory of evolution by natural selection as an explanation for
adaptation and speciation. He defined natural selection as the "principle by which each slight variation [of a
trait], if useful, is preserved".[35] The concept was simple but powerful: individuals best adapted to their
environments are more likely to survive and reproduce. As long as there is some variation between them,
there will be an inevitable selection of individuals with the most advantageous variations. If the variations are
inherited, then differential reproductive success will lead to a progressive evolution of particular populations
of a species, and populations that evolve to be sufficiently different eventually become different species.[36]
Darwin's ideas were inspired by the observations that he had made on the Beagle voyage, and by
the work of a political economist, the Reverend Thomas Malthus, who in An Essay on the Principle of
Population, noted that population (if unchecked) increases exponentially whereas the food supply grows only
arithmetically; thus inevitable limitations of resources would have demographic implications, leading to a
"struggle for existence".[37] When Darwin read Malthus in 1838 he was already primed by his work as a
naturalist to appreciate the "struggle for existence" in nature and it struck him that as population outgrew
resources, "favourable variations would tend to be preserved, and unfavourable ones to be destroyed. The
result of this would be the formation of new species."[38]
Here is Darwin's own summary of the idea, which can be found in the fourth chapter of the Origin:
If during the long course of ages and under varying conditions of life, organic beings vary at all
in the several parts of their organisation, and I think this cannot be disputed; if there be, owing to the
high geometrical powers of increase of each species, at some age, season, or year, a severe struggle
for life, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of
all organic beings to each other and to their conditions of existence, causing an infinite diversity in
structure, constitution, and habits, to be advantageous to them, I think it would be a most extraordinary
fact if no variation ever had occurred useful to each being's own welfare, in the same way as so many
variations have occurred useful to man. But if variations useful to any organic being do occur,
assuredly individuals thus characterised will have the best chance of being preserved in the struggle
for life; and from the strong principle of inheritance they will tend to produce offspring similarly
characterised. This principle of preservation, I have called, for the sake of brevity, Natural Selection.
Once he had his theory "by which to work", Darwin was meticulous about gathering and refining
evidence as his "prime hobby" before making his idea public. He was in the process of writing his "big book"
to present his researches when the naturalist Alfred Russel Wallace independently conceived of the principle
and described it in an essay he sent to Darwin to forward to Charles Lyell. Lyell and Joseph Dalton Hooker
decided (without Wallace's knowledge) to present his essay together with unpublished writings which Darwin
had sent to fellow naturalists, and On the Tendency of Species to form Varieties; and on the Perpetuation of
Varieties and Species by Natural Means of Selection was read to the Linnean Society announcing co-
discovery of the principle in July 1858.[39] Darwin published a detailed account of his evidence and
conclusions in On the Origin of Species in 1859. In the 3rd edition of 1861 Darwin acknowledged that others
— notably William Charles Wells in 1813, and Patrick Matthew in 1831 — had proposed similar ideas, but had
neither developed them nor presented them in notable scientific publications.[40]
Darwin thought of natural selection by analogy to how farmers select crops or livestock for breeding,
which he called "artificial selection"; in his early manuscripts he referred to a 'Nature' which would do the
selection. At the time, other mechanisms of evolution such as evolution by genetic drift were not yet explicitly
formulated, and Darwin believed that selection was likely only part of the story: "I am convinced that [it] has
been the main, but not exclusive means of modification."[41] In a letter to Charles Lyell in September 1860,
Darwin regretted the use of the term "Natural Selection", preferring the term "Natural Preservation".[42]
For Darwin and his contemporaries, natural selection was essentially synonymous with evolution by
natural selection. After the publication of On the Origin of Species, educated people generally accepted that
evolution had occurred in some form. However, natural selection remained controversial as a mechanism,
partly because it was perceived to be too weak to explain the range of observed characteristics of living
organisms, and partly because even supporters of evolution balked at its "unguided" and non-progressive
nature,[43] a response that has been characterized as the single most significant impediment to the idea's
acceptance.[44]
However, some thinkers enthusiastically embraced natural selection; after reading Darwin, Herbert
Spencer introduced the term survival of the fittest, which became a popular summary of the theory.[45] The
fifth edition of On the Origin of Species published in 1869 included Spencer's phrase as an alternative to
natural selection, with credit given: "But the expression often used by Mr. Herbert Spencer, of the Survival of
the Fittest, is more accurate, and is sometimes equally convenient."[46] Although the phrase is still often
used by non-biologists, modern biologists avoid it because it is tautological if "fittest" is read to mean
"functionally superior" and is applied to individuals rather than considered as an averaged quantity over
populations.[47]
[edit] Modern evolutionary synthesis

Main article: Modern evolutionary synthesis
Natural selection relies crucially on the idea of heredity, but it was developed long before the basic
concepts of genetics. Although the Austrian monk Gregor Mendel, the father of modern genetics, was a
contemporary of Darwin's, his work would lie in obscurity until the early 20th century. Only after the
integration of Darwin's theory of evolution with a complex statistical appreciation of Gregor Mendel's 're-
discovered' laws of inheritance did natural selection become generally accepted by scientists.
The work of Ronald Fisher (who developed the required mathematical language and The Genetical
Theory of Natural Selection),[2] J.B.S. Haldane (who introduced the concept of the "cost" of natural
selection),[48] Sewall Wright (who elucidated the nature of selection and adaptation),[49] Theodosius
Dobzhansky (who established the idea that mutation, by creating genetic diversity, supplied the raw material
for natural selection: see Genetics and the Origin of Species),[50] William Hamilton (who conceived of kin
selection), Ernst Mayr (who recognised the key importance of reproductive isolation for speciation: see
Systematics and the Origin of Species)[51] and many others formed the modern evolutionary synthesis. This
synthesis cemented natural selection as the foundation of evolutionary theory, where it remains today.
[edit] Impact of the idea

Darwin's ideas, along with those of Adam Smith and Karl Marx, had a profound influence on 19th
century thought. Perhaps the most radical claim of the theory of evolution through natural selection is that
"elaborately constructed forms, so different from each other, and dependent on each other in so complex a
manner" evolved from the simplest forms of life by a few simple principles. This claim inspired some of
Darwin's most ardent supporters—and provoked the most profound opposition. The radicalism of natural
selection, according to Stephen Jay Gould,[52] lay in its power to "dethrone some of the deepest and most
traditional comforts of Western thought". In particular, it challenged long-standing beliefs in such concepts as
a special and exalted place for humans in the natural world and a benevolent creator whose intentions were
reflected in nature's order and design.
[edit] Cell and molecular biology
In the 19th century, Wilhelm Roux, a founder of modern embryology, wrote a book entitled « Der
Kampf der Teile im Organismus » (The struggle of parts in the organism) in which he suggested that the
development of an organism results from a Darwinian competition between the parts of the embryo,
occurring at all levels, from molecules to organs. In recent years, a modern version of this theory has been
proposed by Jean-Jacques Kupiec. According to this cellular Darwinism, stochasticity at the molecular level
generates diversity in cell types whereas cell interactions impose a characteristic order on the developing
embryo.
[edit] Social and psychological theory

The social implications of the theory of evolution by natural selection also became the source of
continuing controversy. Friedrich Engels, a German political philosopher and co-originator of the ideology of
communism, wrote in 1872 that "Darwin did not know what a bitter satire he wrote on mankind when he
showed that free competition, the struggle for existence, which the economists celebrate as the highest
historical achievement, is the normal state of the animal kingdom".[53] Interpretation of natural selection as
necessarily 'progressive', leading to increasing 'advances' in intelligence and civilisation, was used as a
justification for colonialism and policies of eugenics, as well as broader sociopolitical positions now described
as Social Darwinism. Konrad Lorenz won the Nobel Prize in Physiology or Medicine in 1973 for his analysis
of animal behavior in terms of the role of natural selection (particularly group selection). However, in
Germany in 1940, in writings that he subsequently disowned, he used the theory as a justification for policies
of the Nazi state. He wrote "... selection for toughness, heroism, and social utility...must be accomplished by
some human institution, if mankind, in default of selective factors, is not to be ruined by domestication-
induced degeneracy. The racial idea as the basis of our state has already accomplished much in this
respect."[54] Others have developed ideas that human societies and culture evolve by mechanisms that are
analogous to those that apply to evolution of species.[55]
More recently, work among anthropologists and psychologists has led to the development of
sociobiology and later evolutionary psychology, a field that attempts to explain features of human psychology
in terms of adaptation to the ancestral environment. The most prominent such example, notably advanced in
the early work of Noam Chomsky and later by Steven Pinker, is the hypothesis that the human brain is
adapted to acquire the grammatical rules of natural language.[56] Other aspects of human behavior and
social structures, from specific cultural norms such as incest avoidance to broader patterns such as gender
roles, have been hypothesized to have similar origins as adaptations to the early environment in which
modern humans evolved. By analogy to the action of natural selection on genes, the concept of memes –
"units of cultural transmission", or culture's equivalents of genes undergoing selection and recombination –
has arisen, first described in this form by Richard Dawkins[57] and subsequently expanded upon by
philosophers such as Daniel Dennett as explanations for complex cultural activities, including human
consciousness.[58] Extensions of the theory of natural selection to such a wide range of cultural phenomena
have been distinctly controversial and are not widely accepted.[59]
[edit] Information and systems theory

In 1922, Alfred Lotka proposed that natural selection might be understood as a physical principle
which could be described in terms of the use of energy by a system,[60] a concept that was later developed
by Howard Odum as the maximum power principle whereby evolutionary systems with selective advantage
maximise the rate of useful energy transformation. Such concepts are sometimes relevant in the study of
applied thermodynamics.
The principles of natural selection have inspired a variety of computational techniques, such as "soft"
artificial life, that simulate selective processes and can be highly efficient in 'adapting' entities to an
environment defined by a specified fitness function.[61] For example, a class of heuristic optimization
algorithms known as genetic algorithms, pioneered by John Holland in the 1970s and expanded upon by
David E. Goldberg,[62] identify optimal solutions by simulated reproduction and mutation of a population of
solutions defined by an initial probability distribution.[63] Such algorithms are particularly useful when applied
to problems whose solution landscape is very rough or has many local minima.
[edit] Genetic basis of natural selection

The idea of natural selection predates the understanding of genetics. We now have a much better
idea of the biology underlying heritability, which is the basis of natural selection.
[edit] Genotype and phenotype

See also: Genotype-phenotype distinction.
Natural selection acts on an organism's phenotype, or physical characteristics. Phenotype is
determined by an organism's genetic make-up (genotype) and the environment in which the organism lives.
Often, natural selection acts on specific traits of an individual, and the terms phenotype and genotype are
used narrowly to indicate these specific traits.
When different organisms in a population possess different versions of a gene for a certain trait, each
of these versions is known as an allele. It is this genetic variation that underlies phenotypic traits. A typical
example is that certain combinations of genes for eye color in humans which, for instance, give rise to the
phenotype of blue eyes. (On the other hand, when all the organisms in a population share the same allele for
a particular trait, and this state is stable over time, the allele is said to be fixed in that population.)
Some traits are governed by only a single gene, but most traits are influenced by the interactions of
many genes. A variation in one of the many genes that contributes to a trait may have only a small effect on
the phenotype; together, these genes can produce a continuum of possible phenotypic values.[64]
[edit] Directionality of selection

When some component of a trait is heritable, selection will alter the frequencies of the different
alleles, or variants of the gene that produces the variants of the trait. Selection can be divided into three
classes, on the basis of its effect on allele frequencies.[65]
Directional selection occurs when a certain allele has a greater fitness than others, resulting in an
increase of its frequency. This process can continue until the allele is fixed and the entire population shares
the fitter phenotype. It is directional selection that is illustrated in the antibiotic resistance example above.
Far more common is stabilizing selection (which is commonly confused with purifying selection[66]
[67]), which lowers the frequency of alleles that have a deleterious effect on the phenotype – that is, produce
organisms of lower fitness. This process can continue until the allele is eliminated from the population.
Purifying selection results in functional genetic features, such as protein-coding genes or regulatory
sequences, being conserved over time due to selective pressure against deleterious variants.
Finally, a number of forms of balancing selection exist, which do not result in fixation, but maintain an
allele at intermediate frequencies in a population. This can occur in diploid species (that is, those that have
two pairs of chromosomes) when heterozygote individuals, who have different alleles on each chromosome
at a single genetic locus, have a higher fitness than homozygote individuals that have two of the same
alleles. This is called heterozygote advantage or overdominance, of which the best-known example is the
malarial resistance observed in heterozygous humans who carry only one copy of the gene for sickle cell
anemia. Maintenance of allelic variation can also occur through disruptive or diversifying selection, which
favors genotypes that depart from the average in either direction (that is, the opposite of overdominance),
and can result in a bimodal distribution of trait values. Finally, balancing selection can occur through
frequency-dependent selection, where the fitness of one particular phenotype depends on the distribution of
other phenotypes in the population. The principles of game theory have been applied to understand the
fitness distributions in these situations, particularly in the study of kin selection and the evolution of reciprocal
altruism.[68][69]
[edit] Selection and genetic variation

A portion of all genetic variation is functionally neutral in that it produces no phenotypic effect or
significant difference in fitness; the hypothesis that this variation accounts for a large fraction of observed
genetic diversity is known as the neutral theory of molecular evolution and was originated by Motoo Kimura.
When genetic variation does not result in differences in fitness, selection cannot directly affect the frequency
of such variation. As a result, the genetic variation at those sites will be higher than at sites where variation
does influence fitness.[65] However, after a period with no new mutation, the genetic variation at these sites
will be eliminated due to genetic drift.
[edit] Mutation selection balance

Natural selection results in the reduction of genetic variation through the elimination of maladapted
individuals and consequently of the mutations that caused the maladaptation. At the same time, new
mutations occur, resulting in a mutation-selection balance. The exact outcome of the two processes depends
both on the rate at which new mutations occur and on the strength of the natural selection, which is a function
of how unfavorable the mutation proves to be. Consequently, changes in the mutation rate or the selection
pressure will result in a different mutation-selection balance.
[edit] Genetic linkage
Genetic linkage occurs when the loci of two alleles are linked, or in close proximity to each other on
the chromosome. During the formation of gametes, recombination of the genetic material results in
reshuffling of the alleles. However, the chance that such a reshuffle occurs between two alleles depends on
the distance between those alleles; the closer the alleles are to each other, the less likely it is that such a
reshuffle will occur. Consequently, when selection targets one allele, this automatically results in selection of
the other allele as well; through this mechanism, selection can have a strong influence on patterns of
variation in the genome.
Selective sweeps occur when an allele becomes more common in a population as a result of positive
selection. As the prevalence of one allele increases, linked alleles can also become more common, whether
they are neutral or even slightly deleterious. This is called genetic hitchhiking. A strong selective sweep
results in a region of the genome where the positively selected haplotype (the allele and its neighbours) are
essentially the only ones that exist in the population.
Whether a selective sweep has occurred or not can be investigated by measuring linkage
disequilibrium, or whether a given haplotype is overrepresented in the population. Normally, genetic
recombination results in a reshuffling of the different alleles within a haplotype, and none of the haplotypes
will dominate the population. However, during a selective sweep, selection for a specific allele will also result
in selection of neighbouring alleles. Therefore, the presence of a block of strong linkage disequilibrium might
indicate that there has been a 'recent' selective sweep near the center of the block, and this can be used to
identify sites recently under selection.
Background selection is the opposite of a selective sweep. If a specific site experiences strong and
persistent purifying selection, linked variation will tend to be weeded out along with it, producing a region in
the genome of low overall variability. Because background selection is a result of deleterious new mutations,
which can occur randomly in any haplotype, it does not produce clear blocks of linkage disequilibrium,
although with low recombination it can still lead to slightly negative linkage disequilibrium overall.[70]
[edit] See also

Book:Evolution

• Artificial selection
• Co-evolution
• Evolvability
• Gene-centered view of evolution
• Negative selection
• Unit of selection
[edit] References
1. ^ a b Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the
Preservation of Favoured Races in the Struggle for Life John Murray, London; modern reprint
Charles Darwin, Julian Huxley (2003). On The Origin of Species. Signet Classics. ISBN 0-451-
52906-5. Published online at The complete work of Charles Darwin online: On the origin of species
by means of natural selection, or the preservation of favoured races in the struggle for life.
2. ^ a b Fisher RA (1930) The Genetical Theory of Natural Selection Clarendon Press, Oxford
3. ^ Works employing or describing this usage:
Endler JA (1986). Natural Selection in the Wild. Princeton, New Jersey: Princeton University Press.
ISBN 0-691-00057-3.
Williams GC (1966). Adaptation and Natural Selection. Oxford University Press.
4. ^ Works employing or describing this usage:
Lande R & Arnold SJ (1983) The measurement of selection on correlated characters. Evolution
37:1210-26
Futuyma DJ (2005) Evolution. Sinauer Associates, Inc., Sunderland, Massachusetts. ISBN 0-87893-
187-2
Haldane, J.B.S. 1953. The measurement of natural selection. Proceedings of the 9th International
Congress of Genetics. 1: 480-487
5. ^ Sober E (1984; 1993) The Nature of Selection: Evolutionary Theory in Philosophical Focus
University of Chicago Press ISBN 0-226-76748-5
6. ^ http://www.sciencedaily.com/releases/2011/01/110125172418.htm
7. ^ Modified from Christiansen FB (1984) The definition and measurement of fitness. In:
Evolutionary ecology (ed. Shorrocks B) pp65–79. Blackwell Scientific, Oxford by adding survival
selection in the reproductive phase
8. ^ Pitnick S & Markow TA (1994) Large-male advantage associated with the costs of sperm
production in Drosophila hydei, a species with giant sperm. Proc Natl Acad Sci USA 91:9277-81;
Pitnick S (1996) Investment in testes and the cost of making long sperm in Drosophila. Am Nat
148:57-80
9. ^ Andersson, M (1995). Sexual Selection. Princeton, New Jersey: Princeton University
Press. ISBN 0-691-00057-3.
10.^ Eens M, Pinxten R. (2000). Sex-role reversal in vertebrates: behavioural and
endocrinological accounts. Behav Processes 51(1-3):135-147. PMID 11074317
11.^ Barlow GW. (2005). How Do We Decide that a Species is Sex-Role Reversed? The
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2006-05-06.
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0691.2006.01343.x. PMID 16445718. [1]
14.^ Sylvain Charlat, Emily A. Hornett, James H. Fullard, Neil Davies, George K. Roderick, Nina
Wedell & Gregory D. D. Hurst (2007). "Extraordinary flux in sex ratio". Science 317 (5835): 214.
doi:10.1126/science.1143369. PMID 17626876.
15.^ Kryukov GV, Schmidt S & Sunyaev S (2005) Small fitness effect of mutations in highly
conserved non-coding regions. Human Molecular Genetics 14:2221-9
16.^ Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS & Haussler D (2004)
Ultraconserved elements in the human genome. Science 304:1321-5
17.^ Eyre-Walker A, Woolfit M, Phelps T. (2006). The distribution of fitness effects of new
deleterious amino acid mutations in humans. Genetics 173(2):891-900. PMID 16547091
18.^ Galis F (1999) Why do almost all mammals have seven cervical vertebrae? developmental
constraints, Hox genes, and cancer. J Exp Zool 285:19-26
19.^ Zakany J, FromentalRamain C, Warot X & Duboule D (1997) Regulation of number and
size of digits by posterior Hox genes: a dose-dependent mechanism with potential evolutionary
implications. Proc Natl Acad Sci USA 94:13695-700
20.^ Sanyal S, Jansen HG, de Grip WJ, Nevo E, de Jong WW. (1990). The eye of the blind mole
rat, Spalax ehrenbergi. Rudiment with hidden function? Invest Ophthalmol Vis Sci. 1990 31(7):1398-
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21.^ Salzburger W, Baric S, Sturmbauer C. (2002). Speciation via introgressive hybridization in
East African cichlids? Mol Ecol 11(3): 619–625. PMID 11918795
22.^ Empedocles. On Nature. Book II
23.^ Lucretius. De rerum natura. Book V
24.^ Aristotle. Physics. Book II, Chapters 4 and 8
25.^ Conway Zirkle (1941). Natural Selection before the "Origin of Species", Proceedings of the
American Philosophical Society 84 (1), p. 71-123.
26.^ Mehmet Bayrakdar (Third Quarter, 1983). "Al-Jahiz And the Rise of Biological
Evolutionism", The Islamic Quarterly. London.
27.^ Paul S. Agutter & Denys N. Wheatley (2008). Thinking about Life: The History and
Philosophy of Biology and Other Sciences. Springer. p. 43. ISBN 1402088655
28.^ Jan Z. Wilczynski (December 1959). "On the Presumed Darwinism of Alberuni Eight
Hundred Years before Darwin". Isis 50 (4): 459–466. doi:10.1086/348801
29.^ Farid Alakbarov (Summer 2001). A 13th-Century Darwin? Tusi's Views on Evolution,
Azerbaijan International 9 (2).
30.^ Franz Rosenthal and Ibn Khaldun, Muqaddimah, Chapter 6, Part 5
32.^ Maupertuis, Pierre Louis (1748). "Derivation of the laws of motion and equilibrium from a
metaphysical principle (Original French text)". Histoire de l'academie des sciences et belle lettres de
Berlin 1746: 267–294.
33.^ Chevalier de Lamarck J-B, de Monet PA (1809) Philosophie Zoologique
34.^ Joravsky D. (1959). Soviet Marxism and Biology before Lysenko. Journal of the History of
Ideas 20(1):85-104.
35.^ Darwin 1859, p. 61
36.^ Darwin 1859, p. 5
37.^ T. Robert Malthus (1798). "An Essay on the Principle of Population". Rogers State
University. http://www.faculty.rsu.edu/~felwell/Theorists/Malthus/Essay.htm#112. Retrieved 2008-11-
03.
38.^ Charles Darwin; ed. Nora Barlow (1958). "The autobiography of Charles Darwin 1809-
1882". London: Collins. pp. 120. http://darwin-online.org.uk/content/frameset?
viewtype=text&itemID=F1497&pageseq=124. Retrieved 2008-11-03.
39.^ Wallace, Alfred Russel (1870) Contributions to the Theory of Natural Selection New York:
Macmillan & Co. [2]
40.^ Darwin 1861, p. xiii
41.^ Darwin 1859, p. 6
42.^ "Darwin Correspondence Online Database: Darwin, C. R. to Lyell, Charles, 28 September
1860". http://www.darwinproject.ac.uk/darwinletters/calendar/entry-2931.html. Retrieved 2006-05-
10.
43.^ Eisley L. (1958). Darwin's Century: Evolution and the Men Who Discovered It. Doubleday &
Co: New York, USA.
44.^ Kuhn TS. [1962] (1996). The Structure of Scientific Revolution 3rd ed. University of
Chicago Press: Chicago, Illinois, USA. ISBN 0-226-45808-3
45.^ "Letter 5145 — Darwin, C. R. to Wallace, A. R., 5 July (1866)". Darwin Correspondence
Project. http://www.darwinproject.ac.uk/entry-5145#mark-5145.f3. Retrieved 2010-01-12.
Maurice E. Stucke. "Better Competition Advocacy". http://works.bepress.com/cgi/viewcontent.cgi?
article=1000&context=maurice_stucke. Retrieved 2007-08-29. "Herbert Spencer in his Principles of
Biology of 1864, vol. 1, p. 444, wrote “This survival of the fittest, which I have here sought to express
in mechanical terms, is that which Mr. Darwin has called ‘natural selection’, or the preservation of
favoured races in the struggle for life.”"
46.^ Darwin 1872, p. 49.
47.^ Mills SK, Beatty JH. [1979] (1994). The Propensity Interpretation of Fitness . Originally in
Philosophy of Science (1979) 46: 263-286; republished in Conceptual Issues in Evolutionary Biology
2nd ed. Elliott Sober, ed. MIT Press: Cambridge, Massachusetts, USA. pp3-23. ISBN 0-262-69162-0.
48.^ Haldane JBS (1932) The Causes of Evolution; Haldane JBS (1957) The cost of natural
selection. J Genet 55:511-24([3].
49.^ Wright S (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution
Proc 6th Int Cong Genet 1:356–66
50.^ Dobzhansky Th (1937) Genetics and the Origin of Species Columbia University Press, New
York. (2nd ed., 1941; 3rd edn., 1951)
51.^ Mayr E (1942) Systematics and the Origin of Species Columbia University Press, New
York. ISBN 0-674-86250-3
52.^ The New York Review of Books: Darwinian Fundamentalism (accessed May 6, 2006)
53.^ Engels F (1873-86) Dialectics of Nature 3d ed. Moscow: Progress, 1964 [4]
54.^ Quoted in translation in Eisenberg L (2005) Which image for Lorenz? Am J Psychiatry
162:1760 [5]
55.^ e.g. Wilson, DS (2002) Darwin's Cathedral: Evolution, Religion, and the Nature of Society .
University of Chicago Press, ISBN 0-226-90134-3
56.^ Pinker S. [1994] (1995). The Language Instinct: How the Mind Creates Language.
HarperCollins: New York, NY, USA. ISBN 0-06-097651-9
57.^ Dawkins R. [1976] (1989). The Selfish Gene. Oxford University Press: New York, NY, USA,
p.192. ISBN 0-19-286092-5
58.^ Dennett DC. (1991). Consciousness Explained. Little, Brown, and Co: New York, NY, USA.
ISBN 0-316-18066-1
59.^ For example, see Rose H, Rose SPR, Jencks C. (2000). Alas, Poor Darwin: Arguments
Against Evolutionary Psychology. Harmony Books. ISBN 0-609-60513-5
60.^ Lotka AJ (1922a) Contribution to the energetics of evolution [PDF] Proc Natl Acad Sci USA
8:147–51
Lotka AJ (1922b) Natural selection as a physical principle [PDF] Proc Natl Acad Sci USA 8:151–4
61.^ Kauffman SA (1993) The Origin of order. Self-organization and selection in evolution. New
York: Oxford University Press ISBN 0-19-507951-5
62.^ Goldberg DE. (1989). Genetic Algorithms in Search, Optimization and Machine Learning.
Addison-Wesley: Boston, MA, USA
63.^ Mitchell, Melanie, (1996), An Introduction to Genetic Algorithms, MIT Press, Cambridge,
MA.
64.^ Falconer DS & Mackay TFC (1996) Introduction to Quantitative Genetics Addison Wesley
Longman, Harlow, Essex, UK ISBN 0-582-24302-5
65.^ a b Rice SH. (2004). Evolutionary Theory: Mathematical and Conceptual Foundations.
Sinauer Associates: Sunderland, Massachusetts, USA. ISBN 0-87893-702-1 See esp. ch. 5 and 6 for
a quantitative treatment.
66.^ Lemey, Philippe; Marco Salemi, Anne-Mieke Vandamme (2009). The Phylogenetic
Handbook. Cambridge University Press. ISBN 978-0-521-73071.
67.^ http://www.nature.com/scitable/topicpage/Negative-Selection-1136
68.^ Hamilton WD. (1964). The genetical evolution of social behaviour I and II. Journal of
Theoretical Biology 7: 1-16 and 17-52. PMID 5875341 PMID 5875340
69.^ Trivers RL. (1971). The evolution of reciprocal altruism. Q Rev Biol 46: 35-57.
70.^ Keightley PD. and Otto SP (2006). "Interference among deleterious mutations favours sex
and recombination in finite populations". Nature 443 (7107): 89–92. doi:10.1038/nature05049.
PMID 16957730.
• For technical audiences
• Gould, Stephen Jay (2002). The Structure of Evolutionary Theory. Harvard University
Press. ISBN 0-674-00613-5.
• Maynard Smith, John (1993). The Theory of Evolution: Canto Edition. Cambridge
University Press. ISBN 0-521-45128-0.
• Popper, Karl (1978) Natural selection and the emergence of mind. Dialectica 32:339-
55. See [6]
• Sober, Elliott (1984) The Nature of Selection: Evolutionary Theory in Philosophical
Focus. University of Chicago Press.
• Williams, George C. (1966) Adaptation and Natural Selection: A Critique of Some
Current Evolutionary Thought. Oxford University Press.
• Williams George C. (1992) Natural Selection: Domains, Levels and Challenges.
Oxford University Press.
• For general audiences
• Dawkins, Richard (1996) Climbing Mount Improbable. Penguin Books, ISBN 0-670-
85018-7.
• Dennett, Daniel (1995) Darwin's Dangerous Idea: Evolution and the Meanings of
Life. Simon & Schuster ISBN 0-684-82471-X.
• Gould, Stephen Jay (1997) Ever Since Darwin: Reflections in Natural History.
Norton, ISBN 0-393-06425-5.
• Jones, Steve (2001) Darwin's Ghost: The Origin of Species Updated. Ballantine
Books ISBN 0-345-42277-5. Also published in Britain under the title Almost like a whale: the
origin of species updated. Doubleday. ISBN 1-86230-025-9.
• Lewontin, Richard (1978) Adaptation. Scientific American 239:212-30
• Weiner, Jonathan (1994) The Beak of the Finch: A Story of Evolution in Our Time.
Vintage Books, ISBN 0-679-73337-X.
• Historical
• Zirkle C (1941). Natural Selection before the "Origin of Species", Proceedings of the
American Philosophical Society 84 (1), p. 71-123.
• Kohm M (2004) A Reason for Everything: Natural Selection and the English
Imagination. London: Faber and Faber. ISBN 0-571-22392-3. For review, see [7] van Wyhe J
(2005) Human Nature Review 5:1-4

• On the Origin of Species by Charles Darwin – Chapter 4,Natural Selection
• Natural Selection- Modeling for Understanding in Science Education, University of Wisconsin
• Natural Selection from University of Berkeley education website
• T. Ryan Gregory: Understanding Natural Selection: Essential Concepts and Common
Misconceptions Evolution: Education and Outreach
Processes of
Population genetic
Evolutionary
developmental
concepts
Taxa evolution Birds · Butterflies · Cephalopods · Dinosaurs · Dolphins and whales ·

Fungi · Horses · Humans · Influenza · Insects · Lemur · Life · Molluscs · Plants ·
Modes of

[hide]v · d · eTopics in population genetics
Key concepts Hardy-Weinberg law · Genetic linkage · Linkage disequilibrium · Fisher's

fundamental theorem · Neutral theory · Price equation
Selection Natural · Sexual · Artificial · Ecological

Effects of
selection Genetic hitchhiking · Background selection
on genomic variation
Genetic drift Small population size · Population bottleneck · Founder effect ·

Coalescence · Balding–Nichols model
Founders R. A. Fisher · J. B. S. Haldane · Sewall Wright
Related topics Evolution · Microevolution · Evolutionary game theory · Fitness landscape ·

Genetic genealogy
Retrieved from "http://en.wikipedia.org/wiki/Natural_selection"
Categories: Selection | Evolutionary biology | Ecological processes

W000
Biology

For other uses, see Biology (disambiguation).
Biology deals with the study of the many varieties of living organisms. Clockwise from top left:
Salmonella typhimurium, Phascolarctos cinereus, Athyrium filix-femina, Amanita muscaria, Agalychnis
callidryas, and Brachypelma smithi
Biology is a natural science concerned with the study of life and living organisms, including their
structure, function, growth, origin, evolution, distribution, and taxonomy.[1] Biology is a vast subject
containing many subdivisions, topics, and disciplines. Among the most important topics are five unifying
principles that can be said to be the fundamental axioms of modern biology:[2]
1. Cells are the basic unit of life
2. New species and inherited traits are the product of evolution
3. Genes are the basic unit of heredity
4. An organism regulates its internal environment to maintain a stable and constant condition
5. Living organisms consume and transform energy .
Subdisciplines of biology are recognized on the basis of the scale at which organisms are studied
and the methods used to study them: biochemistry examines the rudimentary chemistry of life; molecular
biology studies the complex interactions of systems of biological molecules; cellular biology examines the
basic building block of all life, the cell; physiology examines the physical and chemical functions of the
tissues, organs, and organ systems of an organism; and ecology examines how various organisms interact
and associate with their environment.[3]
Contents
[hide]
• 1 History
• 2 Foundations of modern biology
• 2.1 Cell theory
• 2.2 Evolution
• 2.3 Genetics
• 2.4 Homeostasis
• 2.5 Energy
• 3 Research
• 3.1 Structural
• 3.2 Physiological
• 3.3 Evolutionary
• 3.4 Systematics
• 3.5 Ecology
• 4 Branches of biology
• 5 See also
• 6 Notes and references
History
Main article: History of biology
Ernst Haeckel's Tree of Life (1879)
The term biology in its modern sense appears to have been introduced independently by Karl
Friedrich Burdach (1800), Gottfried Reinhold Treviranus (Biologie oder Philosophie der lebenden Natur,
1802), and Jean-Baptiste Lamarck (Hydrogéologie, 1802).[4][5] It is a classical compound inspired by the
Greek word βίος, bios, "life" and the suffix -λογία, -logia, "study of."
Although biology in its modern form is a relatively recent development, sciences related to and
included within it have been studied since ancient times. Natural philosophy was studied as early as the
ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, and China. However, the origins of
modern biology and its approach to the study of nature are most often traced back to ancient Greece.[6]
While the formal study of medicine dates back to Hippocrates (ca. 460 BC – ca. 370 BC), it was Aristotle (384
BC – 322 BC) who contributed most extensively to the development of biology. Especially important are his
History of Animals and other works where he showed naturalist leanings, and later more empirical works that
focused on biological causation and the diversity of life. Aristotle's successor at the Lyceum, Theophrastus,
wrote a series of books on botany that survived as the most important contribution of antiquity to the plant
sciences, even into the Middle Ages. Significant advances in the study and development of biology were
promoted through the efforts of such Muslim physicians as the Afro-Arab scholar al-Jahiz (781–869) in
zoology,[7] the Kurdish biologist Al-Dinawari (828–896) in botany,[8] and the Persian physician Rhazes (865–
925) in anatomy and physiology. These philosophers elaborated on, expanded, and improved the Greek
biological theories and systematics. Medicine was especially well studied by Islamic scholars working in
Greek philosopher traditions, while natural history drew heavily on Aristotelian thought, especially in
upholding a fixed hierarchy of life.
Biology began to quickly develop and grow with Antony van Leeuwenhoek's dramatic improvement
of the microscope. It was then that scholars discovered spermatozoa, bacteria, infusoria and the sheer
strangeness and diversity of microscopic life. Investigations by Jan Swammerdam led to new interest in
entomology and built the basic techniques of microscopic dissection and staining.[9]
Advances in microscopy also had a profound impact on biological thinking itself. In the early 19th
century, a number of biologists pointed to the central importance of the cell. In 1838 and 1839, Schleiden and
Schwann began promoting the ideas that (1) the basic unit of organisms is the cell and (2) that individual
cells have all the characteristics of life, although they opposed the idea that (3) all cells come from the
division of other cells. Thanks to the work of Robert Remak and Rudolf Virchow, however, by the 1860s most
biologists accepted all three tenets of what came to be known as cell theory.[10]
Meanwhile, taxonomy and classification became a focus in the study of natural history. Carolus
Linnaeus published a basic taxonomy for the natural world in 1735 (variations of which have been in use ever
since), and in the 1750s introduced scientific names for all his species.[11] Georges-Louis Leclerc, Comte de
Buffon, treated species as artificial categories and living forms as malleable—even suggesting the possibility
of common descent. Though he was opposed to evolution, Buffon is a key figure in the history of evolutionary
thought; his work influenced the evolutionary theories of both Lamarck and Darwin.[12]
Serious evolutionary thinking originated with the works of Jean-Baptiste Lamarck. However, it was
the British naturalist Charles Darwin, combining the biogeographical approach of Humboldt, the
uniformitarian geology of Lyell, Thomas Malthus's writings on population growth, and his own morphological
expertise, that created a more successful evolutionary theory based on natural selection; similar reasoning
and evidence led Alfred Russel Wallace to independently reach the same conclusions.[13]
The discovery of the physical representation of heredity came along with evolutionary principles and
population genetics. In the 1940s and early 1950s, experiments pointed to DNA as the component of
chromosomes that held genes. A focus on new model organisms such as viruses and bacteria, along with
the discovery of the double helical structure of DNA in 1953, marked the transition to the era of molecular
genetics. From the 1950s to present times, biology has been vastly extended in the molecular domain. The
genetic code was cracked by Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg after
DNA was understood to contain codons. Finally, the Human Genome Project was launched in 1990 with the
goal of mapping the general human genome. This project was essentially completed in 2003,[14] with further
analysis still being published. The Human Genome Project was the first step in a globalized effort to
incorporate accumulated knowledge of biology into a functional, molecular definition of the human body and
the bodies of other organisms.
Foundations of modern biology

Much of modern biology can be encompassed within five unifying principles: cell theory, evolution,
genetics, homeostasis, and energy.[2]
Cell theory
Main article: Cell theory
Cells in culture, stained for keratin (red) and DNA (green)
Cell theory states that the cell is the fundamental unit of life, and that all living things are composed
of one or more cells or the secreted products of those cells (e.g. shells). All cells arise from other cells
through cell division. In multicellular organisms, every cell in the organism's body derives ultimately from a
single cell in a fertilized egg. The cell is also considered to be the basic unit in many pathological processes.
[15] Additionally, the phenomenon of energy flow occurs in cells in processes that are part of the function
known as metabolism. Finally, cells contain hereditary information (DNA) which is passed from cell to cell
during cell division.
Evolution
Natural selection of a population for dark coloration.

Main article: Evolution
A central organizing concept in biology is that life changes and develops through evolution, and that
all life-forms known have a common origin. Introduced into the scientific lexicon by Jean-Baptiste de Lamarck
in 1809,[16] evolution was established by Charles Darwin fifty years later as a viable theory when he
articulated its driving force: natural selection.[17][18] (Alfred Russel Wallace is recognized as the co-
discoverer of this concept as he helped research and experiment with the concept of evolution.)[19] Evolution
is now used to explain the great variations of life found on Earth.
Darwin theorized that species and breeds developed through the processes of natural selection and
artificial selection or selective breeding.[20] Genetic drift was embraced as an additional mechanism of
evolutionary development in the modern synthesis of the theory.[21]
The evolutionary history of the species—which describes the characteristics of the various species
from which it descended—together with its genealogical relationship to every other species is known as its
phylogeny. Widely varied approaches to biology generate information about phylogeny. These include the
comparisons of DNA sequences conducted within molecular biology or genomics, and comparisons of fossils
or other records of ancient organisms in paleontology.[22] Biologists organize and analyze evolutionary
relationships through various methods, including phylogenetics, phenetics, and cladistics. (For a summary of
major events in the evolution of life as currently understood by biologists, see evolutionary timeline.)
The theory of evolution postulates that all organisms on the Earth, both living and extinct, have
descended from a common ancestor or an ancestral gene pool. This last universal common ancestor of all
organisms is believed to have appeared about 3.5 billion years ago.[23] Biologists generally regard the
universality and ubiquity of the genetic code as definitive evidence in favor of the theory of universal common
descent for all bacteria, archaea, and eukaryotes (see: origin of life).[24]
Genetics
Main article: Genetics
A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b)
blossoms
Genes are the primary units of inheritance in all organisms. A gene is a unit of heredity and
corresponds to a region of DNA that influences the form or function of an organism in specific ways. All
organisms, from bacteria to animals, share the same basic machinery that copies and translates DNA into
proteins. Cells transcribe a DNA gene into an RNA version of the gene, and a ribosome then translates the
RNA into a protein, a sequence of amino acids. The translation code from RNA codon to amino acid is the
same for most organisms, but slightly different for some. For example, a sequence of DNA that codes for
insulin in humans also codes for insulin when inserted into other organisms, such as plants.[25][26]
DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes.
A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell
and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively
known as its genome. In eukaryotes, genomic DNA is located in the cell nucleus, along with small amounts in
mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the
cytoplasm called the nucleoid.[27] The genetic information in a genome is held within genes, and the
complete assemblage of this information in an organism is called its genotype.[28]
Homeostasis
Main article: Homeostasis
The hypothalamus secretes CRH, which directs the pituitary gland to secrete ACTH. In turn, ACTH
directs the adrenal cortex to secrete glucocorticoids, such as cortisol. The GCs then reduce the rate of
secretion by the hypothalamus and the pituitary gland once a sufficient amount of GCs has been released.
[29]
Homeostasis is the ability of an open system to regulate its internal environment to maintain stable
conditions by means of multiple dynamic equilibrium adjustments controlled by interrelated regulation
mechanisms. All living organisms, whether unicellular or multicellular, exhibit homeostasis.[30]
To maintain dynamic equilibrium and effectively carry out certain functions, a system must detect and
respond to perturbations. After the detection of a perturbation, a biological system normally respond through
negative feedback. This means stabilizing conditions by either reducing or increasing the activity of an organ
or system. One example is the release of glucagon when sugar levels are too low.
Energy
Basic overview of energy and human life.

The survival of a living organism depends on the continuous input of energy. Chemical reactions that
are responsible for its structure and function are tuned to extract energy from substances that act as its food
and transform them to help form new cells and sustain them. In this process, molecules of chemical
substances that constitute food play two roles; first, they contain energy that can be transformed for
biological chemical reactions; second, they develop new molecular structures made up of biomolecules.
The organisms responsible for the introduction of energy into an ecosystem are known as producers
or autotrophs. Nearly all of these organisms originally draw energy from the sun.[31] Plants and other
phototrophs use solar energy via a process known as photosynthesis to convert raw materials into organic
molecules, such as ATP, whose bonds can be broken to release energy.[32] A few ecosystems, however,
depend entirely on energy extracted by chemotrophs from methane, sulfides, or other non-luminal energy
sources.[33]
Some of the captured energy is used to produce biomass to sustain life and provide energy for
growth and development. The majority of the rest of this energy is lost as heat and waste molecules. The
most important processes for converting the energy trapped in chemical substances into energy useful to
sustain life are metabolism[34] and cellular respiration.[35]
Research
Structural
Schematic of typical animal cell depicting the various organelles and structures.
Main articles: Molecular biology, Cell biology, Genetics, and Developmental biology
Molecular biology is the study of biology at a molecular level.[36] This field overlaps with other areas
of biology, particularly with genetics and biochemistry. Molecular biology chiefly concerns itself with
understanding the interactions between the various systems of a cell, including the interrelationship of DNA,
RNA, and protein synthesis and learning how these interactions are regulated.
Cell biology studies the structural and physiological properties of cells, including their behaviors,
interactions, and environment. This is done on both the microscopic and molecular levels, for single-celled
organisms such as bacteria as well as the specialized cells in multicellular organisms such as humans.
Understanding the structure and function of cells is fundamental to all of the biological sciences. The
similarities and differences between cell types are particularly relevant to molecular biology.
Anatomy considers the forms of macroscopic structures such as organs and organ systems.[37]
Genetics is the science of genes, heredity, and the variation of organisms.[38][39] Genes encode the
information necessary for synthesizing proteins, which in turn play a large role in influencing (though, in many
instances, not completely determining) the final phenotype of the organism. In modern research, genetics
provides important tools in the investigation of the function of a particular gene, or the analysis of genetic
interactions. Within organisms, genetic information generally is carried in chromosomes, where it is
represented in the chemical structure of particular DNA molecules.
Developmental biology studies the process by which organisms grow and develop. Originating in
embryology, modern developmental biology studies the genetic control of cell growth, differentiation, and
"morphogenesis," which is the process that progressively gives rise to tissues, organs, and anatomy. Model
organisms for developmental biology include the round worm Caenorhabditis elegans,[40] the fruit fly
Drosophila melanogaster,[41] the zebrafish Danio rerio,[42] the mouse Mus musculus,[43], and the weed
Arabidopsis thaliana.[44][45] (A model organism is a species that is extensively studied to understand
particular biological phenomena, with the expectation that discoveries made in that organism provide insight
into the workings of other organisms.)[46]
Physiological
Main article: Physiology
Physiology studies the mechanical, physical, and biochemical processes of living organisms by
attempting to understand how all of the structures function as a whole. The theme of "structure to function" is
central to biology. Physiological studies have traditionally been divided into plant physiology and animal
physiology, but some principles of physiology are universal, no matter what particular organism is being
studied. For example, what is learned about the physiology of yeast cells can also apply to human cells. The
field of animal physiology extends the tools and methods of human physiology to non-human species. Plant
physiology borrows techniques from both research fields.
Physiology studies how for example nervous, immune, endocrine, respiratory, and circulatory
systems, function and interact. The study of these systems is shared with medically oriented disciplines such
as neurology and immunology.
Evolutionary
Evolutionary research is concerned with the origin and descent of species, as well as their change
over time, and includes scientists from many taxonomically oriented disciplines. For example, it generally
involves scientists who have special training in particular organisms such as mammalogy, ornithology,
botany, or herpetology, but use those organisms as systems to answer general questions about evolution.
Evolutionary biology is partly based on paleontology, which uses the fossil record to answer
questions about the mode and tempo of evolution,[47] and partly on the developments in areas such as
population genetics[48] and evolutionary theory. In the 1980s, developmental biology re-entered evolutionary
biology from its initial exclusion from the modern synthesis through the study of evolutionary developmental
biology.[49] Related fields often considered part of evolutionary biology are phylogenetics, systematics, and
taxonomy.
Systematics
A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three
domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with
other genes are generally similar, although they may place some early-branching groups very differently,
presumably owing to rapid rRNA evolution. The exact relationships of the three domains are still being
debated.
Main article: Systematics
Multiple speciation events create a tree structured system of relationships between species. The role
of systematics is to study these relationships and thus the differences and similarities between species and
groups of species.[50] However, systematics was an active field of research long before evolutionary thinking
was common.[51] The classification, taxonomy, and nomenclature of biological organisms is administered by
the International Code of Zoological Nomenclature, International Code of Botanical Nomenclature, and
International Code of Nomenclature of Bacteria for animals, plants, and bacteria, respectively. The
classification of viruses, viroids, prions, and all other sub-viral agents that demonstrate biological
characteristics is conducted by the International Code of Virus classification and nomenclature.[52][53][54]
[55] However, several other viral classification systems do exist.
Traditionally, living things have been divided into five kingdoms: Monera; Protista; Fungi; Plantae;
Animalia.[56]
However, many scientists now consider this five-kingdom system outdated. Modern alternative
classification systems generally begin with the three-domain system: Archaea (originally Archaebacteria);
Bacteria (originally Eubacteria); Eukaryota (including protists, fungi, plants, and animals)[57] These domains
reflect whether the cells have nuclei or not, as well as differences in the chemical composition of the cell
exteriors.[57]
Further, each kingdom is broken down recursively until each species is separately classified. The
order is: Domain; Kingdom; Phylum; Class; Order; Family; Genus; Species.
There is also a series of intracellular parasites that are "on the edge of life"[58] in terms of metabolic
activity, meaning that many scientists do not actually classify these structures as alive, due to their lack of at
least one or more of the fundamental functions that define life. They are classified as viruses, viroids, prions,
or satellites.
The scientific name of an organism is generated from its genus and species. For example, humans
are listed as Homo sapiens. Homo is the genus, and sapiens the species. When writing the scientific name of
an organism, it is proper to capitalize the first letter in the genus and put all of the species in lowercase.
Additionally, the entire term may be italicized or underlined.[59][60]
The dominant classification system is called the Linnaean taxonomy. It includes ranks and binomial
nomenclature. How organisms are named is governed by international agreements such as the International
Code of Botanical Nomenclature (ICBN), the International Code of Zoological Nomenclature (ICZN), and the
International Code of Nomenclature of Bacteria (ICNB).
A merging draft, BioCode, was published in 1997 in an attempt to standardize nomenclature in these
three areas, but has yet to be formally adopted.[61] The BioCode draft has received little attention since
1997; its originally planned implementation date of January 1, 2000, has passed unnoticed. However, a 2004
paper concerning the cyanobacteria does advocate a future adoption of a BioCode and interim steps
consisting of reducing the differences between the codes.[62] The International Code of Virus Classification
and Nomenclature (ICVCN) remains outside the BioCode.
Ecology
Mutual symbiosis between clownfish of the genus Amphiprion that dwell among the tentacles of
tropical sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the
stinging tentacles of the anemone protects the clown fish from its predators
Main articles: Ecology, Ethology, Behavior, and Biogeography
Ecology studies the distribution and abundance of living organisms, and the interactions between
organisms and their environment.[63] The habitat of an organism can be described as the local abiotic
factors such as climate and ecology, in addition to the other organisms and biotic factors that share its
environment.[64] One reason that biological systems can be difficult to study is that so many different
interactions with other organisms and the environment are possible, even on the smallest of scales. A
microscopic bacterium responding to a local sugar gradient is responding to its environment as much as a
lion is responding to its environment when it searches for food in the African savanna. For any given species,
behaviors can be co-operative, aggressive, parasitic, or symbiotic. Matters become more complex when two
or more different species interact in an ecosystem. Studies of this type are within the province of ecology.
Ecological systems are studied at several different levels, from individuals and populations to
ecosystems and the biosphere. The term population biology is often used interchangeably with population
ecology, although population biology is more frequently used when studying diseases, viruses, and
microbes, while population ecology is more commonly when studying plants and animals. As can be
surmised, ecology is a science that draws on several disciplines.
Ethology studies animal behavior (particularly that of social animals such as primates and canids),
and is sometimes considered a branch of zoology. Ethologists have been particularly concerned with the
evolution of behavior and the understanding of behavior in terms of the theory of natural selection. In one
sense, the first modern ethologist was Charles Darwin, whose book, The Expression of the Emotions in Man
and Animals, influenced many ethologists to come.[65]
Biogeography studies the spatial distribution of organisms on the Earth,[66] focusing on topics like
plate tectonics, climate change, dispersal and migration, and cladistics.
Branches of biology
Main article: List of biology disciplines
These are the main branches of biology:[67][68]
• Aerobiology — the study of airborne organic particles
• Agriculture — the study of producing crops from the land, with an emphasis on practical
applications
• Anatomy — the study of form and function, in plants, animals, and other organisms, or
specifically in humans
• Astrobiology- the study of evolution, distribution, and future of life in the universe—also known
as exobiology, exopaleontology, and bioastronomy
• Biochemistry — the study of the chemical reactions required for life to exist and function,
usually a focus on the cellular level
• Bioengineering — the study of biology through the means of engineering with an emphasis on
applied knowledge and especially related to biotechnology
• Bioinformatics — the use of information technology for the study, collection, and storage of
genomic and other biological data
• Biomathematics or Mathematical Biology — the quantitative or mathematical study of
biological processes, with an emphasis on modeling
• Biomechanics — often considered a branch of medicine, the study of the mechanics of living
beings, with an emphasis on applied use through prosthetics or orthotics
• Biomedical research — the study of the human body in health and disease
• Biophysics — the study of biological processes through physics, by applying the theories and
methods traditionally used in the physical sciences
• Biotechnology — a new and sometimes controversial branch of biology that studies the
manipulation of living matter, including genetic modification and synthetic biology
• Building biology — the study of the indoor living environment
• Botany — the study of plants
• Cell biology — the study of the cell as a complete unit, and the molecular and chemical
interactions that occur within a living cell
• Conservation Biology — the study of the preservation, protection, or restoration of the natural
environment, natural ecosystems, vegetation, and wildlife
• Cryobiology — the study of the effects of lower than normally preferred temperatures on living
beings.
• Developmental biology — the study of the processes through which an organism forms, from
zygote to full structure
• Ecology — the study of the interactions of living organisms with one another and with the non-
living elements of their environment
• Embryology — the study of the development of embryo (from fecundation to birth). See also
topobiology.
• Entomology — the study of insects
• Environmental Biology — the study of the natural world, as a whole or in a particular area,
especially as affected by human activity
• Epidemiology — a major component of public health research, studying factors affecting the
health of populations
• Ethology — the study of animal behavior
• Evolutionary Biology — the study of the origin and descent of species over time
• Genetics — the study of genes and heredity
• Herpetology — the study of reptiles and amphibians
• Histology — the study of cells and tissues, a microscopic branch of anatomy
• Ichthyology — the study of fish
• Integrative biology — the study of whole organisms
• Limnology — the study of inland waters
• Mammalogy — the study of mammals
• Marine Biology — the study of ocean ecosystems, plants, animals, and other living beings
• Microbiology — the study of microscopic organisms (microorganisms) and their interactions
with other living things
• Molecular Biology — the study of biology and biological functions at the molecular level, some
cross over with biochemistry
• Mycology — the study of fungi
• Neurobiology — the study of the nervous system, including anatomy, physiology and
pathology
• Oceanography — the study of the ocean, including ocean life, environment, geography,
weather, and other aspects influencing the ocean
• Oncology — the study of cancer processes, including virus or mutation oncogenesis,
angiogenesis and tissues remoldings
• Ornithology — the study of birds
• Population biology — the study of groups of conspecific organisms, including
• Population ecology — the study of how population dynamics and extinction
• Population genetics — the study of changes in gene frequencies in populations of
organisms
• Paleontology — the study of fossils and sometimes geographic evidence of prehistoric life
• Pathobiology or pathology — the study of diseases, and the causes, processes, nature, and
development of disease
• Parasitology — the study of parasites and parasitism
• Pharmacology — the study and practical application of preparation, use, and effects of drugs
and synthetic medicines
• Physiology — the study of the functioning of living organisms and the organs and parts of
living organisms
• Phytopathology — the study of plant diseases (also called Plant Pathology)
• Psychobiology — the study of the biological bases of psychology
• Sociobiology — the study of the biological bases of sociology
• Structural biology — a branch of molecular biology, biochemistry, and biophysics concerned
with the molecular structure of biological macromolecules
• Virology — the study of viruses and some other virus-like agents
• Zoology — the study of animals, including classification, physiology, development, and
behavior (See also Entomology, Ethology, Herpetology, Ichthyology, Mammalogy, and Ornithology)
See also
Biology portal
Environment portal
Ecology portal
Earth_sciences portal
Main article: Outline of biology
• Conservation biology
• The Journal of Life Sciences
• List of biological websites
• List of biologists
• List of Russian biologists
• List of biology topics
• Lists of biology journals and magazines
• Periodic Table of Life Sciences in Tinbergen's four questions
[show]v · d · eTopics related to biology
People and Biologist · Notable biologists · History of biology · Nobel Prize in

history Physiology or Medicine · Timeline of biology and organic chemistry · List of
geneticists and biochemists
Institutions,
publications Bachelor of Science · Publications
Terms and Omne vivum ex ovo · In vivo · In vitro · In utero · In silico

phrases
Related Medicine (Physician) · Physical anthropology · Environmental science ·

disciplines Life Sciences · Biotechnology
Other List of conservation topics · Altricial and Precocial development strategies
Notes and references

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doi:10.1073/pnas.87.12.4576. PMID 2112744. PMC 54159.
http://www.pnas.org/cgi/reprint/87/12/4576.
58.^ Rybicki EP (1990) "The classification of organisms at the edge of life, or problems with
virus systematics." S Aft J Sci 86:182–186
59.^ Heather Silyn-Roberts (2000). Writing for Science and Engineering: Papers, Presentation .
Oxford: Butterworth-Heinemann. pp. 198. ISBN 0750646365. http://books.google.com/?
id=hVUU7Gq8QskC&lpg=PA198&dq=species%20epithet
%20capitalize&pg=PA198#v=onepage&q=species%20epithet%20capitalize.
60.^ "Recommendation 60F". International Code of Botanical Nomenclature, Vienna Code.
2006. pp. 60F.1. http://ibot.sav.sk/icbn/frameset/0065Ch7OaGoNSec1a60.htm#recF.
61.^ John McNeill (1996-11-04). "The BioCode: Integrated biological nomenclature for the 21st
century?". Proceedings of a Mini-Symposium on Biological Nomenclature in the 21st Century .
62.^ Ahoren Oren (2004). "A proposal for further integration of the cyanobacteria under the
Bacteriological Code". Int. J. Syst. Evol. Microbiol. 54 (Pt 5): 1895–1902. doi:10.1099/ijs.0.03008-0.
PMID 15388760.
63.^ Begon, M.; Townsend, C. R., Harper, J. L. (2006). Ecology: From individuals to
ecosystems. (4th ed.). Blackwell. ISBN 1405111178.
64.^ Habitats of the world. New York: Marshall Cavendish. 2004. pp. 238. ISBN 978-0-7614-
7523-1. http://books.google.com/?id=U-_mlcy8rGgC&pg=PA238.
65.^ Black, J (Jun 2002). "Darwin in the world of emotions" (Free full text). Journal of the Royal
Society of Medicine 95 (6): 311–3. doi:10.1258/jrsm.95.6.311. ISSN 0141-0768. PMID 12042386.
PMC 1279921. http://www.jrsm.org/cgi/pmidlookup?view=long&pmid=12042386.
66.^ Wiley, 1981
67.^ Branches of Biology on biology-online.org
68.^ Biology on bellaonline.com
Further reading
• Alberts, Bruce; Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter, P (2002). Molecular
Biology of the Cell (4th ed.). Garland. ISBN 978-0815332183. OCLC 48122761 57023651 69932405
145080076 48122761 57023651 69932405.
• Begon, Michael; Townsend, CR & Harper, JL (2005). Ecology: From Individuals to
Ecosystems (4th ed.). Blackwell Publishing Limited. ISBN 978-1405111171. OCLC 57675855
62131207 57639896 57675855 62131207.
• Campbell, Neil (2004). Biology (7th ed.). Benjamin-Cummings Publishing Company. ISBN 0-
8053-7146-X. OCLC 71890442.
• Colinvaux, Paul (1979). Why Big Fierce Animals are Rare: An Ecologist's Perspective
(reissue ed.). Princeton University Press. ISBN 0691023646. OCLC 24132192 10081738 24132192.
• Hoagland, Mahlon (2001). The Way Life Works (reprint ed.). Jones and Bartlett Publishers
inc. ISBN 076371688X. OCLC 45487537 223090105 45487537.
• Janovy, John Jr. (2004). On Becoming a Biologist (2nd ed.). Bison Books.
ISBN 0803276206. OCLC 56964280 55138571 56964280.
• Johnson, George B. (2005). Biology, Visualizing Life. Holt, Rinehart, and Winston. ISBN 0-
03-016723-X. OCLC 36306648.
• Tobin, Allan; Dusheck, Jennie (2005). Asking About Life (3rd ed.). Belmont, CA: Wadsworth.
ISBN 0-534-40653X.
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Cell (biology)

Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from
Micrographia which is the origin of the word "cell" being used to describe the smallest unit of a living
organism
Cells in culture, stained for keratin (red) and DNA (green)
The cell is the functional basic unit of life. It was discovered by Robert Hooke and is the functional
unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often
called the building block of life.[1] Some organisms, such as most bacteria, are unicellular (consist of a single
cell). Other organisms, such as humans, are multicellular. Humans have about 100 trillion or 1014 cells; a
typical cell size is 10 µm and a typical cell mass is 1 nanogram. The largest cells are about 135 µm in the
anterior horn in the spinal cord while granule cells in the cerebellum, the smallest, can be some 4 µm and the
longest cell can reach from the toe to the lower brain stem (Pseudounipolar cells).[2] The largest known cells
are unfertilised ostrich egg cells which weigh 3.3 pounds.[3][4]
In 1835, before the final cell theory was developed, Jan Evangelista Purkyně observed small
"granules" while looking at the plant tissue through a microscope. The cell theory, first developed in 1839 by
Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more
cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that
all cells contain the hereditary information necessary for regulating cell functions and for transmitting
information to the next generation of cells.[5]
The word cell comes from the Latin cellula, meaning, a small room. The descriptive term for the
smallest living biological structure was coined by Robert Hooke in a book he published in 1665 when he
compared the cork cells he saw through his microscope to the small rooms monks lived in.[6]
Contents
[hide]
• 1 Anatomy
• 1.1 Prokaryotic cells
• 1.2 Eukaryotic cells
• 2 Subcellular components
• 2.1 Membrane
• 2.2 Cytoskeleton
• 2.3 Genetic material
• 2.4 Organelles
• 3 Structures outside the cell wall
• 3.1 Capsule
• 3.2 Flagella
• 3.3 Fimbriae (pili)
• 4 Functions
• 4.1 Growth and metabolism
• 4.2 Creation
• 4.3 Protein synthesis
• 5 Movement or motility
• 6 Evolution
• 6.1 Origin of the first cell
• 6.2 Origin of eukaryotic cells
Anatomy
There are two types of cells: eukaryotic and prokaryotic. Prokaryotic cells are usually independent,
while eukaryotic cells are often found in multicellular organisms.
Prokaryotic cells
Main article: Prokaryote
Diagram of a typical prokaryotic cell
The prokaryote cell is simpler, and therefore smaller, than a eukaryote cell, lacking a nucleus and
most of the other organelles of eukaryotes. There are two kinds of prokaryotes: bacteria and archaea; these
share a similar structure.
Nuclear material of prokaryotic cell consist of a single chromosome which is in direct contact with
cytoplasm. Here the undefined nuclear region in the cytoplasm is called nucleoid.
A prokaryotic cell has three architectural regions:
• On the outside, flagella and pili project from the cell's surface. These are structures (not
present in all prokaryotes) made of proteins that facilitate movement and communication between
cells;
• Enclosing the cell is the cell envelope – generally consisting of a cell wall covering a plasma
membrane though some bacteria also have a further covering layer called a capsule. The envelope
gives rigidity to the cell and separates the interior of the cell from its environment, serving as a
protective filter. Though most prokaryotes have a cell wall, there are exceptions such as Mycoplasma
(bacteria) and Thermoplasma (archaea). The cell wall consists of peptidoglycan in bacteria, and acts
as an additional barrier against exterior forces. It also prevents the cell from expanding and finally
bursting (cytolysis) from osmotic pressure against a hypotonic environment. Some eukaryote cells
(plant cells and fungi cells) also have a cell wall;
• Inside the cell is the cytoplasmic region that contains the cell genome (DNA) and ribosomes
and various sorts of inclusions. A prokaryotic chromosome is usually a circular molecule (an
exception is that of the bacterium Borrelia burgdorferi, which causes Lyme disease). Though not
forming a nucleus, the DNA is condensed in a nucleoid. Prokaryotes can carry extrachromosomal
DNA elements called plasmids, which are usually circular. Plasmids enable additional functions, such
as antibiotic resistance.
Eukaryotic cells
Main article: Eukaryote
Diagram of a typical animal (eukaryotic) cell, showing subcellular components.

Organelles:
(1) nucleolus
(2) nucleus
(3) ribosome
(4) vesicle
(5) rough endoplasmic reticulum (ER)
(6) Golgi apparatus
(7) Cytoskeleton
(8) smooth endoplasmic reticulum
(9) mitochondria
(10) vacuole
(11) cytoplasm
(12) lysosome
(13) centrioles within centrosome
Eukaryotic cells are about 15 times wider than a typical prokaryote and can be as much as 1000
times greater in volume. The major difference between prokaryotes and eukaryotes is that eukaryotic cells
contain membrane-bound compartments in which specific metabolic activities take place. Most important
among these is a cell nucleus, a membrane-delineated compartment that houses the eukaryotic cell's DNA.
This nucleus gives the eukaryote its name, which means "true nucleus." Other differences include:
• The plasma membrane resembles that of prokaryotes in function, with minor differences in
the setup. Cell walls may or may not be present.
• The eukaryotic DNA is organized in one or more linear molecules, called chromosomes,
which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus,
separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria
also contain some DNA.
• Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in
chemosensation, mechanosensation, and thermosensation. Cilia may thus be "viewed as sensory
cellular antennae that coordinate a large number of cellular signaling pathways, sometimes coupling
the signaling to ciliary motility or alternatively to cell division and differentiation."[7]
• Eukaryotes can move using motile cilia or flagella. The flagella are more complex than those
of prokaryotes.
Table 1: Comparison of features of prokaryotic and eukaryotic cells
Prokaryotes Eukaryotes
Typical organisms bacteria, archaea protists, fungi, plants, animals
~ 10–100 µm (sperm cells, apart from the

Typical size ~ 1–10 µm
tail, are smaller)
nucleoid region; no
Type of nucleus real nucleus with double membrane
real nucleus
linear molecules (chromosomes) with

DNA circular (usually)
histone proteins
RNA-/protein- coupled in RNA-synthesis inside the nucleus

synthesis cytoplasm protein synthesis in cytoplasm
Ribosomes 50S+30S 60S+40S
Cytoplasmatic very few structures highly structured by endomembranes and

structure a cytoskeleton
flagella made of flagella and cilia containing microtubules;

Cell movement
flagellin lamellipodia and filopodia containing actin
one to several thousand (though some

Mitochondria none
lack mitochondria)
Chloroplasts none in algae and plants
single cells, colonies, higher multicellular

Organization usually single cells
organisms with specialized cells
Binary fission Mitosis (fission or budding)

Cell division
(simple division) Meiosis
Table 2: Comparison of structures between animal and plant cells

Typical animal cell Typical plant cell
Organelles • Nucleus • Nucleus

• Nucleolus (within • Nucleolus (within
nucleus) nucleus)
• Rough endoplasmic • Rough ER
reticulum (ER) • Smooth ER
• Smooth ER
• Ribosomes
• Ribosomes
• Cytoskeleton
• Cytoskeleton
• Golgi apparatus
• Golgi apparatus
(dictiosomes)
• Cytoplasm
• Cytoplasm
• Mitochondria
• Mitochondria
• Vesicles
• Plastids and its derivatives
• Lysosomes
• Vacuole(s)
• Centrosome
• Cell wall
• Centrioles
Subcellular components
The cells of eukaryotes (left) and prokaryotes (right)

All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, separates its
interior from its environment, regulates what moves in and out (selectively permeable), and maintains the
electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All
cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build
various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules
in cells. This article will list these primary components of the cell, then briefly describe their function.
Membrane
Main article: Cell membrane
The cytoplasm of a cell is surrounded by a cell membrane or plasma membrane. The plasma
membrane in plants and prokaryotes is usually covered by a cell wall. This membrane serves to separate
and protect a cell from its surrounding environment and is made mostly from a double layer of lipids
(hydrophobic fat-like molecules) and hydrophilic phosphorus molecules. Hence, the layer is called a
phospholipid bilayer. It may also be called a fluid mosaic membrane. Embedded within this membrane is a
variety of protein molecules that act as channels and pumps that move different molecules into and out of the
cell. The membrane is said to be 'semi-permeable', in that it can either let a substance (molecule or ion) pass
through freely, pass through to a limited extent or not pass through at all. Cell surface membranes also
contain receptor proteins that allow cells to detect external signaling molecules such as hormones.
Cytoskeleton
Main article: Cytoskeleton
Bovine Pulmonary Artery Endothelial cell: nuclei stained blue, mitochondria stained red, and F-actin,
an important component in microfilaments, stained green. Cell imaged on a fluorescent microscope.
The cytoskeleton acts to organize and maintain the cell's shape; anchors organelles in place; helps
during endocytosis, the uptake of external materials by a cell, and cytokinesis, the separation of daughter
cells after cell division; and moves parts of the cell in processes of growth and mobility. The eukaryotic
cytoskeleton is composed of microfilaments, intermediate filaments and microtubules. There is a great
number of proteins associated with them, each controlling a cell's structure by directing, bundling, and
aligning filaments. The prokaryotic cytoskeleton is less well-studied but is involved in the maintenance of cell
shape, polarity and cytokinesis.[8]
Genetic material
Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). Most organisms use DNA for their long-term information storage, but some viruses (e.g., retroviruses)
have RNA as their genetic material. The biological information contained in an organism is encoded in its
DNA or RNA sequence. RNA is also used for information transport (e.g., mRNA) and enzymatic functions
(e.g., ribosomal RNA) in organisms that use DNA for the genetic code itself. Transfer RNA (tRNA) molecules
are used to add amino acids during protein translation.
Prokaryotic genetic material is organized in a simple circular DNA molecule (the bacterial
chromosome) in the nucleoid region of the cytoplasm. Eukaryotic genetic material is divided into different,
linear molecules called chromosomes inside a discrete nucleus, usually with additional genetic material in
some organelles like mitochondria and chloroplasts (see endosymbiotic theory).
A human cell has genetic material contained in the cell nucleus (the nuclear genome) and in the
mitochondria (the mitochondrial genome). In humans the nuclear genome is divided into 23 pairs of linear
DNA molecules called chromosomes. The mitochondrial genome is a circular DNA molecule distinct from the
nuclear DNA. Although the mitochondrial DNA is very small compared to nuclear chromosomes, it codes for
13 proteins involved in mitochondrial energy production and specific tRNAs.
Foreign genetic material (most commonly DNA) can also be artificially introduced into the cell by a
process called transfection. This can be transient, if the DNA is not inserted into the cell's genome, or stable,
if it is. Certain viruses also insert their genetic material into the genome.
Organelles
Main article: Organelle
The human body contains many different organs, such as the heart, lung, and kidney, with each
organ performing a different function. Cells also have a set of "little organs," called organelles, that are
adapted and/or specialized for carrying out one or more vital functions. Both eukaryotic and prokaryotic cells
have organelles but organelles in eukaryotes are generally more complex and may be membrane bound.
There are several types of organelles in a cell. Some (such as the nucleus and golgi apparatus) are
typically solitary, while others (such as mitochondria, peroxisomes and lysosomes) can be numerous
(hundreds to thousands). The cytosol is the gelatinous fluid that fills the cell and surrounds the organelles.
Cell nucleus – eukaryotes only - a cell's information
center
The cell nucleus is the most conspicuous
organelle found in a eukaryotic cell. It houses the cell's
chromosomes, and is the place where almost all DNA
replication and RNA synthesis (transcription) occur.
The nucleus is spherical and separated from the
cytoplasm by a double membrane called the nuclear
envelope. The nuclear envelope isolates and protects
a cell's DNA from various molecules that could
accidentally damage its structure or interfere with its
processing. During processing, DNA is transcribed, or
copied into a special RNA, called messenger RNA
(mRNA). This mRNA is then transported out of the
nucleus, where it is translated into a specific protein
Diagram of a cell nucleus
molecule. The nucleolus is a specialized region within
the nucleus where ribosome subunits are assembled.
In prokaryotes, DNA processing takes place in the
cytoplasm.
Mitochondria and Chloroplasts – eukaryotes only -

the power generators
Mitochondria are self-replicating organelles
that occur in various numbers, shapes, and sizes in
the cytoplasm of all eukaryotic cells. Mitochondria play
a critical role in generating energy in the eukaryotic
cell. Mitochondria generate the cell's energy by
oxidative phosphorylation, using oxygen to release
energy stored in cellular nutrients (typically pertaining
to glucose) to generate ATP. Mitochondria multiply by
splitting in two. Respiration occurs in the cell
mitochondria.
Organelles that are modified chloroplasts are
broadly called plastids, and are involved in energy
storage through photosynthesis, which uses solar
energy to generate carbohydrates and oxygen from
carbon dioxide and water.[citation needed]
Mitochondria and chloroplasts each contain
their own genome, which is separate and distinct from
the nuclear genome of a cell. Both organelles contain
this DNA in circular plasmids, much like prokaryotic
cells, strongly supporting the evolutionary theory of
endosymbiosis; since these organelles contain their
own genomes and have other similarities to
prokaryotes, they are thought to have developed
through a symbiotic relationship after being engulfed
by a primitive cell.[citation needed]
Endoplasmic reticulum – eukaryotes only

The endoplasmic reticulum (ER) is the
transport network for molecules targeted for certain
modifications and specific destinations, as compared
to molecules that will float freely in the cytoplasm. The
ER has two forms: the rough ER, which has ribosomes
on its surface and secretes proteins into the
cytoplasm, and the smooth ER, which lacks them.
Smooth ER plays a role in calcium sequestration and
release.
Golgi apparatus – eukaryotes only
The primary function of the Golgi apparatus is
to process and package the macromolecules such as
proteins and lipids that are synthesized by the cell. It is
particularly important in the processing of proteins for
secretion. The Golgi apparatus forms a part of the
endomembrane system of eukaryotic cells. Vesicles
that enter the Golgi apparatus are processed in a cis
to trans direction, meaning they coalesce on the cis
side of the apparatus and after processing pinch off on
the opposite (trans) side to form a new vesicle in the
animal cell.[citation needed]
Diagram of an endomembrane system

Ribosomes
The ribosome is a large complex of RNA and
protein molecules. They each consist of two subunits,
and act as an assembly line where RNA from the
nucleus is used to synthesise proteins from amino
acids. Ribosomes can be found either floating freely or
bound to a membrane (the rough endoplasmatic
reticulum in eukaryotes, or the cell membrane in
prokaryotes).[9]
Lysosomes and Peroxisomes – eukaryotes only

Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out
organelles, food particles, and engulfed viruses or bacteria. Peroxisomes have enzymes that rid the
cell of toxic peroxides. The cell could not house these destructive enzymes if they were not contained
in a membrane-bound system. These organelles are often called a "suicide bag" because of their
ability to detonate and destroy the cell.[citation needed]
Centrosome – the cytoskeleton organiser

The centrosome produces the microtubules of a cell – a key component of the cytoskeleton. It
directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two
centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single
centrosome is present in the animal cells. They are also found in some fungi and algae cells.[ citation
needed]
Vacuoles
Vacuoles store food and waste. Some vacuoles store extra water. They are often described
as liquid filled space and are surrounded by a membrane. Some cells, most notably Amoeba, have
contractile vacuoles, which can pump water out of the cell if there is too much water. The vacuoles of
eukaryotic cells are usually larger in those of plants than animals.
Structures outside the cell wall
Capsule
A gelatinous capsule is present in some bacteria outside the cell wall. The capsule may be
polysaccharide as in pneumococci, meningococci or polypeptide as Bacillus anthracis or hyaluronic acid as
in streptococci.[citation needed] Capsules are not marked by ordinary stain and can be detected by special
stain. The capsule is antigenic. The capsule has antiphagocytic function so it determines the virulence of
many bacteria. It also plays a role in attachment of the organism to mucous membranes.[ citation needed]
Flagella
Flagella are the organelles of cellular mobility. They arise from cytoplasm and extrude through the
cell wall. They are long and thick thread-like appendages, protein in nature. Are most commonly found in
bacteria cells but are found in animal cells as well.
Fimbriae (pili)
They are short and thin hair like filaments, formed of protein called pilin (antigenic). Fimbriae are
responsible for attachment of bacteria to specific receptors of human cell (adherence). There are special
types of pili called (sex pili) involved in conjunction.[ citation needed]
Functions
Growth and metabolism
Main articles: Cell growth and Metabolism
Between successive cell divisions, cells grow through the functioning of cellular metabolism. Cell
metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct
divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing
power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules
and perform other biological functions. Complex sugars consumed by the organism can be broken down into
a less chemically complex sugar molecule called glucose. Once inside the cell, glucose is broken down to
make adenosine triphosphate (ATP), a form of energy, through two different pathways.
The first pathway, glycolysis, requires no oxygen and is referred to as anaerobic metabolism. Each
reaction is designed to produce some hydrogen ions that can then be used to make energy packets (ATP). In
prokaryotes, glycolysis is the only method used for converting energy.
The second pathway, called the Krebs cycle, or citric acid cycle, occurs inside the mitochondria and
can generate enough ATP to run all the cell functions.
An overview of protein synthesis.
Within the nucleus of the cell (light blue), genes (DNA, dark blue) are transcribed into RNA. This RNA is then
subject to post-transcriptional modification and control, resulting in a mature mRNA (red) that is then
transported out of the nucleus and into the cytoplasm (peach), where it undergoes translation into a protein.
mRNA is translated by ribosomes (purple) that match the three-base codons of the mRNA to the three-base
anti-codons of the appropriate tRNA. Newly synthesized proteins (black) are often further modified, such as
by binding to an effector molecule (orange), to become fully active.
Creation
Main article: Cell division
Cell division involves a single cell (called a mother cell) dividing into two daughter cells. This leads to
growth in multicellular organisms (the growth of tissue) and to procreation (vegetative reproduction) in
unicellular organisms.
Prokaryotic cells divide by binary fission. Eukaryotic cells usually undergo a process of nuclear
division, called mitosis, followed by division of the cell, called cytokinesis. A diploid cell may also undergo
meiosis to produce haploid cells, usually four. Haploid cells serve as gametes in multicellular organisms,
fusing to form new diploid cells.
DNA replication, or the process of duplicating a cell's genome, is required every time a cell divides.
Replication, like all cellular activities, requires specialized proteins for carrying out the job.
Protein synthesis
Main article: Protein biosynthesis
Cells are capable of synthesizing new proteins, which are essential for the modulation and
maintenance of cellular activities. This process involves the formation of new protein molecules from amino
acid building blocks based on information encoded in DNA/RNA. Protein synthesis generally consists of two
major steps: transcription and translation.
Transcription is the process where genetic information in DNA is used to produce a complementary
RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate
through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol,
where they are translated into polypeptide sequences. The ribosome mediates the formation of a polypeptide
sequence based on the mRNA sequence. The mRNA sequence directly relates to the polypeptide sequence
by binding to transfer RNA (tRNA) adapter molecules in binding pockets within the ribosome. The new
polypeptide then folds into a functional three-dimensional protein molecule.
Movement or motility
Cells can move during many processes: such as wound healing, the immune response and cancer
metastasis. For wound healing to occur, white blood cells and cells that ingest bacteria move to the wound
site to kill the microorganisms that cause infection.
At the same time fibroblasts (connective tissue cells) move there to remodel damaged structures. In the case
of tumor development, cells from a primary tumor move away and spread to other parts of the body. Cell
motility involves many receptors, crosslinking, bundling, binding, adhesion, motor and other proteins.[10] The
process is divided into three steps – protrusion of the leading edge of the cell, adhesion of the leading edge
and de-adhesion at the cell body and rear, and cytoskeletal contraction to pull the cell forward. Each step is
driven by physical forces generated by unique segments of the cytoskeleton.[11][12]
Evolution
Main article: Evolutionary history of life
The origin of cells has to do with the origin of life, which began the history of life on Earth.
Origin of the first cell

Further information: Abiogenesis
There are several theories about the origin of small molecules that could lead to life in an early Earth.
One is that they came from meteorites (see Murchison meteorite). Another is that they were created at deep-
sea vents. A third is that they were synthesized by lightning in a reducing atmosphere ( see Miller–Urey
experiment); although it is not clear if Earth had such an atmosphere. There are essentially no experimental
data defining what the first self-replicating forms were. RNA is generally assumed to be the earliest self-
replicating molecule, as it is capable of both storing genetic information and catalyzing chemical reactions
(see RNA world hypothesis). But some other entity with the potential to self-replicate could have preceded
RNA, like clay or peptide nucleic acid.[13]
Cells emerged at least 4.0–4.3 billion years ago. The current belief is that these cells were
heterotrophs. An important characteristic of cells is the cell membrane, composed of a bilayer of lipids. The
early cell membranes were probably more simple and permeable than modern ones, with only a single fatty
acid chain per lipid. Lipids are known to spontaneously form bilayered vesicles in water, and could have
preceded RNA. But the first cell membranes could also have been produced by catalytic RNA, or even have
required structural proteins before they could form.[14]
Origin of eukaryotic cells
The eukaryotic cell seems to have evolved from a symbiotic community of prokaryotic cells. DNA-
bearing organelles like the mitochondria and the chloroplasts are almost certainly what remains of ancient
symbiotic oxygen-breathing proteobacteria and cyanobacteria, respectively, where the rest of the cell seems
to be derived from an ancestral archaean prokaryote cell – a theory termed the endosymbiotic theory.
There is still considerable debate about whether organelles like the hydrogenosome predated the
origin of mitochondria, or viceversa: see the hydrogen hypothesis for the origin of eukaryotic cells.
Sex, as the stereotyped choreography of meiosis and syngamy that persists in nearly all extant
eukaryotes, may have played a role in the transition from prokaryotes to eukaryotes. An 'origin of sex as
vaccination' theory suggests that the eukaryote genome accreted from prokaryan parasite genomes in
numerous rounds of lateral gene transfer. Sex-as-syngamy (fusion sex) arose when infected hosts began
swapping nuclearized genomes containing co-evolved, vertically transmitted symbionts that conveyed
protection against horizontal infection by more virulent symbionts.[15]
History
• 1632–1723: Antonie van Leeuwenhoek teaches himself to grind lenses, builds a microscope
and draws protozoa, such as Vorticella from rain water, and bacteria from his own mouth.
• 1665: Robert Hooke discovers cells in cork, then in living plant tissue using an early
microscope.[6]
• 1839: Theodor Schwann and Matthias Jakob Schleiden elucidate the principle that plants
and animals are made of cells, concluding that cells are a common unit of structure and
development, and thus founding the cell theory.
• The belief that life forms can occur spontaneously ( generatio spontanea) is contradicted by
Louis Pasteur (1822–1895) (although Francesco Redi had performed an experiment in 1668 that
suggested the same conclusion).
• 1855: Rudolf Virchow states that cells always emerge from cell divisions (omnis cellula ex
cellula).
• 1931: Ernst Ruska builds first transmission electron microscope (TEM) at the University of
Berlin. By 1935, he has built an EM with twice the resolution of a light microscope, revealing
previously unresolvable organelles.
• 1953: Watson and Crick made their first announcement on the double-helix structure for DNA
on February 28.
• 1981: Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic
theory.
See also
Wikimedia Commons has media related to: Cell biology
Main article: Topic outline of cell biology

• Cell biology
• Cell culture
• Cell type
• Cellular component
• Cytorrhysis
• Cytotoxicity
• Plasmolysis
• Stem cell
• Syncytium
References
1. ^ Cell Movements and the Shaping of the Vertebrate Body in Chapter 21 of Molecular
Biology of the Cell fourth edition, edited by Bruce Alberts (2002) published by Garland Science.
The Alberts text discusses how the "cellular building blocks" move to shape developing embryos. It is
also common to describe small molecules such as amino acids as "molecular building blocks".
2. ^ Integrative Biology 131 - Lecture 03: Skeletal System at YouTube first 12 minutes of the
lecture covers cells (by Marian Diamond).
3. ^ Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life.
Boston, Massachusetts: Pearson Prentice Hall. ISBN 0-13-250882-6.
http://www.phschool.com/el_marketing.html.
4. ^ Mitzi Perdue. "Facts about Birds and Eggs". http://www.eggscape.com/birds.htm. Retrieved
2010-04-15.
5. ^ Maton, Anthea; Hopkins, Jean Johnson, Susan LaHart, David Quon Warner, Maryanna
Wright, Jill D (1997). Cells Building Blocks of Life. New Jersey: Prentice Hall. ISBN 0-13-423476-6.
6. ^ a b "... I could exceedingly plainly perceive it to be all perforated and porous, much like a
Honey-comb, but that the pores of it were not regular [..] these pores, or cells, [..] were indeed the
first microscopical pores I ever saw, and perhaps, that were ever seen, for I had not met with any
Writer or Person, that had made any mention of them before this. . ." – Hooke describing his
observations on a thin slice of cork. Robert Hooke
7. ^ Satir, P; Christensen, ST; Søren T. Christensen (2008-03-26). "Structure and function of
mammalian cilia". Histochemistry and Cell Biology (Springer Berlin / Heidelberg) 129 (6): 687–693.
doi:10.1007/s00418-008-0416-9. 1432-119X. PMID 18365235. PMC 2386530.
http://www.springerlink.com/content/x5051hq648t3152q/. Retrieved 2009-09-12.
8. ^ Michie K, Löwe J (2006). "Dynamic filaments of the bacterial cytoskeleton". Annu Rev
Biochem 75: 467–92. doi:10.1146/annurev.biochem.75.103004.142452. PMID 16756499.
9. ^ Ménétret JF, Schaletzky J, Clemons WM, et al., CW; Akey (December 2007). "Ribosome
binding of a single copy of the SecY complex: implications for protein translocation". Mol. Cell 28 (6):
1083–92. doi:10.1016/j.molcel.2007.10.034. PMID 18158904.
10.^ Revathi Ananthakrishnan1 *, Allen Ehrlicher2 ✉. "The Forces Behind Cell Movement".
Biolsci.org. http://www.biolsci.org/v03p0303.htm. Retrieved 2009-04-17.
11.^ Alberts B, Johnson A, Lewis J. et al. Molecular Biology of the Cell, 4e. Garland Science.
2002
12.^ Ananthakrishnan R, Ehrlicher A. The Forces Behind Cell Movement. Int J Biol Sci 2007;
3:303–317. http://www.biolsci.org/v03p0303.htm
13.^ Orgel LE (1998). "The origin of life--a review of facts and speculations". Trends Biochem
Sci 23 (12): 491–5. doi:10.1016/S0968-0004(98)01300-0. PMID 9868373.
14.^ Griffiths G (December 2007). "Cell evolution and the problem of membrane topology".
Nature reviews. Molecular cell biology 8 (12): 1018–24. doi:10.1038/nrm2287. PMID 17971839.
15.^ Sterrer W (2002). "On the origin of sex as vaccination". Journal of Theoretical Biology 216:
387–396. doi:10.1006/jtbi.2002.3008. PMID 12151256.
• This article incorporates public domain material from the NCBI document "Science
Primer".
External links
• Inside the Cell
• Virtual Cell's Educational Animations
• The Inner Life of A Cell, a flash video showing what happens inside of a cell
• The Virtual Cell
• Cells Alive!
• Journal of Cell Biology
• The Biology Project > Cell Biology
• Centre of the Cell online
• The Image & Video Library of The American Society for Cell Biology , a collection of peer-
reviewed still images, video clips and digital books that illustrate the structure, function and biology of
the cell.
Textbooks
• Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the
Cell (4th ed.). Garland. ISBN 0815332181. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?
rid=mboc4.TOC&depth=2.
• Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J
(2004). Molecular Cell Biology (5th ed.). WH Freeman: New York, NY. ISBN 978-0716743668.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.TOC.
• Cooper GM (2000). The cell: a molecular approach (2nd ed.). Washington, D.C: ASM Press.
ISBN 0-87893-102-3. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.TOC&depth=2.
[hide]v · d · eStructures of the cell / organelles
Cell membrane · Nucleus (and Nucleolus) · Endoplasmic reticulum ·

Golgi apparatus · Parenthesome · Autophagosome
Endomembrane
system Vesicles (Exosome · Lysosome · Endosome · Phagosome · Vacuole)
Cytoplasmic granules: Melanosome · Microbody (Glyoxysome,
Peroxisome) · Weibel-Palade body
Microfilaments · Intermediate filaments · Microtubules · Prokaryotic

cytoskeleton
Cytoskeleton
MTOCs: Centrosome/Centriole · Basal body · Spindle pole body
Myofibril
Endosymbionts Mitochondrion · Plastids (Chloroplast · Chromoplast · Leucoplast)

RNA: Ribosome · Vault
Other internal
Cytoplasm · Proteasome
Undulipodium: Cilium/Flagellum · Axoneme · Radial spoke

External
Cell wall · Acrosome
B strc: edmb (perx), skel (ctrs), epit, cili, mito, nucl (chro)
[hide]v · d · eHierarchy of life
Biosphere > Ecosystem > Community (Biocoenosis) > Population > Organism > Organ system
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Retrieved from "http://en.wikipedia.org/wiki/Cell_(biology)"
Categories: Cell biology

W000
Brown algae

Brown algae
Temporal range: 150–0 Ma[1][2]
PreЄ
g
Giant kelp (Macrocystis pyrifera)
Domain: Eukaryota
Kingdom: Chromalveolata
Division: Heterokontophyta
Phaeophyceae
Class:
Kjellman, 1891[3]
Orders
see Classification.
Synonyms
Fucophyceae
Melanophyceae
Phaeophyta
The Phaeophyceae or brown algae (singular: alga), is a large group of mostly marine multicellular
algae, including many seaweeds of colder Northern Hemisphere waters. They play an important role in
marine environments both as food, and for the habitats they form. For instance Macrocystis, a member of the
Laminariales or kelps, may reach 60 m in length, and forms prominent underwater forests. Another example
is Sargassum, which creates unique habitats in the tropical waters of the Sargasso Sea. Many brown algae
such as members of the order Fucales are commonly found along rocky seashores. Some members of the
class are used as food for humans.
Worldwide there are about 1500-2000 species of brown algae.[4] Some species are of sufficient
commercial importance, such as Ascophyllum nodosum, that they have become subjects of extensive
research in their own right.[5]
Brown algae belong to a very large group, the Heterokontophyta, a eukaryotic group of organisms
distinguished most prominently by having chloroplasts surrounded by four membranes, suggesting an origin
from a symbiotic relationship between a basal eukaryote and another eukaryotic organism. Most brown algae
contain the pigment fucoxanthin, which is responsible for the distinctive greenish-brown color that gives them
their name. Brown algae are unique among heterokonts in developing into multicellular forms with
differentiated tissues, but they reproduce by means of flagellate spores and gametes, which closely resemble
other heterokont cells. Genetic studies show their closest relatives to be the yellow-green algae.
Contents
[hide]
• 1 Morphology
• 1.1 Visible structures
• 1.2 Tissue organisation
• 1.3 Growth
• 2.1 Fossils
• 4 Life cycle
• 5 Ecology
• 6 Chemistry
• 7 Importance and uses
• 8 See also
• 9 References
[edit] Morphology
Brown algae exist in a wide range of sizes and forms. The smallest members of the group grow as
tiny, feathery tufts of threadlike cells no more than a few centimeters long.[6] Some species even have a
stage in their life cycle that consists of only a few cells, making the entire alga microscopic. Other groups of
brown algae grow to much larger sizes. The leathery kelps and rockweeds are often the most conspicuous
algae in their habitats.[7] Kelps can range in size from the two-foot-tall sea palm ( Postelsia) to the giant kelp
Macrocystis pyrifera, which grows to over 45 m (150 ft) long[8][9] and is the largest of all the algae. In form,
the brown algae range from small crusts or cushions[10] to leafy free-floating mats formed by species of
Sargassum. They may consist of delicate felt-like strands of cells, as in Ectocarpus, or of foot-long flattened
branches resembling a fan, as in Padina.
Reagrdless of size or form, two visible features set the Phaeophyceae apart from all other algae.
First, members of the group possess a characteristic color that ranges from an olive green to various shades
of brown. The particular shade depends on the amount of fucoxanthin present in the alga.[11] Second, all
brown algae are multicellular. There are no known species that exist as single cells or as colonies of
cells[11], and the brown algae are the only major group of seaweeds that does not include such forms.
However, this may be the result of classification rather than evolutionary, as all the groups hypothesized to
be the closest relatives of the browns include single-celled or colonial forms.
[edit] Visible structures
Two specimens of Laminaria hyperborea, each showing the rootlike holdfast at lower left, a divided
blade at upper right, and a stemlike stipe connecting the blade to the holdfast.
Further information: Thallus, Holdfast, Stipe (botany), Lamina (algae), and Pneumatocyst
Whatever their form, the body of all brown algae is termed a thallus, indicating that it lacks the
complex xylem and phloem of vascular plants. This does not mean that brown algae completely lack
specialized structures. But, because some botanists define "true" stems, leaves, and roots by the presence of
these tissues, their absence in the brown algae means that the stem-like and leaf-like structures found in
some groups of brown algae must be described using different terminology.[12] Although not all brown algae
are structurally complex, those that are typically possess one or more characteristic parts.
A holdfast is a rootlike structure present at the base of the alga. Like a root system in plants, a
holdfast serves to anchor the alga in place on the substrate where it grows, and thus prevents the alga from
being carried away by the current. Unlike a root system, the holdfast generally does not serve as the primary
organ for water uptake, nor does it take in nutrients from the substrate. The overall physical appearance of
the holdfast differs among various brown algae and among various substrates. It may be heavily branched,
or it may be cup-like in appearance. A single alga typically has just one holdfast, although some species
have more than one stipe growing from their holdfast.
A stipe is a stalk or stemlike structure present in an alga. It may grow as a short structure near the
base of the alga (as in Laminaria), or it may develop into a large, complex structure running throughout the
algal body (as in Sargassum or Macrocystis). In the most structurally differentiated brown algae (such as
Fucus), the tissues within the stipe are divided into three distinct layers or regions. These regions include a
central pith, a surrounding cortex, and an outer epidermis, each of which has an analog in the stem of a
vascular plant. In some brown algae, the pith region includes a core of elongated cells that resemble the
phloem of vascular plants both in structure and function. In others (such as Nereocystis), the center of the
stipe is hollow and filled with gas that serves to keep that part of the alga buoyant. The stipe may be relatively
flexible and elastic in species like Macrocystis pyrifera that grow in strong currents, or may be more rigid in
species like Postelsia palmaeformis that are exposed to the atmosphere at low tide.
Many algae have a flattened portion that may resemble a leaf, and this is termed a blade, lamina, or
frond. The name blade is most often applied to a single undivided structure, while frond may be applied to all
or most of an algal body that is flattened, but this distinction is not universally applied. The name lamina
refers to that portion of a structurally differentiated alga that is flattened. It may be a single or a divided
structure, and may be spread over a substantial portion of the alga. In rockweeds, for example, the lamina is
a broad wing of tissue that runs continuously along both sides of a branched midrib. The midrib and lamina
together constitute almost all of a rockweed, so that the lamina is spread throughout the alga rather than
existing as a localized portion of it.
Species like Fucus vesiculosus produce numerous gas-filled pneumatocysts (air bladders) to
increase buoyancy.
In some brown algae, there is a single lamina or blade, while in others there may be many separate
blades. Even in those species that initially produce a single blade, the structure may tear with rough currents
or as part of maturation to form additional blades. These blades may be attached directly to the stipe, to a
holdfast with no stipe present, or there may be an air bladder between the stipe and blade. The surface of the
lamina or blade may be smooth or wrinkled; its tissues may be thin and flexible or thick and leathery. In
species like Egregia menziesii, this characteristic may change depending upon the turbulence of the waters
in which it grows.[6] In other species, the surface of the blade is coated with slime to discourage the
attachment of epiphytes or to deter herbivores. Blades are also often the parts of the alga that bear the
reproductive structures.
Gas-filled floats called pneumatocysts provide buoyancy in many kelps and members of the Fucales.
These bladder-like structures occur in or near the lamina, so that it is held nearer the water surface and thus
receives more light for photosynthesis. Pneumatocysts are most often spherical or ellipsoidal, but can vary in
shape among different species. Species such as Nereocystis luetkeana and Pelagophycus porra bear a
single large pneumatocyst between the top of the stipe and the base of the blades. In contrast, the giant kelp
Macrocystis pyrifera bears many blades along its stipe, with a pneumatocyst at the base of each blade where
it attaches to the main stipe. Species of Sargassum also bear many blades and pneumatocysts, but both
kinds of structures are attached separately to the stipe by short stalks. In species of Fucus, the
pneumatocysts develop within the lamina itself, either as discrete spherical bladders or as elongated gas-
filled regions that take the outline of the lamina in which they develop.
[edit] Tissue organisation

The simplest browns are filamentous - that is, their cells are elongate and have septa cutting across
their width. They branch by getting wider at their tip, and then dividing the widening.[13]
Aside from filamentous forms, there are two main types of tissue organization in the brown algae:
pseudoparenchymatous (haplostichous) and parenchymatous (polystichous).[14] The fronds may be
multiaxial or monoaxial.
The cell wall consists of two layers; the inner layer bears the strength, and consists of cellulose; the
outer wall layer is mainly algin, and is gummy when wet but becomes hard and brittle when it dries out.[15]
[edit] Growth
Growth in Dictyota dichotoma occurs at each frond tip, where new cells are produced.
The brown algae include the largest and fastest growing of seaweeds.[6] Fronds of Macrocystis may
grow as much as 50 centimetres (20 in) per day, and the stipes can grow 6 centimetres (2.4 in) in a single
day.[16]
Growth in most brown algae occurs at the tips of structures as a result of divisions in a single apical
cell or in a row of such cells.[7] As this apical cell divides, the new cells that it produces develop into all the
tissues of the alga. Branchings and other lateral structures appear when the apical cell divides to produce
two new apical cells. However, a few groups (such as Ectocarpus) grow by a diffuse, unlocalized production
of new cells that can occur anywhere on the thallus.[11]
Genetic and ultrastructural evidence place the Phaeophyceae among the heterokonts
(Stramenopiles)[17], a large assemblage of organisms that includes both photosynthetic members with
plastids (such as the diatoms) as well as non-photosynthetic groups (such as the slime nets and water
moulds). Although some heterokont relatives of the brown algae lack plastids in their cells, scientists believe
this is a result of evolutionary loss of that organelle in those groups rather than independent acquisition by
the several photosynthetic members.[18] Thus, all heterokonts are believed to descend from a single
heterotrophic ancestor that became photosynthetic when it acquired plastids through endosymbiosis of
another unicellular eukaryote.[4]
The closest relatives of the brown algae include unicellular and filamentous species, but no
unicellular species of brown algae are known. However, most scientists assume that the Phaeophyceae
evolved from unicellular ancestors.[19] DNA sequence comparison also suggests that the brown algae
evolved from the filamentous Phaeothamniophyceae[20], Xanthophyceae[21], or the Chrysophyceae[22]
between 150[1] and 200 million years ago.[2] In many ways, the evolution of the brown algae parallels that of
the green algae and red algae,[23] as all three groups possess complex multicellular species with an
alternation of generations. Analysis of 5S rRNA sequences reveals much smaller evolutionary distances
among genera of the brown algae than among genera of red or green algae,[2][24] which suggests that the
brown algae have diversified much more recently than the other two groups.
[edit] Fossils
The occurrence of Phaeophyceae as fossils is rare due to their generally soft-bodied nature[25], and
scientists continue to debate the identification of some finds.[26] Part of the problem with identification lies in
the convergent evolution of morphologies between many brown and red algae.[27] Most fossils of soft-tissue
algae preserve only a flattened outline, without the microscopic features that permit the major groups of
multicellular algae to be reliably distinguished. Among the brown algae, only species of the genus Padina
deposit significant quantities of minerals in or around their cell walls.[28] Other algal groups, such as the red
algae and green algae, have a number of calcareous members. Because of this, they are more likely to leave
evidence in the fossil record than the soft bodies of most brown algae and more often can be precisely
classified.[29]
Fossils comparable in morphology to brown algae are known from strata as old as the Upper
Ordovician[30], but the taxonomic affinity of these impression fossils is far from certain.[31] Claims that
earlier Ediacaran fossils are brown algae[32] have since been dismissed.[20] While many carbonaceous
fossils have been described from the Precambrian, they are typically preserved as flattened outlines or
fragments measuring only millimeters long.[33] Because these fossils lack features diagnostic for
identification at even the highest level, they are assigned to fossil form taxa according to their shape and
other gross morphological features.[34] A number of Devonian fossils termed fucoids, from their resemblance
in outline to species in the genus Fucus, have proven to be inorganic rather than true fossils.[25] The
Devonian megafossil Prototaxites, which consists of masses of filaments grouped into trunk-like axes, has
been considered a possible brown alga.[11] However, modern research favors reinterpretation of this fossil
as a terrestrial fungus or fungal-like organism.[35] Likewise, the fossil Protosalvinia was once considered a
possible brown alga, but is now thought to be an early land plant.[36]
A number of Paleozoic fossils have been tentatively classified with the brown algae, although most
have also been compared to known red algae species. Phascolophyllaphycus possesses numerous
elongate, inflated blades attached to a stipe. It is the most abundant of algal fossils found in a collection
made from Carboniferous strata in Illinois.[37] Each hollow blade bears up to eight pneumatocysts at its
base, and the stipes appear to have been hollow and inflated as well. This combination of characteristics is
similar to certain modern genera in the order Laminariales (kelps). Several fossils of Drydenia and a single
specimen of Hungerfordia from the Upper Devonian of New York have also been compared to both brown
and red algae.[27] Fossils of Drydenia consist of an elliptical blade attached to a branching filamentous
holdfast, not unlike some species of Laminaria, Porphyra, or Gigartina. The single known specimen of
Hungerfordia branches dichotomously into lobes and resembles genera like Chondrus and Fucus[27] or
Dictyota.[38]
The earliest known fossils that can be assigned reliably to the Phaeophyceae come from Miocene
diatomite deposits of the Monterey Formation in California.[4] Several soft-bodied brown macroalgae, such
as Julescraneia, have been found.[39]
Further information: List of brown algal genera
This is a list of the orders in the class Phaeophyceae:[40]
• Ascoseirales Petrov • Nemodermatales M. Parente, R.L.
• Cutleriales Fletcher, F. Rousseau & N. Phillips
Oltmanns • Onslowiales Draisma & Prud'homme
• Desmarestiales van Reine ex Phillips et al.
Setchell & Gardner • Ralfsiales Nakamura
• Dictyotales Kjellman • Scytosiphonales Feldmann
• Discosporangiales • Scytothamnales A. F. Peters & M. N.
• Ectocarpales Clayton
Setchell & Gardner • Sphacelariales Migula
• Fucales Kylin • Sporochnales Sauvageau
• Ishigeales G.Y. Cho • Syringodermatales E. C. Henry
& Boo • Tilopteridales Bessey
• Laminariales Migula
[edit] Life cycle

The life cycle shows great variability from one group to another. However the life cycle of Laminaria
consists of the diploid generation, that is the large kelp well known to most people, producing sporangia from
specialised microscopic structures, which divide meiotically before they are released. As they are haploid
there are equal numbers of male and female spores.[41] With the exception of the Fucales all brown algae
have a life cycle which consists of an alternation between haploid and diploid forms.
[edit] Ecology
Saccharina latissima on a beach.

Brown algae have adapted to a wide variety of marine ecological niches including the tidal splash
zone, rock pools, the whole intertidal zone and relatively deep near shore waters. They are an important
constituent of some brackish water ecosystems, and four species are restricted to life in fresh water.[20] A
large number of Phaeophyceae are intertidal or upper littoral,[20] and they are predominantly cool and cold
water organisms that benefit from nutrients in up welling cold water currents and inflows from land;
Sargassum being a prominent exception to this generalisation.
Brown algae growing in brackish waters are almost solely asexual.[20]
[edit] Chemistry
Algal group δ13C range[42]
HCO3-using red algae −22.5‰ – −9.6‰
CO2-using red algae −34.5‰ – −29.9‰
Brown algae −20.8‰ – −10.5‰
Green algae −20.3‰ – −8.8‰
Brown algae have a δ13C value between −-20.8‰ – −10.5‰, in contrast with red algae and greens.
This reflects their different metabolic pathways.[43]
They have Cellulose walls with alginic acid; fucoidin also important in amorphous section of cell
walls. A few species (of Padina) calcify with aragonite needles.[20]
Brown algae produce a specific type of tannin, called phlorotannins.
[edit] Importance and uses

The brown algae include a number of edible seaweeds.
[edit] See also

• Wrack (seaweed)
[edit] References
1. ^ a b Medlin, L. K.; Kooistra, W. H. F.; Potter, D.; Saunders, G. W.; Andersen, R. A. (1997).
"Phylogenetic relationships of the 'golden algae' (haptophytes, heterokont chromophytes) and their
plastids" (PDF). Origins of algae and their plastids: 187–219.
http://epic.awi.de/Publications/Med1997c.pdf.
2. ^ a b c Lim, B.-L.; Kawai, H.; Hori, H.; Osawa, S. (1986). "Molecular evolution of 5S ribosomal
RNA from red and brown algae". Idengaku Zasshi (Japanese Journal of Genetics) 61 (2): 169–176.
3. ^ Kjellman, F.R. (1891). "Phaeophyceae (Fucoideae)". In Engler, A. & Prantl, K. (eds.). Die
natürlichen Pflanzenfamilien. 1 (2). Leipzig: Wilhelm Engelmann. pp. 176–192.
4. ^ a b c Hoek, C. van den; D. G. Mann; H. M. Jahns (1995). Algae: An Introduction to
Phycology. Cambridge: Cambridge University Press. pp. 165–218. ISBN 0-521-31687-1.
5. ^ T. L. Senn (1987). Seaweed and Plant Growth. Clemson, S.C.: T.L. Senn. p. 181 pp.
ISBN 0-939241-01-3.
6. ^ a b c Connor, J.; Baxter, C. (1989). Kelp Forests. Monterey Bay Aquarium.
ISBN 1878244019.
7. ^ a b Dittmer, Howard J. (1964). Phylogeny and Form in the Plant Kingdom. Princeton, NJ: D.
Van Nostrand Company. pp. 115–137. ISBN 0882751670.
8. ^ Abbott, I. A.; Hollenberg, G. J. (1976). Marine Algae of California. California: Stanford
9. ^ Cribb, A. B. (1953). "Macrocystis pyrifera (L.) Ag. in Tasmanian waters". Australian Journal
of Marine and Freshwater Research 5 (1): 1–34. doi:10.1071/MF9540001.
10.^ Jones, W. E. (1962). "A key to the genera of the British seaweeds". Field Studies 1 (4): 1–
32.
11.^ a b c d Bold, H. C.; Alexopoulos, C. J.; Delevoryas, T. (1987). Morphology of Plants and
Fungi (5th ed.). New York: Harper & Row Publishers. pp. 112–131, 174–186. ISBN 0060408391.
12.^ Raven, P. H.; Evert, R. F.; Eichhorn, S. E. (2005). Biology of Plants (7th ed.). New York: W.
H. Freeman and Company. pp. 316–321, 347. ISBN 0716710072.
13.^ Lobban, Christopher S; Wynne, Michael James (1981). The Biology of seaweeds.
ISBN 9780520045859. http://books.google.com/?id=QG4tqjFPWJ0C&pg=PA52.
14.^ Sharma, O. P (1986-01-01). Textbook of Algae. ISBN 9780074519288.
http://books.google.ca/books?id=hOa74Hm4zDIC&pg=PA298&lpg=PA298.
15.^ Sharma, O. P (1986-01-01). Textbook of Algae. ISBN 9780074519288.
http://books.google.ca/books?id=hOa74Hm4zDIC&pg=PA298&lpg=PA298.
16.^ Round, F. E. (1981). The Ecology of Algae. Cambridge: Cambridge University Press.
p. 103. ISBN 0521269067.
17.^ Adl SM, Simpson AG, Farmer MA, et al. (2005). "The new higher level classification of
eukaryotes with emphasis on the taxonomy of protists". J. Eukaryot. Microbiol. 52 (5): 399–451.
doi:10.1111/j.1550-7408.2005.00053.x. PMID 16248873.
18.^ Lane, C. E.; Archibald, J. M. (2008). "The eukaryotic tree of life: endosymbiosis takes its
TOL". Trends in Ecology and Evolution 23 (5): 268–275. doi:10.1016/j.tree.2008.02.004.
PMID 18378040.
19.^ Niklas, Karl J. (1997). The Evolutionary Biology of Plants. Chicago: The University of
Chicago Press. p. 156. ISBN 0226580822.
20.^ a b c d e f Lee, R.E. (2008). Phycology (4th ed.). Cambridge University Press. ISBN 978-
0521638838.
21.^ Ariztia, E. V.; Andersen, R. A.; Sogin, M. L. (1991). "A new phylogeny of chromophyte
algae using 16S-like rRNA sequences from Mallomonas papillosa (Synurophyceae) and Tribonema
aequale (Xanthophyceae)". Journal of Phycology 27: 428–436. doi:10.1111/j.0022-
3646.1991.00428.x.
22.^ Taylor, T. N.; E. L. Taylor (1993). The Biology and Evolution of Fossil Plants. Englewood
Cliffs, NJ: Prentice Hall. pp. 128–131. ISBN 0-13-651589-4.
23.^ Dittmer, H. J. (1964). Phylogeny and Form in the Plant Kingdom. Princeton, N. J.: D. Van
Nostrand Company, Inc.. pp. 115–137. ISBN 0882751670.
24.^ Hori, H.; Osawa, S. (1987). "Origin and evolution of organisms as deduced from 5S
ribosomal RNS sequences". Molecular Biology and Evolution. 4 (5): 445–472. PMID 2452957.
25.^ a b Arnold, C. A. (1947). An Introduction to Paleobotany (1st ed.). New York; London:
McGraw-Hill Book Company, Inc.. p. 48. ISBN 1406718610.
26.^ Coyer, J.A.; G.J. Smith, R.A. Anderson (2001). "Evolution of Macrocystis spp.
(Phaeophyta) as determined by ITS1 and ITS2 sequences". Journal of Phycology (Blackwell
Publishing) 37: 574–585. doi:10.1046/j.1529-8817.2001.037001574.x.
27.^ a b c Fry, W. L.; Banks, H. P. (1955). "Three new genera of algae from the Upper Devonian
of New York". Journal of Paleontology 29: 37–44.
28.^ Prescott, G. W. (1968). The Algae: A Review. Boston: Houghton Mifflin Company. pp. 207–
231, 371–372. ISBN 3874292444.
29.^ Simpson, G. G. (1953). Life of the Past: An Introduction to Paleontology . New Haven: Yale
University Press. pp. 158–159.
30.^ Fry, W. L. (1983). "An algal flora from the Upper Ordovician of the Lake Winnipeg region,
Manitoba, Canada". Review of Palaeobotany and Palynology 39: 313–341. doi:10.1016/0034-
6667(83)90018-0.
31.^ Speer, B. R.; Waggoner, B. M. (2000). "Phaeophyta: Fossil Record".
http://www.ucmp.berkeley.edu/chromista/browns/phaeofr.html.
32.^ Loeblich, A. R. (1974). "Protistan Phylogeny as Indicated by the Fossil Record". Taxon
(International Association for Plant Taxonomy (IAPT)) 23 (2/3): 277–290. doi:10.2307/1218707.
http://links.jstor.org/sici?sici=0040-0262(197405)23%3A2%2F3%3C277%3APPAIBT%3E2.0.CO
%3B2-8.
33.^ Hofmann, H. J. (1985). "Precambrian Carbonaceous Megafossils". In D. F. Toomey & M. H.
Nitecki. Paleoalgology: Contemporary Research and Applications . Berlin: Springer-Verlag. pp. 20–
33.
34.^ Hofmann, H. J. (1994). "Proterozoic carbonaceous compressions ("metaphytes" and
"worms")". In S. Bengtson. Life on Earth. Nobel Symposium No. 84. New York: Columbia University
Press. pp. 342–357.
35.^ Hueber, F.M. (2001). "Rotted wood-alga-fungus: the history and life of Prototaxites Dawson
1859". Review of Palaeobotany and Palynology 116 (1): 123–158. doi:10.1016/S0034-
6667(01)00058-6.
36.^ Taylor, W. A.; Taylor, T. N. (1987). "Spore wall ultrastructure of Protosalvinia". American
Journal of Botany 74 (3): 437–433. doi:10.2307/2443819. http://jstor.org/stable/2443819.
37.^ Leary, R. L. (1986). "Three new genera of fossil noncalcareous algae from Valmeyeran
(Mississippian) strata of Illinois". American Journal of Botany 73 (3): 369–375. doi:10.2307/2444080.
38.^ Bold, H. C.; Wynne, M. J. (1978). Introduction to the Algae (2nd ed.). pp. 27.
ISBN 0134777867.
39.^ Parker, B. C.; Dawson, E. Y. (1965). "Non-calcareous marine algae from California
Miocene deposits". Nova Hedwigia 10: 273–295; plates 76–96.
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ISBN 0565091751.
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by marine plants", Oecologia 91: 481, doi:10.1007/BF00650320
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doi:10.1111/j.1472-4677.2004.00026.x

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W000
Bear

"Ursine" redirects here. For the village, see Ursine, Nevada.
For other uses, see Bear (disambiguation).
Bears
PreЄ
g Late Eocene - Recent
American Black Bear, Ursus americanus
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Carnivora
Suborder: Caniformia
Ursidae
Family:
G. Fischer de Waldheim, 1817
Genera
• Ailuropoda
• Helarctos
• Melursus
• Ursus
• Tremarctos
• Agriarctos †
• Agriotherium †
• Amphicticeps †
• Amphicynodon †
• Arctotherium †
• Arctodus †
• Indarctos †
• Kolponomos †
• Parictis †
• Plionarctos †
• Ursavus †
Bears are mammals of the family Ursidae. Bears are classified as caniforms, or doglike carnivorans,
with the pinnipeds being their closest living relatives. Although there are only eight living species of bear,
they are widespread, appearing in a wide variety of habitats throughout the Northern Hemisphere and
partially in the Southern Hemisphere. Bears are found in the continents of North America, South America,
Europe, and Asia.
Common characteristics of modern bears include a large body with stocky legs, a long snout, shaggy
hair, plantigrade paws with five nonretractile claws, and a short tail. While the polar bear is mostly
carnivorous and the giant panda feeds almost entirely on bamboo, the remaining six species are omnivorous,
with largely varied diets including both plants and animals.
With the exceptions of courting individuals and mothers with their young, bears are typically solitary
animals. They are generally diurnal, but may be active during the night (nocturnal) or twilight (crepuscular),
particularly around humans. Bears are aided by an excellent sense of smell, and despite their heavy build
and awkward gait, they can run quickly and are adept climbers and swimmers. In autumn some bear species
forage large amounts of fermented fruits which affects their behaviour.[1] Bears use shelters such as caves
and burrows as their dens, which are occupied by most species during the winter for a long period of sleep
similar to hibernation.
Bears have been hunted since prehistoric times for their meat and fur. To this day, they play a
prominent role in the arts, mythology, and other cultural aspects of various human societies. In modern times,
the bear's existence has been pressured through the encroachment on its habitats and the illegal trade of
bears and bear parts, including the Asian bile bear market. The IUCN lists six bear species as vulnerable or
endangered, and even least concern species such as the brown bear are at risk of extirpation in certain
countries. The poaching and international trade of these most threatened populations is prohibited, but still
ongoing.
Contents
[hide]
• 1.1 Fossil bears
• 1.2 Taxonomic revisions of living bear species
• 3 Biology
• 3.1 Morphology
• 3.1.1 Dentition
• 3.2 Distribution and habitat
• 3.3 Behaviour
• 3.4 Vocalizations
• 3.5 Diet and interspecific interactions
• 3.6 Breeding
• 3.7 Winter dormancy
• 4 Relationship with humans
• 4.1 Bears as food and medicine
• 5 Culture
• 5.1 Names
• 5.2 Myth and legend
• 5.3 Symbolic use
• 5.4 Figures of speech
The family Ursidae is one of nine families in the suborder Caniformia, or "doglike" carnivores, within
the order Carnivora. Bears' closest living relatives are the pinnipeds (seals and kin).
The following synapomorphic (derived) traits set bears apart from related families:
• presence of an alisphenoid canal
• paroccipital processes that are large and not fused to the auditory bullae
• auditory bullae are not enlarged
• lacrimal bone is vestigial
• cheek teeth are bunodont and hence indicative of a broad, hypocarnivorous (non-strictly
meat-eating) diet (although hypercarnivorous (strictly meat-eating) taxa are known from the fossil
record)[2]
• carnassials are flattened
Additionally, members of this family possess posteriorly oriented M2 postprotocrista molars,
elongated m2 molars, and a reduction of the premolars.
Modern bears comprise eight species in three subfamilies: Ailuropodinae (monotypic with the giant
panda), Tremarctinae (monotypic with the Spectacled Bear), and Ursinae (containing six species divided into
one to three genera, depending upon authority).
Fossil bears
The earliest members of Ursidae belong to the extinct subfamily Amphicynodontinae, including
Parictis (late Eocene to early middle Miocene, 38-18 million years (Ma) ago) and the slightly younger
Allocyon (early Oligocene, 34-30 Ma), both from North America. These animals looked very different from
today's bears, being small and raccoon-like in overall appearance, and a diet perhaps more similar to that of
a badger. Parictis does not appear in Eurasia and Africa until the Miocene.[3] It is unclear whether late
Eocene ursids were also present in Eurasia, although faunal exchange across the Bering land bridge may
have been possible during a major sea level low stand as early as the late Eocene (~37 Ma) and continuing
into the early Oligocene.[4] European genera morphologically very similar to Allocyon, and also the much
younger American Kolponomos (~18 Ma), are known from the Oligocene, including Amphicticeps and
Amphicynodon.
Plithocyon armagnacensis skull

The raccoon-sized, dog-like Cephalogale is the oldest-known member of the subfamily
Hemicyoninae which first appeared during the middle Oligocene in Eurasia ~30 Ma ago. The subfamily also
includes the younger genera Phoberocyon (~20-15 Ma), and Plithocyon (~15-7 Ma).
A Cephalogale-like species gave rise to the genus Ursavus during the early Oligocene (30-28 Ma);
this genus proliferated into many species in Asia and is ancestral to all living bears. Species of Ursavus
subsequently entered North America together with Amphicynodon and Cephalogale during the early Miocene
(21-18 Ma).
Members of living lineages of bears diverged from Ursavus ~20 Ma ago, likely via the species
Ursavus elmensis. Based on genetic and morphological data, the subfamily Ailuropodinae (pandas) was the
first to diverge from other living bears ~19 Ma ago, although no fossils of this group have been found pre-
dating about 5 Ma.[5]
The New World short-faced bears (Tremarctinae) differentiated from Ursinae following a dispersal
event into North America during the mid Miocene (~13 Ma).[5] They invaded South America (~1 Ma)
following formation of the Isthmus of Panama.[6] Their earliest fossil representative is Plionarctos in North
America (~10-2 Ma). This genus is probably the direct ancestor to the North American short-faced bears
(genus Arctodus), the South American short-faced bears (Pararctotherium and Arctotherium), and the
spectacled bears, Tremarctos, represented by both an extinct North American species ( T. floridanus), and
the lone surviving representative of the Tremarctinae, the South American spectacled bear (T. ornatus).
Fossil of Cave bear (Ursus spelaeus)
The subfamily Ursinae experienced a dramatic proliferation of taxa ~5.3-4.5 Ma ago coincident with
major environmental changes, with the first members of the genus Ursus also appearing around this time.[5]
The sloth bear is a modern survivor of one of the earliest lineages to diverge during this radiation event (~5.3
Ma); it took on its peculiar morphology related to its diet on termites and ants no later than by the early
Pleistocene. By 3-4 Ma ago, the species Ursus minimus appears in the fossil record of Europe, which apart
from size is nearly identical to today's Asiatic black bear. It is likely ancestral to all bears within Ursinae,
perhaps aside from the sloth bear. Two lineages evolved from U. minimus, the black bears (including the sun
bear, the Asiatic black bear, and the American black bear), and the brown bears. Modern brown bears
evolved from U. minimus via Ursus etruscus, which itself is ancestral to both the extinct Pleistocene cave
bear and the ancestor of today's brown and polar bears. Species of Ursinae have migrated repeatedly into N.
America from Eurasia as early as 4 Ma ago during the early Pliocene.[7]
The fossil record of bears is exceptionally good. Direct ancestor-descendent relationships between
individual species are often fairly well-established, with sufficient intermediate forms known to make the
precise cut-off between an ancestral and its daughter species subjective.[8]
Other extinct bear genera include Agriarctos, Indarctos, and Agriotherium (sometimes placed within
hemicyonids).
Taxonomic revisions of living bear species

The giant panda's taxonomy (subfamily Ailuropodinae) has long been debated. Its original
classification by Armand David in 1869 was within the bear genus Ursus, but in 1870 it was reclassified by
Alphonse Milne-Edwards to the raccoon family.[9] In recent studies, the majority of DNA analyses suggest
that the giant panda has a much closer relationship to other bears and should be considered a member of the
family Ursidae.[10] Estimates of divergence dates place the giant panda as the most ancient offshoot among
living taxa within Ursidae, having split from other bears 17.9 to 22.1 Ma ago.[5] The red panda was included
within Ursidae in the past. However, more recent research does not support such a conclusion and instead
places it in its own family Ailuridae, in superfamily Musteloidea along with Mustelidae, Procyonidae, and
Mephitidae.[11][12][13] Multiple similarities between the two pandas, including the presence of false thumbs,
are thus thought to represent an example of convergent evolution for feeding primarily on bamboo.
There is also evidence that, unlike their neighbors elsewhere, the brown bears of Alaska's ABC
islands are more closely related to polar bears than they are to other brown bears in the world. Researchers
Gerald Shields and Sandra Talbot of the University of Alaska Fairbanks Institute of Arctic Biology studied the
DNA of several samples of the species and found that their DNA is different from that of other brown bears.
The researchers discovered that their DNA was unique compared to brown bears anywhere else in the world.
The discovery has shown that while all other brown bears share a brown bear as their closest relative, those
of Alaska's ABC Islands differ and share their closest relation with the polar bear.[14] There is also the very
rare Tibetan blue bear, which is a type of brown bear. This animal has never been photographed.
Koalas are often referred to as bears due to their appearance; they are not bears, however, but
marsupials.
Classification
Brown bear Ursus arctos, at the Moscow Zoo

Asian black bear Ursus thibetanus, at the Wrocław Zoo, Poland
Sun bear Helarctos malayanus, at the Columbus Zoo
Giant panda Ailuropoda melanoleuca, "Tian Tian"

• Family Ursidae
• Subfamily Ailuropodinae
• †Ailurarctos
• †Ailurarctos lufengensis
• †Ailurarctos yuanmouenensis
• Ailuropoda (pandas)
• †Ailuropoda baconi
• †Ailuropoda fovealis
• Ailuropoda melanoleuca, giant panda
• Ailuropoda melanoleuca melanoleuca , giant panda
• Ailuropoda melanoleuca qinlingensis , Qinling panda
• †Ailuropoda microta
• †Ailuropoda wulingshanensis
• Subfamily Tremarctinae
• Tremarctos (Spectacled bears)
• Tremarctos ornatus, spectacled bear
• †Tremarctos floridanus
• †Arctodus
• †Arctodus simus
• †Arctodus pristinus
• †Arctotherium
• †Arctotherium angustidens
• †Arctotherium bonariense
• †Arctotherium brasilense
• †Arctotherium latidens
• †Arctotherium tarijense
• †Arctotherium vetustum
• †Arctotherium wingei
• †Plionarctos
• †Plionarctos edensis
• †Plionarctos harroldorum
• Subfamily Ursinae
• †Agriotherium
• †Agriotherium inexpetans
• †Agriotherium schneideri
• †Agriotherium sivalensis
• Helarctos
• Helarctos malayanus, Sun bear
• Helarctos malayanus malayanus
• Helarctos malayanus euryspilus, Borneo sun bear
• †Indarctos
• †Indarctos anthraciti
• †Indarctos arctoides
• †Indarctos atticus
• †Indarctos nevadensis
• †Indarctos oregonensis
• †Indarctos salmontanus
• †Indarctos vireti
• †Indarctos zdanskyi
• Melursus
• Melursus ursinus, sloth bear
• Melursus ursinus inornatus, Sri Lankan sloth bear
• Melursus ursinus ursinus, Indian sloth bear
• †Ursavus
• †Ursavus brevirhinus
• †Ursavus depereti
• †Ursavus elmensis
• †Ursavus pawniensis
• †Ursavus primaevus
• Ursus
• †Ursus abstrusus
• Ursus americanus, American black bear
• Ursus americanus altifrontalis, Olympic black bear
• Ursus americanus amblyceps, New Mexico black bear
• Ursus americanus americanus, Eastern black bear
• Ursus americanus californiensis, California black bear
• Ursus americanus carlottae, Haida Gwaii black bear or
Queen Charlotte black bear
• Ursus americanus cinnamomum, cinnamon bear
• Ursus americanus emmonsii, Glacier bear
• Ursus americanus eremicus, Mexican black bear
• Ursus americanus floridanus, Florida black bear
• Ursus americanus hamiltoni, Newfoundland black bear
• Ursus americanus kermodei, Kermode bear or spirit bear
• Ursus americanus luteolus, Louisiana black bear
• Ursus americanus machetes, West Mexico black bear
• Ursus americanus perniger, Kenai black bear
• Ursus americanus pugnax, Dall black bear
• Ursus americanus vancouveri, Vancouver Island black bear
• Ursus arctos, brown bear
• Ursus arctos arctos, Eurasian brown bear
• Ursus arctos alascensis
• Ursus arctos beringianus, Kamchatka brown bear or Far
Eastern brown bear
• †Ursus arctos californicus, California golden bear
• †Ursus arctos crowtheri, Atlas bear
• †Ursus arctos dalli
• Ursus arctos gobiensis, Gobi bear (very rare)
• Ursus arctos horribilis, grizzly bear
• Ursus arctos isabellinus, Himalayan brown bear or
Himalayan red bear
• Ursus arctos lasiotus, Ussuri brown bear or black grizzly
• Ursus arctos middendorffi, Kodiak bear
• †Ursus arctos nelsoni, Mexican grizzly bear
• Ursus arctos piscator, Bergman's bear (extinct?)
• Ursus arctos pruinosus, Tibetan blue bear or Tibetan bear or
Himalayan blue bear
• Ursus arctos sitkensis
• Ursus arctos syriacus Syrian (brown) bear
• †Ursus deningeri
• †Ursus etruscus
• †Ursus inopinatus, MacFarlane's bear (cryptid; if an authentic
species, extinct)
• †Ursus minimus
• Ursus maritimus, polar bear
• Ursus maritimus maritimus
• †Ursus maritimus tyrannus
• †Ursus rossicus
• †Ursus sackdillingensis
• †Ursus spelaeus, cave bear
• Ursus thibetanus, Asian black bear
• Ursus thibetanus formosanus, Formosan black bear
• Ursus thibetanus gedrosianus
• Ursus thibetanus japonicus
• Ursus thibetanus laniger
• Ursus thibetanus mupinensis
• Ursus thibetanus thibetanus
• Ursus thibetanus ussuricus
• †Kolponomos
• †Kolponomos clallamensis
• †Kolponomos newportensis
The genera Melursus and Helarctos are sometimes also included in Ursus. The Asiatic black bear
and the polar bear used to be placed in their own genera, Selenarctos and Thalarctos which are now placed
at subgenus rank.
A number of hybrids have been bred between American black, brown, and polar bears (see Ursid
hybrids).
Biology
Morphology
Despite being quadrupeds, bears can stand and sit similarly to humans.
Unlike other carnivora, bears have plantigrade hind feet
Bears are generally bulky and robust animals with relatively short legs. Bears are sexually dimorphic
with regard to size, with the males being larger. Larger species tend to show increased levels of sexual
dimorphism in comparison to smaller species, and where a species varies in size across its distribution
individuals from larger sized areas tend also to vary more. Bears are the most massive terrestrial members of
the order Carnivora, with some Polar Bears and Brown Bears weighing over 750 kilograms (1,700 lb). As to
which species is the largest may depend on whether the assessment is based on which species has the
largest individuals (brown bears) or on the largest average size (polar bears). The smallest bears are the Sun
Bears of Asia, which weigh an average of 65 kilograms (140 lb) for the males and 45 kilograms (99 lb) for the
females.[15]
Unlike other land carnivorans, bears are plantigrade. They distribute their weight toward the hind feet
which makes them look lumbering when they walk. They are still quite fast with the brown bear reaching
30 miles per hour (48 km/h) although they are still slower than felines and canines. Bears can stand on their
hind feet and sit up straight with remarkable balance. Bears have non-retractable claws which are used for
digging, climbing, tearing and catching prey. Their ears are rounded.
Bears have an excellent sense of smell, a better sense of smell in fact than the dogs (Canidae), or
possibly any other mammal. This sense of smell is used for signalling between bears (either to warn off rivals
or detect mates) and for finding food. Smell is the principal sense used by bears to find most of their diet.[15]
Dentition
Unlike most other members of the Carnivora, bears have relatively undeveloped carnassial teeth,
and their teeth are adapted for a diet that includes a significant amount of vegetable matter. The canine teeth
are large, and the molar teeth flat and crushing. There is considerable variation in dental formula even within
a given species. It has been suggested that this indicates bears are still in the process of evolving from a
carnivorous to a predominantly herbivorous diet. Polar bears appear to have secondarily re-evolved fully
functional carnassials, as their diet has switched back towards carnivory.[16] The dental formula for living
bears is:
Distribution and habitat

The bears are mostly found in the northern hemisphere, with a single species, the spectacled bear,
occurring in South America. The Atlas Bear, a subspecies of the Brown Bear, was the only bear native to
Africa. It was distributed in North Africa from Morocco to Libya, but has been extinct since around the 1870s.
All the other species are found in North America, Asia and Europe. The most widespread species is the
Brown Bear, which occurs from Western Europe eastwards through Asia to the western areas of North
America. The American Black Bear is restricted to North America, and the Polar bear is restricted to the
Arctic Sea. All the remaining species are Asian.[15]
With the exception of the Polar Bear the bears are mostly forest species. Some species, particularly
the Brown Bear, may inhabit or seasonally use other areas such as alpine scrub or tundra.
Behaviour
While many people think that bears are nocturnal, they are in fact generally diurnal, active for the
most part during the day. The belief that they are nocturnal apparently comes from the habits of bears that
live near humans which engage in some nocturnal activities, such as raiding trash cans or crops while
avoiding humans. The sloth bear of Asia is the most nocturnal of the bears, but this varies by individual and
females with cubs are often diurnal in order to avoid competition with males and nocturnal predators.[15]
Bears are overwhelmingly solitary and are considered to be the most asocial of all the Carnivora. Liaisons
between breeding bears are brief, and the only times bears are encountered in small groups are mothers
with young or occasional seasonal bounties of rich food (such as salmon runs).[15]
Vocalizations
Bears produce a variety of vocalizations such as:
• Moaning: produced mostly as mild warnings to potential threats or in fear.
• Barking: produced during times of alarm, excitement or to give away the animal's position.
• Huffing: made during courtship or between mother and cubs to warn of danger.
• Growling: produced as strong warnings to potential threats or in anger.
• Roaring: used much for the same reasons as growls and also to proclaim territory and for
intimidation.
Diet and interspecific interactions
Asian black bear feeding on berries

Brown bears make use of infrequent but predictable salmon runs in order to feed
Their carnivorous reputation non-withstanding, most bears have adopted a diet of more plant than
animal matter and are completely opportunistic omnivores. Some bears will climb trees in order to obtain
mast (edible vegatative or reproductive parts such as acorns); smaller species which are more able to climb
include a greater amount of this in their diet.[17] Such masts can be very important to the diet of these
species, and mast failures may result in long range movements by bears looking for alternate sources of
food.[18] One exception is the polar bear, which has adopted a diet mainly of marine mammals to survive in
the Arctic. The other exception is the giant panda which has adopted a diet mainly of bamboo. Stable isotope
analysis of the extinct giant short-faced bear (Arctodus simus) shows that it was also an exclusive meat
eater, probably a scavenger.[19] The sloth bear, though not as specialized as the previous two species, has
lost several front teeth usually seen in bears and developed a long, suctioning tongue in order to feed on the
ants, termites and other burrowing insects that they favour. At certain times of the year these insects can
make up 90% of their diet.[20] All bears will feed on any food source that becomes available, and the nature
of that varies seasonally. A study of Asiatic black bears in Taiwan found that they would consume large
numbers of acorns when they were most common, and switch to ungulates in other times of the year.[21]
When taking warm-blooded animals, bears will typically take small or young animals, as they are
easier to catch. Although (besides polar bears) both species of black bear and the brown bear can
sometimes take large prey, such as ungulates.[21][22] Often, bears will feed on other large animals when
they encounter a carcass, whether or not the carcass is claimed by or is the kill of another predator. This
competition is the main source of interspecies conflict. Bears are typically the apex predators in their range
due to their size and power, and can defend a carcass against nearly all comers. Mother bears also can
usually defend their cubs against other predators. The tiger is the only known predator known to regularly
prey on adult bears, including sloth bears, Asiatic black bears, giant pandas, sun bears and small brown
bears.
Breeding
Bear cubs, like this American Black Bear, are sometimes killed by males
The age at which bears reach sexual maturity is highly variable, both between and within species.
Sexual maturity is dependent on body condition, which is in turn dependent upon the food supply available to
the growing individual. In the females of smaller species may have young in as little as two years, whereas
the larger species may not rear young until they are four or even nine years old. First breeding may be even
later in males, where competition for mates may leave younger males without access to females.[15]
American Black Bears mating
The bear's courtship period is very brief. Bears in northern climates reproduce seasonally, usually
after a period of inactivity similar to hibernation, although tropical species breed all year round. Cubs are born
toothless, blind, and bald. The cubs of brown bears, usually born in litters of 1–3, will typically stay with the
mother for two full seasons. They feed on their mother's milk through the duration of their relationship with
their mother, although as the cubs continue to grow, nursing becomes less frequent and cubs learn to begin
hunting with the mother. They will remain with the mother for approximately three years, until she enters the
next cycle of estrus and drives the cubs off. Bears will reach sexual maturity in five to seven years. Male
bears, especially Polar and Brown Bears, will kill and sometimes devour cubs born to another father in order
to induce a female to breed again. Female bears are often successful in driving off males in protection of their
cubs, despite being rather smaller.
Winter dormancy
Polar bear mother is nursing her cub

Many bears of northern regions are assumed to hibernate in the winter. While many bear species do
go into a physiological state often colloquially called "hibernation" or "winter sleep", it is not true hibernation.
In true hibernators, body temperatures drop to near ambient and heart rate slows drastically, but the animals
periodically rouse themselves to urinate or defecate and to eat from stored food. The body temperature of
bears, on the other hand, drops only a few degrees from normal and heart rate slows only slightly. They
normally do not wake during this "hibernation", and therefore do not eat, drink, urinate or defecate the entire
period. Higher body heat and being easily roused may be adaptations, because females give birth to their
cubs during this winter sleep.
Relationship with humans
Polar bear at Wapusk National Park, Canada

See also: Bear danger
Some species, such as the polar bear, American black bear, sloth bear and the brown bear, are
dangerous to humans, especially in areas where they have become used to people. All bears are physically
powerful and are likely capable of fatally attacking a person, but they, for the most part, are shy, are easily
frightened and will avoid humans. Injuries caused by bears are rare, but are often widely reported.[23] The
danger that bears pose is often vastly exaggerated, in part by the human imagination. However, when a
mother feels her cubs are threatened, she will behave ferociously. It is recommended to give all bears a wide
berth because they are behaviorally unpredictable.
Bears may also come into conflict with humans where they raid crops or attack livestock.[24][25]
These problems may be the work of only a few bears but create a climate of conflict as farmers and ranchers
may perceive all losses as due to bears and advocate the preventive removal of all bears.[25] Mitigation
methods may be used to reduce bear damage to crops, and reduce local antipathy towards bears.[24]
Bear danger area closure sign of a type used in Denali National Park in Alaska
Laws have been passed in many areas of the world to protect bears from hunters' habitat
destruction. Public perception of bears is often very positive, as people identify with bears due to their
omnivorous diet, ability to stand on two legs, and symbolic importance,[26] and there is widespread support
for bear protection, at least in more affluent societies.[27] In more rural and poorer regions attitudes may be
more shaped by the dangers posed by bears and the economic costs that they incur to farmers and ranchers.
[25] Some populated areas with bear populations have also outlawed the feeding of bears, including allowing
them access to garbage or other food waste. Bears in captivity have been trained to dance, box, or ride
bicycles; however, this use of the animals became controversial in the late 20th century. Bears were kept for
baiting in Europe at least since the 16th century.
Bears as food and medicine

Many people[citation needed] enjoy hunting bears and eating them. Their meat is dark and stringy,
like a tough cut of beef. In Cantonese cuisine, bear paws are considered a delicacy. The peoples of China,
Japan, and Korea use bears' body parts and secretions (notably their gallbladders and bile) as part of
traditional Chinese medicine. It is believed more than 12,000 bile bears are kept on farms, farmed for their
bile, in China, Vietnam and South Korea.[28] Bear meat must be cooked thoroughly as it can often be
infected with trichinellosis.[29][30][31]
Culture
Names
The English word "bear" comes from Old English bera and belongs to a family of names for the bear
in Germanic languages, in origin from an adjective meaning "brown".[32] In Scandinavia the word for bear is
björn (or bjørn), and is a relatively common given name for males. The use of this name is ancient and has
been found mentioned in several runestone inscriptions.[33] In Germanic culture, the bear was a symbol of
the warrior, as evident from the Old English term beorn which can take the meaning of both "bear" and
"warrior".
The reconstructed Proto-Indo-European name of the bear is *hŕ̥tḱos , whence Sanskrit r̥kṣa, Avestan
arša, Greek ἄρκτος, Latin ursus, Welsh arth (whence perhaps the given name "Arthur"). Also compared is
Hittite ḫartagga-, the name of a monster or predator.[32] In the binomial name of the brown bear, Ursus
arctos, Linné simply combined the Latin and Greek names.
In addition, the Proto-Indo-European word for bear, *hŕ̥tḱos (ancestral to the Greek arktos, Latin
ursus, Welsh arth (cf. Arthur), Albanian ari, Armenian arj, Sanskrit ṛkṣa, Hittite ḫartagga) seems to have been
subject to taboo deformation or replacement in some languages (as was the word for wolf, wlkwos), resulting
in the use of numerous unrelated words with meanings like "brown one" (English bruin) and "honey-eater"
(Slavic medved).[34] Thus some Indo-European language groups do not share the same PIE root. The
theory of the bear taboo is taught to almost all beginning students of Indo-European and historical linguistics;
the putative original PIE word for bear is itself descriptive, because a cognate word in Sanskrit is rakṣas,
meaning "harm, injury".[35]
The female first name "Ursula", originally derived from a Christian saint's name and common in
English- and German-speaking countries, means "little she-bear" (dimunitive of Latin ursa). In Switzerland
the male first name "Urs" is especially popular, whereas the name of the canton and city of Bern is derived
from bär, German for bear.
In Russian and other Slavic languages, the word for bear, "Medved" (медведь), and variants or
derivatives such as Medvedev are common surnames.
The Irish family name "McMahon" means "Son of Bear" in Irish.
In East European Jewish communities, the name "Ber" (‫ — )בער‬Yiddish cognate of "Bear" — has been
attested as a common male first name, at least since the 18th century, and was among others the name of
several prominent Rabbis. The Yiddish "Ber" is still in use among Orthodox Jewish communities in Israel, the
US and other countries.
With the transition from Yiddish to Hebrew under the influence of Zionism, the Hebrew word for
"bear", "Dov" (‫)דב‬, was taken up in contemporary Israel and is at present among the commonly used male
first names in that country.
"Ten Bears" (Paruasemana) was the name of a well-known 19th Century chieftain among the
Comanche. Also among other Native American tribes, bear-related names are attested.
Myth and legend
"En uheldig bjørnejakt" (An Unfortunate Bear Hunt) by Theodor Kittelsen.

Onikuma from Ehon Hyaku Monogatari
According to his hagiography, a bear killed Saint Corbinian's pack horse on the way to Rome and so
the saint commanded it to carry his load. Once he arrived in Rome, however, he let the bear go.
There is evidence of prehistoric bear worship, see Arctic, Arcturus, Great Bear, Berserker, Kalevala.
Anthropologists such as Joseph Campbell have regarded this as a common feature in most of the fishing and
hunting-tribes. The prehistoric Finns, along with most Finno-Ugric peoples, considered the bear as the spirit
of one's forefathers. This is why the bear (karhu) was a greatly respected animal, with several euphemistic
names (such as otso, mesikämmen and kontio). The bear is the national animal of Finland.
This kind of attitude is reflected in the traditional Russian fairy tale "Morozko", whose arrogant
protagonist Ivan tries to kill a mother bear and her cubs — and is punished and humbled by having his own
head turned magically into a bear's head and being subsequently shunned by human society.
"The Brown Bear of Norway" is a Scottish fairy tale telling the adventures of a girl who married a
prince magically turned into a bear, and who managed to get him back into a human form by the force of her
love and after many trials and difficulties.
There has been evidence about early bear worship in China and among the Ainu culture as well (see
Iomante). Korean people in their mythology identify the bear as their ancestor and symbolic animal.
According to the Korean legend, a god imposed a difficult test on a she-bear, and when she passed it the god
turned her into a woman and married her.
The saddled "bear of St. Corbinian" the emblem of Freising, here incorporated in the arms of Pope
Benedict XVI
Legends of saints taming bears are common in the Alpine zone. In the arms of the bishopric of
Freising (see illustration) the bear is the dangerous totem animal tamed by St. Corbinian and made to carry
his civilised baggage over the mountains. A bear also features prominently in the legend of St. Romedius,
who is also said to have tamed one of these animals and had the same bear carry him from his hermitage in
the mountains to the city of Trento.
Coat of Arms of the Abbey of Saint Gall
Similar stories are told of Saint Gall and Saint Columbanus.
This recurrent motif was used by the Church as a symbol of the victory of Christianity over Paganism.
[36] In the Norse settlements of northern England during the tenth century a type of "hogback" grave cover of
a long narrow block of stone with a shaped apex like the roof beam of a long house, is carved with a
muzzled, thus Christianised, bear clasping each gable end. Though the best collection of these is in the
church at Brompton, North Yorkshire,[37] their distribution ranges across northern England and southern
Scotland, with a scattered few in the north Midlands and single survivals in Wales, Cornwall and Ireland; a
late group is found in the Orkneys.
"The Three Bears", Arthur Rackham's illustration to English Fairy Tales, by Flora Annie Steel
Bears are a popular feature of many children's stories including Goldilocks and The Story of the
Three Bears, the Berenstein Bears, and Winnie the Pooh.
The constellations Ursa Major and Ursa Minor represent bears.
Symbolic use
For more details on this topic, see Bears in heraldry.
The British Lion, the Persian Cat and the Russian Bear (see The Great Game)
The Russian bear is a common National personification for Russia (as well as the Soviet Union) and
even Germany. The brown bear is Finland's national animal.
The flag of California
In the United States, the black bear is the state animal of Louisiana, New Mexico, and West Virginia;
the grizzly bear is the state animal of both Montana and California.
In the UK, the bear and staff has long featured on the heraldic arms of Warwickshire county.[38]
Bears appear in the canting arms of Bern and Berlin.
Also, "bear", "bruin", or specific types of bears are popular nicknames or mascots, e.g. for sports
teams (Chicago Bears, California Golden Bears, UCLA Bruins, Boston Bruins); and a bear cub called Misha
was mascot of the 1980 Summer Olympics in Moscow, USSR.
Smokey Bear
Smokey Bear has become a part of American culture since his introduction in 1944. Known to almost
all Americans, he and his message, "Only You Can Prevent Forest Fires" (updated in 2001 to "Only You Can
Prevent Wildfires") has been a symbol of preserving woodlands.[39] Smokey wears a hat similar to one worn
by many U.S. state police officers, giving rise to the CB slang "bear" or "Smokey" for the highway patrol.
The name Beowulf means "bear".[citation needed]
Figures of speech
The physical attributes and behaviours of bears are commonly used in figures of speech in English.
• In the stock market, a bear market is a period of declining prices. Pessimistic forecasting or
negative activity is said to be bearish (due to the stereotypical posture of bears looking downwards),
and one who expresses bearish sentiment is a bear. Its opposite is a bull market, and bullish
sentiment from bulls.
• In gay slang, the term "bear" refers to male individuals who possess physical attributes much
like a bear, such as a heavy build, abundant body hair, and commonly facial hair.
• A bear hug is typically a tight hug that involves wrapping one's arms around another person,
often leaving that person's arms immobile. It was used in the Ronald Reagan political ad "Bear in the
woods".
• Bear tracking - in the old Western states of the U.S. and to this day in the former Dakota
Territory, the expression, "You ain't just a bear trackin'.", is used to mean "You ain't lying" or "That's
for sure" or "You're not just blowing smoke". This expression evolved as an outgrowth of the
experience pioneer hunters and mountainmen had when tracking bear. Bears often lay down false
tracks and are notorious for doubling back on anything tracking them. If you are not following bear
tracks, you are not following false trails or leads in your thoughts, words or deeds.
• In Korean culture a person is referred to as being "like a bear" when they are stubborn or not
sensitive to what is happening around their surroundings. Used as a phrase to call a person
"stubborn bear."
• The Bible compares King David's "bitter warriors", who fight with such fury that they could
overcome many times their number of opponents, with "a bear robbed of her whelps in the field" (2
Samuel 17:8 s:Bible (King James)/2 Samuel#Chapter 17). The term "a bereaved bear" (‫)דב שכול‬,
derived from this Biblical source, is still used in the literary Hebrew of contemporary Israel.
Teddy bears
Main article: Teddy bear
Around the world, many children have stuffed toys in the form of bears.
Scientific/Conservation Organizations
The two authoritative organizations for seeking scientific information (e.g., natural history,
management, conservation, etc.) on bear species of the world are the International Association for Bear
Research & Management (International Bear Association- IBA) and the Bear Specialist Group of the Species
Survival Commission - International Union for the Conservation of Nature.
See also
• Bear hunting
• List of bears
• List of fatal bear attacks in North America
• List of fictional bears
• List of mammals
• List of non-fictional bears
• Mammal classification
• Sankebetsu brown bear incident
References
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http://www.nhm.org/expeditions/rrc/wang/documents/Wangetal2005ShandGolarctoids.pdf. [dead
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3. ^ Kemp, T.S. (2005). The Origin and Evolution of Mammals. Oxford University Press.
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Matheus, P.; Cooper, A.; Slatkin, M.; Pääbo, S.; Hofreiter, M. (2008-07-28). "Mitochondrial genomes
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8. ^ Kurtén, B., 1995. The cave bear story: life and death of a vanished animal, Björn Kurtén,
Columbia University Press
9. ^ Lindburg, Donald G. (2004). Giant Pandas: Biology and Conservation, pp. 7–9. University of
California Press
10.^ Olaf R. P. Bininda-Emonds. "Phylogenetic Position of the Giant Panda". In Lindburg,
Donald G. (2004) Giant Pandas: Biology and Conservation, pp. 11–35. University of California Press
11.^ Flynn, J. J.; Nedbal, M. A.; Dragoo, J. W.; Honeycutt, R. L. (2000). "Whence the Red
Panda?". Molecular Phylogenetics and Evolution 17 (2): 190–199. doi:10.1006/mpev.2000.0819.
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09-23.
12.^ Flynn, J. J.; Finarelli, J. A.; Zehr, S.; Hsu, J.; Nedbal, M. A. (2005). "Molecular phylogeny of
the carnivora (mammalia): assessing the impact of increased sampling on resolving enigmatic
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13.^ Flynn, J. J.; Nedbal, M. A. (1998). "Abstract". Molecular Phylogenetics and Evolution 9 (3):
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15.^ a b c d e f Garshelis, David L. (2009). "Family Ursidae (Bears)". In Wilson, Don; Mittermeier,
Russell. Handbook of the Mammals of the World. Volume 1: Carnivores. Barcelona: Lynx Edicions.
ISBN 978-84-96553-49-1.
16.^ Bunnell, Fred (1984). Macdonald, D.. ed. The Encyclopedia of Mammals. New York: Facts
on File. p. 87. ISBN 978-0-87196-871-5.
17.^ Mattson, David J. (1998). "Diet and Morphology of Extant and Recently Extinct Northern
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mast production on black bear non-hunting mortalities in West Virginia". Ursus 18 (1): 46–53.
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Brown Bears in Eastern Beringia". Quaternary Research 44 (3): 447–453.
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and Geographical Comparisons". Ursus 13: 111–125.
22.^ Zager, Peter; Beecham, John (2006). "The role of American black bears and brown bears
as predators on ungulates in North America". Ursus 17 (2): 95–108. doi:10.2192/1537-
6176(2006)17[95:TROABB]2.0.CO;2.
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2000". Ursus 14 (1): 65–71.
24.^ a b Fredriksson, Gabriella (2005). "Human–sun bear conflicts in East Kalimantan,
Indonesian Borneo". Ursus 16 (1): 130–137. doi:10.2192/1537-
6176(2005)016[0130:HBCIEK]2.0.CO;2.
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Francisco; Castellanos, Armando (2006). "Andean bear–livestock conflicts: a review". Ursus 17 (1): 8–
15. doi:10.2192/1537-6176(2006)17[8:ABCAR]2.0.CO;2.
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Their Biology and Management 9 (1): 43–50. doi:10.2307/3872683. http://jstor.org/stable/3872683.
27.^ Andersone, Žanete; Ozolinš, Jānis (2004). "Public perception of large carnivores in Latvia".
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36.^ Michel Pastoreau (2007)L'ours. Historie d'un roi déchu
37.^ Noted and illustrated in Richard Hall, Viking Age Archaeology 1995:43 and fig. 22.
38.^ WARWICKSHIRE COUNTY COUNCIL Civic heraldry
39.^ "Forest Fire Prevention - Smokey Bear (1944–Present)". Ad Council. 1944-08-09. Archived
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Further reading
• Bears of the World, Terry Domico, Photographs by Terry Domico and Mark Newman, Facts
on File, Inc, 1988, hardcover, ISBN 978-0-8160-1536-8
• The Bear by William Faulkner
• Brunner, Bernd: Bears — A Brief History. New Haven and London: Yale University Press,
2007
External links
Find more about Bears on Wikipedia's sister projects:
Definitions from Wiktionary
Images and media from Commons
Learning resources from Wikiversity
News stories from Wikinews
Quotations from Wikiquote
Source texts from Wikisource
Textbooks from Wikibooks
Species directories Ursidae from Wikispecies
• The Bears Project Information, reports and images of European brown bears and other living
species
• Grizzly Bear Outreach Project Information on the history, biology, and conservation of North
American Grizzly Bears
[hide]v · d · eExtant Carnivora species
Kingdom: Animalia · Phylum: Chordata · Class: Mammalia · Infraclass: Eutheria · Superorder:

Laurasiatheria
[show] Suborder Feliformia
Nandiniidae African palm civet (N.

Nandinia
binotata)
Atilax Marsh Mongoose (A. paludinosus)
Bushy-tailed Mongoose (B. crassicauda) · Jackson's

Bdeogale Mongoose (B. jacksoni) · Black-footed Mongoose (B.
nigripes)
Alexander's Kusimanse (C. alexandri) · Angolan

Crossarchus Kusimanse (C. ansorgei) · Common Kusimanse (C.
obscurus) · Flat-headed Kusimanse (C. platycephalus)
Cynictis Yellow Mongoose (C. penicillata)

[hide]v · d · eHeraldic creatures
Beasts Bear · Boar · Bull · Dog · Camelopard · Hind · Kangaroo ·

Lion · Ox · Stag · Tiger · Wolf (Borz)
Birds Cock · Dove · Eagle · Pelican · Rook
Legendary Alce · Basilisk · Biscione · Cockatrice · Dragon · Enfield

creatures beast · Griffin · Keythong · Tikbalang · Lindworm · Manticore ·
Martlet · Opinicus · Phoenix · Salamander · Turul · Unicorn · Wyvern
Fish Dolphin · Ged · Lucy · Scallop
Others Bat · Bee · Crapaudy · Emmet · Serpent
Retrieved from "http://en.wikipedia.org/wiki/Bear"
Categories: Bears | Predators

W000
Trilobite

For the robot vacuum cleaner, see Electrolux Trilobite.
Trilobite
Trilobites
Temporal range: Atdabanian – Late Permian
PreЄ
g
Kainops invius
Kingdom: Animalia
Arthropoda
Phylum:
Walch, 1771[1]
Orders
• Agnostida
• Asaphida
• Corynexochida
• Harpetida
• Nectaspida
• Redlichiida
• Lichida
• Phacopida
• Proetida
• Ptychopariida
Trilobites (pronounced /ˈtraɪləbaɪt/, meaning "three lobes") are a well-known fossil group of extinct
marine arthropods that form the class Trilobita. The first appearance of trilobites in the fossil record defines
the base of the Atdabanian stage of the Early Cambrian period (526 million years ago), and they flourished
throughout the lower Paleozoic era before beginning a drawn-out decline to extinction when, during the
Devonian, all trilobite orders, with the sole exception of Proetida, died out. Trilobites finally disappeared in the
mass extinction at the end of the Permian about 250 million years ago.
When trilobites first appeared in the fossil record they were already highly diverse and geographically
dispersed. Because trilobites had wide diversity and an easily fossilized exoskeleton an extensive fossil
record was left, with some 17,000 known species spanning Paleozoic time. The study of these fossils has
facilitated important contributions to biostratigraphy, paleontology, evolutionary biology and plate tectonics.
Trilobites are often placed within the arthropod subphylum Schizoramia within the superclass
Arachnomorpha (equivalent to the Arachnata),[2] although several alternative taxonomies are found in the
literature.
Trilobites had many life styles; some moved over the sea-bed as predators, scavengers or filter
feeders and some swam, feeding on plankton. Most life styles expected of modern marine arthropods are
seen in trilobites, with the possible exception of parasitism (where there is still scientific debate).[3] Some
trilobites (particularly the family Olenidae) are even thought to have evolved a symbiotic relationship with
sulfur-eating bacteria from which they derived food.[4]
Contents
[hide]
• 1 Phylogeny
• 2 Relationship to other taxa
• 3 Physical description
• 3.1 Exoskeleton
• 3.1.1 Terminology
• 3.1.2 Cephalon
• 3.1.3 Thorax
• 3.1.4 Pygidium
• 3.1.5 Prosopon (surface sculpture)
• 3.1.6 Spines
• 3.2 Soft body parts
• 3.2.1 Appendages
• 3.2.2 Digestive tract
• 3.2.3 Internal organs
• 3.2.4 Musculature
• 4 Sensory organs
• 4.1 Antennae
• 4.2 Eyes
• 4.3 Sensory pits
• 5 Development
[edit] Phylogeny
Redlichida, such as this Paradoxides, may represent the ancestral trilobites.

Despite their rich fossil record with thousands of genera found throughout the world, the taxonomy
and phylogeny of trilobites have many uncertainties.[5] The systematic division of trilobites into nine distinct
orders is represented by a widely held view that will inevitably change as new data emerges. Except possibly
for the members of order Phacopida, all trilobite orders appeared prior to the end of the Cambrian. Most
scientists believe that order Redlichiida, and more specifically its suborder Redlichiina, contains a common
ancestor of all other orders, with the possible exception of the Agnostina. While many potential phylogenies
are found in the literature, most have suborder Redlichiina giving rise to orders Corynexochida and
Ptychopariida during the Lower Cambrian, and the Lichida descending from either the Redlichiida or
Corynexochida in the Middle Cambrian. Order Ptychopariida is the most problematic order for trilobite
classification. In the 1959 Treatise on Invertebrate Paleontology,[6] what are now members of orders
Ptychopariida, Asaphida, Proetida, and Harpetida were grouped together as order Ptychopariida; subclass
Librostoma was erected in 1990[7] to encompass all of these orders, based on their shared ancestral
character of a natant (unattached) hypostome. The most recently recognized of the nine trilobite orders,
Harpetida, was erected in 2002.[8] The progenitor of order Phacopida is unclear.
[edit] Relationship to other taxa

Once soft-part anatomy had been recovered, the trilobites were originally allied to the Crustacea;
however, this suggestion has since fallen out of favour. A relationship with the Chelicerata, in a clade termed
Arachnomorpha (Arachnata), was in vogue for some time; a position in the Mandibulata (=Myriapoda +
Crustacea + Hexapoda) stem-group may be a more parsimonious alternative.[9]
[edit] Physical description
Cast of Isotelus rex, the largest known trilobite.

When trilobites are found, only the exoskeleton is preserved (often in an incomplete state) in all but a
handful of locations. A few locations (Lagerstätten) preserve identifiable soft body parts (legs, gills,
musculature & digestive tract) and enigmatic traces of other structures (e.g. fine details of eye structure) as
well as the exoskeleton.
Trilobites range in length from 1 millimetre (0.04 in) to 72 centimetres (28 in), with a typical size
range of 3–10 cm (1.2–3.9 in). The world's largest trilobite, Isotelus rex, was found in 1998 by Canadian
scientists in Ordovician rocks on the shores of Hudson Bay.[10]
[edit] Exoskeleton
Trilobite external morphology
The exoskeleton is composed of calcite and
calcium phosphate minerals in a protein lattice of
chitin that covers the upper surface (dorsal) of the
trilobite and curled round the lower edge to
produce a small fringe called the "doublure".
Three distinctive tagmata (sections) are present:
cephalon (head); thorax (body) and pygidium
(tail).
[edit] Terminology
As might be expected for a group of animals
comprising c. 5,000 genera,[11] the morphology
and description of trilobites can be complex.
However, despite morphological complexity and
an unclear position within higher classifications,
The trilobite body is
Trilobites are so divided into three major
named for the three sections (tagmata): 1–
longitudinal lobes: 1 – left cephalon; 2 – thorax; 3–
pleural lobe; 2 – axial lobe; pygidium
3 – right pleural lobe
there are a number of characters that distinguish the trilobites from other arthropods: a generally sub-
elliptical, dorsal, chitinous exoskeleton divided longitudinally into three distinct lobes (from which the group
gets its name); having a distinct, relatively large head shield (cephalon) articulating axially with a thorax
comprising articulated transverse segments, the hindmost of which are almost invariably fused to form a tail
shield (pygidium). When describing differences between trilobite taxa, the presence, size, and shape of the
cephalic features are often mentioned.
During moulting, the exoskeleton generally split between the head and thorax, which is why so many
trilobite fossils are missing one or the other. In most groups facial sutures on the cephalon helped facilitate
moulting. Similar to lobsters and crabs, trilobites would have physically "grown" between the moult stage and
the hardening of the new exoskeleton.
[edit] Cephalon
Main article: Cephalon (arthropod anatomy)
[edit] Thorax
An enrolled phacopid trilobite Phacops rana crassituberculata

The thorax is a series of articulated segments that lie between the cephalon and pygidium. The
number of segments varies between 2 and 61 with most species in the 2 to 16 range.[12]
Each segment consists of the central axial ring and the outer plurae which protected the limbs and
gills. The plurae are sometimes abbreviated to save weight or extended to form long spines. Apodemes are
bulbous projections on the ventral surface of the exoskeleton to which most leg muscles attached, although
some leg muscles attached directly to the exoskeleton.[13] Distinguishing where the thorax ends and the
pygidium begins can be problematic and many segment counts suffer from this problem.[12]
Trilobite fossils are often found "enrolled" (curled up) like modern pill-bugs for protection; evidence
suggests enrollment helped protect against the inherent weakness of the arthropod cuticle that was exploited
by anomalocarid predators.[14]
Some trilobites achieved a fully closed capsule (e.g. Phacops), while others with long pleural spines
(e.g. Selenopeltis) left a gap at the sides or those with a small pygidium (e.g. Paradoxides) left a gap
between the cephalon and pygidium.[12] In Phacops, the pleurae overlap a smooth bevel (facet) allowing a
close seal with the doublure.[13] The doublure carries a panderian notch or protuberance on each segment
to prevent over rotation and achieve a good seal.[13] Even in an agnostid, with only 2 articulating thoracic
segments, the process of enrollment required a complex musculature to contract the exoskeleton and return
to the flat condition.[15]
[edit] Pygidium
The pygidium is formed from a number of segments and the telson fused together. Segments in the
pygidium are similar to the thoracic segments (bearing biramous limbs) but are not articulated. Trilobites can
be described based on the pydigium being micropygous (pydigium smaller than cephalon), isopygous
(pydigium equal in size to cephalon), or macropygous (pydigium larger than cephalon).
[edit] Prosopon (surface sculpture)

Trilobite exoskeletons show a variety of small-scale structures collectively called prosopon. Prosopon
does not include large scale extensions of the cuticle (e.g. hollow pleural spines) but to finer scale features,
such as ribbing, domes, pustules, pitting, ridging and perforations. The exact purpose of the prosopon is not
resolved but suggestions include structural strengthening, sensory pits or hairs, preventing predator attacks
and maintaining aeration while enrolled.[12] In one example, alimentary ridge networks (easily visible in
Cambrian trilobites) might have been either digestive or respiratory tubes in the cephalon and other regions.
[16]
[edit] Spines
Koneprusia brutoni, an example of a species with elaborate spines from the Devonian Hamar
Laghdad Formation, Alnif, Morocco
Some trilobites such as those of the order Lichida evolved elaborate spiny forms, from the Ordovician
until the end of the Devonian period. Examples of these specimens have been found in the Hamar Laghdad
Formation of Alnif in Morocco. There is, however, a serious counterfeiting and fakery problem with much of
the Moroccan material that is offered commercially. Spectacular spined trilobites have also been found in
western Russia; Oklahoma, USA; and Ontario, Canada.
Some trilobites had horns on their heads similar to those of modern beetles. Based on the size,
location, and shape of the horns the most likely use of the horns was combat for mates, making the Asaphida
family Raphiophoridae the earliest exemplars of this behavior.[17] A conclusion likely to be applicable to
other trilobites as well, such as in the Phacopid trilobite genus Walliserops that developed spectacular
tridents.[18]
An exceptionally well preserved trilobite from the Burgess Shale. The antennæ and legs are
preserved as reflective carbon films.
[edit] Soft body parts

Only 21 or so species are described from which soft body parts are preserved,[13][19] so some
features (e.g. the posterior antenniform cerci preserved only in Olenoides serratus)[20] remain difficult to
assess in the wider picture.[21]
[edit] Appendages
Trilobites had a single pair of preoral antennae and otherwise undifferentiated biramous limbs (2, 3 or
4 cephalic pairs, followed by a variable number of thorax + pygidium pairs).[13][19] Each exopodite (walking
leg) had 6 or 7 segments,[19] homologous to other early arthropods.[21] Expodites are attached to the coxa
which also bore a feather-like epipodite, or gill branch, which was used for respiration and, in some species,
swimming.[21] The base of the coxa, the gnathobase, sometimes have heavy, spiny adaptations which were
used to tear at the tissues of prey.[22] The last exopodite segment usually had claws or spines.[13] Many
examples of hairs on the legs suggest adaptations for feeding (as for the gnathobases) or sensory organs to
help with walking.[21]
[edit] Digestive tract

The toothless mouth of trilobites was situated on the rear edge of the hypostome (facing backwards),
in front of the legs attached to the cephalon. The mouth is linked by a small esophagus to the stomach that
lay forward of the mouth, below the glabella. The "intestine" led backwards from there to the pygidium.[13]
The "feeding limbs" attached to the cephalon are thought to have fed food into the mouth, possibly "slicing"
the food on the hypostome and/or gnathobases first. Alternative lifestyles are suggested, with the cephalic
legs used to disturb the sediment to make food available. A large glabella, (implying a large stomach),
coupled with an impendent hypostome has been used as evidence of more complex food sources, i.e.
possibly a carnivorous lifestyle.[3]
[edit] Internal organs

While there is direct and implied evidence for the presence and location of the mouth, stomach and
digestive tract (see above) the presence of heart, brain and liver are only implied (although "present" in many
reconstructions) with little direct geological evidence.[21]
[edit] Musculature
Although rarely preserved, long lateral muscles extended from the cephalon to mid way down the
pygidium, attaching to the axial rings allowing enrollment while separate muscles on the legs tucked them out
of the way.[13]
[edit] Sensory organs

Many trilobites had complex eyes; they also had a pair of antennae. Some trilobites were blind,
probably living too deep in the sea for light to reach them. As such, they became secondarily blind in this
branch of trilobite evolution. Other trilobites (e.g. Phacops rana and Erbenochile erbeni) had large eyes that
were for use in more well lit, predator-filled waters.
[edit] Antennae
The pair of antennae suspected in most trilobites (and preserved in a few examples) were highly
flexible to allow them to be retracted when the trilobite was enrolled. Also, one species ( Olenoides serratus)
preserves antennae-like cerci that project from the rear of the trilobite.[20]
[edit] Eyes
Even the earliest trilobites had complex, compound eyes with lenses made of calcite (a characteristic
of all trilobite eyes), confirming that the eyes of arthropods and probably other animals could have developed
before the Cambrian.[23] Improving eyesight of both predator and prey in marine environments has been
suggested as one of the evolutionary pressures furthering an apparent rapid development of new life forms
during what is known as the Cambrian Explosion.[24]
Trilobite eyes were typically compound, with each lens being an elongated prism.[25] The number of
lenses in such an eye varied: some trilobites had only one, while some had thousands of lenses in a single
eye. In compound eyes, the lenses were typically arranged hexagonally.[16] The fossil record of trilobite eyes
is complete enough that their evolution can be studied through time, which compensates to some extent the
lack of preservation of soft internal parts.[26]
Lenses of trilobites' eyes were made of calcite (calcium carbonate, CaCO3). Pure forms of calcite are
transparent, and some trilobites used crystallographically oriented, clear calcite crystals to form each lens of
each of their eyes.[27] Rigid calcite lenses would have been unable to accommodate to a change of focus
like the soft lens in a human eye would; however, in some trilobites the calcite formed an internal doublet
structure,[28] giving superb depth of field and minimal spherical aberration, as discovered by French scientist
René Descartes and Dutch physicist Christiaan Huygens in the 17th century.[25][28] A living species with
similar lenses is the brittle star Ophiocoma wendtii.[29]
In other trilobites, with a Huygens interface apparently missing, a gradient index lens is invoked with
the refractive index of the lens changing towards the center.[30]
• Holochroal eyes had a great number (sometimes over 15,000) of small (30–100 μm, rarely
larger)[26] lenses. Lenses were hexagonally close packed, touching each other, with a single corneal
membrane covering all lenses.[27] Holochroal eyes had no sclera, the white layer covering the eyes
of most modern arthropods. Holochroal eyes are the ancestral eye of trilobites, and are by far the
most common, found in all orders and through the entirety of the Trilobites' existence.[26] Little is
known of the early history of holochroal eyes; Lower and Middle Cambrian trilobites rarely preserve
the visual surface.[26]
The schizochroal eye of Erbenochile erbenii; the eye shade is unequivocal evidence that some
trilobites were diurnal.[31]
• Schizochroal eyes typically had fewer (to around 700), larger lenses than holochroal eyes
and are found only in Phacopida. Lenses were separate, with each lens having an individual cornea
which extended into a rather large sclera.[27] Schizochroal eyes appear quite suddenly in the early
Ordovician, and were presumably derived from a holochroal ancestor.[26] Field of view (all around
vision), eye placement and coincidental development of more efficient enrollment mechanisms point
to the eye as a more defensive "early warning" system than directly aiding in the hunt for food.[26]
Modern eyes which are functionally equivalent to the schizochroal eye were not thought to exist,[27]
but are found in the modern insect species Xenos peckii.[32]
• Abathochroal eyes are found only in Cambrian Eodiscina, had around 70 small separate
lenses that had individual cornea.[33] The sclera was separate from the cornea, and did not run as
deep as the sclera in schizochroal eyes.[27] Although well preserved examples are sparse in the
early fossil record, abathochroal eyes have been recorded in the lower Cambrian, making them
among the oldest known.[27] Environmental conditions seem to have resulted in the later loss of
visual organs in many Eodiscina.[27]
Secondary blindness is not uncommon, particularly in long lived groups such as the Agnostida and
Trinucleioidea. In Proetida and Phacopina from western Europe and particularly Tropidocoryphinae from
France (where there is good stratigraphic control), there are well studied trends showing progressive eye
reduction between closely related species that eventually leads to blindness.[27]
Several other structures on trilobites have been explained as photo-receptors.[27] Of particular
interest are "macula", the small areas of thinned cuticle on the underside of the hypostome. In some trilobites
macula are suggested to function as simple "ventral eyes" that could have detected night and day or allowed
a trilobite to navigate while swimming (or turned) upside down.[30]
[edit] Sensory pits

There are several types of prosopon that have been suggested as sensory apparatus collecting
chemical or vibrational signals. The connection between large pitted fringes on the cephalon of Harpetida
and Trinucleoidea with corresponding small or absent eyes makes for an interesting possibility of the fringe
as a "compound ear".[27]
[edit] Development
Trilobites grew through successive moult stages called instars, in which existing segments increased
in size and new trunk segments appeared at a sub-terminal generative zone during the anamorphic phase of
development. This was followed by the epimorphic developmental phase, in which the animal continued to
grow and moult, but no new trunk segments were expressed in the exoskeleton. The combination of
anamorphic and epimorphic growth constitutes the hemianamorphic developmental mode that is common
among many living arthropods.[34]
Trilobite development was unusual in the way in which articulations developed between segments,
and changes in the development of articulation gave rise to the conventionally recognized developmental
phases of the trilobite life cycle (divided into 3 stages), which are not readily compared with those of other
arthropods. Actual growth and change in external form of the trilobite would have occurred when the trilobite
was soft shelled, following moulting and before the next exoskeleton hardened.[35]
Trilobite larvae are known from the Cambrian to the Carboniferous[36] and from all sub-orders.[35]
[37] As instars from closely related taxa are more similar than instars from distantly related taxa, trilobite
larvae provide morphological information important in evaluating high-level phylogenetic relationships among
trilobites.[35]
By comparison with living arthropods, trilobites are thought to have reproduced sexually, producing
eggs,[38] albeit without undoubted examples in the fossil record.[35] Some species may have kept eggs or
larvae in a brood pouch forward of the glabella,[39] particularly when the ecological niche was challenging to
larvae.[4] Size and morphology of the first calcified stage are highly variable between (but not within) trilobite
taxa, suggesting some trilobites passed through more growth within the egg than others. Early
developmental stages prior to calcification of the exoskeleton are a possibility (suggested for fallotaspids),
[40] but so is calcification and hatching coinciding.[35]
The earliest post-embryonic trilobite growth stage known with certainty are the "protaspid" stages
(anamorphic phase).[35] Starting with an indistinguishable proto-cephalon and proto-pygidium (anaprotaspid)
a number of changes occur ending with a transverse furrow separating the proto-cephalon and proto-
pygidium (metaprotaspid) that can continue to add segments. Segments are added at the posterior part of
the pygidium but, all segments remain fused together.[35][37]
The "meraspid" stages (anamorphic phase) are marked by the appearance of an articulation
between the head and the fused trunk. Prior to the onset of the first meraspid stage the animal had a two-part
structure — the head and the plate of fused trunk segments, the pygidium. During the meraspid stages, new
segments appeared near the rear of the pygidium as well as additional articulations developing at the front of
the pygidium, releasing freely articulating segments into the thorax. Segments are generally added one per
moult (although two per moult and one every alternate moult are also recorded), with number of stages equal
to the number of thoracic segments. A substantial amount of growth, from less than 25% up to 30%–40%,
probably took place in the meraspid stages.[35]
The "holaspid" stages (epimorphic phase) commence when a stable, mature number of segments
has been released into the thorax. Moulting continued during the holaspid stages, with no changes in
thoracic segment number.[35] Some trilobites are suggested to have continued moulting and growing
throughout the life of the individual, albeit at a slower rate on reaching maturity.
Some trilobites showed a marked transition in morphology at one particular instar, which has been
called "trilobite metamorphosis". Radical change in morphology is linked to the loss or gain of distinctive
features that mark a change in mode of life.[41] A change in lifestyle during development has significance in
terms of evolutionary pressure, as the trilobite could pass through several ecological niches on the way to
adult development and changes would strongly affect survivor-ship and dispersal of trilobite taxa.[35] It is
worth noting that trilobites with all protaspid stages solely planktonic and later meraspid stages benthic (e.g.
asaphids) failed to last through the Ordovician extinctions, while trilobites that were planktonic for only the
first protaspid stage before metamorphosing into benthic forms survived (e.g. lichids, phacopids).[41] Pelagic
larval life-style proved ill-adapted to the rapid onset of global climatic cooling and loss of tropical shelf
habitats during the Ordovician.[10]
Walliserops trifurcatus, from Djebel Oufaten, Morocco

The earliest trilobites known from the fossil record are fallotaspids (order Redlichiida, suborder
Olenellina, superfamily Fallotaspidoidea) and bigotinids (order Ptychopariida, superfamily
Ellipsocephaloidea) dated to some 540 to 520 million years ago.[42][43] Contenders for the earliest trilobites
include Profallotaspis jakutensis (Siberia), Fritzaspis sp. (western USA), Hupetina antiqua (Morocco)[44] and
Serrania gordaensis (Spain).[45] All trilobites are thought to have originated in present day Siberia, with
subsequent distribution and radiation from this location.[43]
Fallotaspids lack facial sutures, that is to say fallotaspids are thought to pre-date facial sutures (as
opposed to a group that secondarily lost facial sutures).[43] Fallotaspids are strongly suggested to be the
ancestral trilobite stock: absence of facial sutures; apparently un-calcified protaspid stages and fallotaspids
underlying (pre-dating) or co-existing with all other trilobite occurrences.[40] However, recent
developments[46] suggest the picture is more complicated,[47] and likely to change as more information
comes to light.[43]
[edit] Origins
Early trilobites show all of the features of the trilobite group as a whole; there do not seem to be any
transitional or ancestral forms showing or combining the features of trilobites with other groups (e.g. early
arthropods).[16] Morphological similarities between trilobites and early arthropod-like creatures such as
Spriggina, Parvancorina, and other "trilobitomorphs" of the Ediacaran period of the Precambrian are
ambiguous enough to make detailed analysis of their ancestry far from compelling.[48][40] Morphological
similarities between early trilobites and other Cambrian arthropods (e.g. the Burgess Shale fauna and the
Maotianshan shales fauna) make analysis of ancestral relationships difficult.[49] However, it is still
reasonable to assume that the trilobites share a common ancestor with other arthropods prior to the
Ediacaran-Cambrian boundary. Evidence suggests significant diversification had already occurred prior to
the preservation of trilobites in the fossil record, easily allowing for the "sudden" appearance of diverse
trilobite groups with complex, derived characteristics (e.g. eyes).[23][43]
[edit] Radiation and extinction

For such a long lasting group of animals, it is no surprise that trilobite evolutionary history is marked
by a number of extinction events where unsuccessful groups perished while surviving groups diversified to fill
ecological niches with more successful adaptations. Generally, trilobites maintained high diversity levels
throughout the Cambrian and Ordovician periods before entering a drawn out decline in the Devonian
culminating in final extinction of the last few survivors at the end of the Permian period.[16]
[edit] Evolutionary trends

Principal evolutionary trends from primitive morphologies (e.g. eoredlichids)[50] include the origin of
new types of eyes, improvement of enrollment and articulation mechanisms, increased size of pygidium
(micropygy to isopygy) and development of extreme spinosity in certain groups.[16] Changes also included
narrowing of the thorax and increasing or decreasing numbers of thoracic segments.[50] Specific changes to
the cephalon are also noted; variable glabella size and shape, position of eyes and facial sutures &
hypostome specialization.[50] Several morphologies appeared independently within different major taxa (e.g.
eye reduction or miniaturization).[50]
[edit] Pre-Cambrian
Phylogenetic biogeographic analysis of Early Cambrian Olenellidae and Redlichidae suggests that a
uniform trilobite fauna existed over Laurentia, Gondwana and Siberia before the tectonic breakup of the
super-continent Pannotia between 600 million years ago and 550 million years ago.[43] Tectonic break up of
Pannotia then allowed for the diversification and radiation expressed later in the Cambrian as the distinctive
olenellid province (Laurentia, Siberia and Baltica) and the separate Redlichid province (Australia, Antarctica
and China).[43][51] Break up of Pannotia significantly pre-dates the first appearance of trilobites in the fossil
record, supporting a long and cryptic development of trilobites extending perhaps as far back as 700 million
years ago or possibly further.[51]
[edit] Cambrian
Olenoides erratus from the Mt. Stephen Trilobite Beds (Middle Cambrian) near Field, British
Columbia, Canada
Very shortly after trilobite fossils appeared in the lower Cambrian, they rapidly diversified into the
major orders that typified the Cambrian - Redlichiida, Ptychopariida, Agnostida and Corynexochida. The first
major crisis in the trilobite fossil record occurred in the Middle Cambrian, surviving orders developed
isopygus or macropygius bodies and developed thicker cuticles, allowing better defense against predators
(see Thorax above).[14] The end Cambrian mass extinction event marked a major change in trilobite fauna;
almost all Redlichiida (including the Olenelloidea) and most Late Cambrian stocks went extinct.[16] A
continuing decrease in Laurentian continental shelf area[10] is recorded at the same time as the extinctions,
suggesting major environmental upheaval.
[edit] Ordovician
Cheirurus sp., middle Ordovician age, Volkhov River, Russia

The Early Ordovician is marked by vigorous radiations of articulate brachiopods, bryozoans,
bivalves, echinoderms, and graptoloids with many groups appearing in the fossil record for the first time.[16]
Although intra-species trilobite diversity seems to have peaked during the Cambrian,[52] trilobites were still
active participants in the Ordovician radiation event with a new fauna taking over from the old Cambrian one.
[53] Phacopida and Trinucleioidea are characteristic forms, highly differentiated and diverse, most with
uncertain ancestors.[16] The Phacopida and other "new" clades almost certainly had Cambrian forebears,
but the fact that they have avoided detection is a strong indication that novel morphologies were developing
very rapidly.[40] Changes within the trilobite fauna during the Ordovician foreshadowed the mass extinction
at the end of the Ordovician allowing many families to continue into the Silurian with little disturbance.[53]
Ordovician trilobites were successful at exploiting new environments, notably reefs. However, the end
Ordovician mass extinction did not leave the trilobites unscathed; some distinctive and previously successful
forms such as the Trinucleioidea and Agnostida became extinct. The Ordovician marks the last great
diversification period amongst the trilobites, very few entirely new patterns of organisation arose post-
Ordovician; later evolution in trilobites was largely a matter of variations upon the Ordovician themes. By the
Ordovician mass extinction vigorous trilobite radiation has stopped and gradual decline beckons.[16]
[edit] Silurian and Devonian
Phacopid trilobite, Devonian age, Ohio, United States

Most Early Silurian families constitute a subgroup of the Late Ordovocian fauna. Few, if any, of the
dominant Early Ordovician fauna survived to the end of the Ordovician, yet 74% of the dominant Late
Ordovician trilobite fauna survived the Ordovician. Late Ordovician survivors account for all post-Ordovician
trilobite groups except the Harpetida.[53]
Silurian and Devonian trilobite assemblages are superficially similar to Ordovician assemblages,
dominated by Lichida and Phacopida (including the well-known Calymenina). However, a number of
characteristic forms do not extend far into the Devonian and almost all the remainder were wiped out by a
series of drastic Middle and Late Devonian extinctions.[50] Three orders and all but five families were
exterminated by the combination of sea level changes and a break in the redox equilibrium (a meteorite
impact has also been suggested as a cause).[50] Only a single order, the Proetida, survived into the
Carboniferous.[16]
[edit] Carboniferous and Permian

The Proetida survived for millions of years, continued through the Carboniferous period and lasted
until the end of the Permian (where the vast majority of species on Earth were wiped out).[16] It is unknown
why order Proetida alone survived the Devonian. The Proetida maintained relatively diverse faunas in deep
water and shallow water, shelf environments throughout the Carboniferous.[50] For many millions of years
the Proetida existed untroubled in their ecological niche.[16] An analogy would be today's crinoids which
mostly exist as deep water species; in the Paleozoic era, vast 'forests' of crinoids lived in shallow near-shore
environments.[16]
[edit] Final extinction

Exactly why the trilobites became extinct is not clear; with repeated extinction events (often followed
by apparent recovery) throughout the trilobite fossil record, a combination of causes is likely. After the
extinction event at the end of the Devonian period, what trilobite diversity remained was bottlenecked into the
order Proetida. Decreasing diversity[54] of genera limited to shallow water, shelf habitats coupled with a
drastic lowering of sea level (regression) meant that the final decline of trilobites happened shortly before the
end Permian mass extinction event.[50] With so many marine species involved in the Permian extinction, the
end of nearly 300 million successful years for the trilobite is hardly surprising.[54]
The closest extant relatives of trilobites may be the horseshoe crabs,[42] or the cephalocarids.[55]
[edit] Fossil distribution
Cruziana, fossil trilobite furrowing trace

A trilobite fragment (T) in a thin-section of an Ordovician limestone; E=echinoderm; scale bar is 2 mm
Trilobites appear to have been exclusively marine organisms, since the fossilized remains of
trilobites are always found in rocks containing fossils of other salt-water animals such as brachiopods,
crinoids, and corals. Within the marine paleoenvironment, trilobites were found in a broad range from
extremely shallow water to very deep water. Trilobites, like brachiopods, crinoids, and corals, are found on all
modern continents, and occupied every ancient ocean from which Paleozoic fossils have been collected. The
remnants of trilobites can range from the preserved body to pieces of the exoskeleton, which it sheds in the
process known as ecdysis. In addition, the tracks left behind by trilobites living on the sea floor are often
preserved as trace fossils.
There are three main forms of trace fossils associated with trilobites: Rusophycus; Cruziana &
Diplichnites – such trace fossils represent the preserved life activity of trilobites active upon the sea floor.
Rusophycus, the resting trace, are trilobite excavations which involve little or no forward movement and
ethological interpretations suggest resting, protection and hunting.[56] Cruziana, the feeding trace, are
furrows through the sediment, which are believed to represent the movement of trilobites while deposit
feeding.[57] Many of the Diplichnites fossils are believed to be traces made by trilobites walking on the
sediment surface.[57] However, care must be taken as similar trace fossils are recorded in freshwater[58]
and post Paleozoic deposits,[59] representing non-trilobite origins.
Trilobite fossils are found worldwide, with many thousands of known species. Because they
appeared quickly in geological time, and moulted like other arthropods, trilobites serve as excellent index
fossils, enabling geologists to date the age of the rocks in which they are found. They were among the first
fossils to attract widespread attention, and new species are being discovered every year.
Rusophycus, a "resting trace" of a trilobite; Ordovician of southern Ohio. Scale bar is 10 mm.
A famous location for trilobite fossils in the United Kingdom is Wren's Nest, Dudley in the West
Midlands, where Calymene blumenbachi is found in the Silurian Wenlock Group. This trilobite is featured on
the town's coat of arms and was named the Dudley Bug or Dudley Locust by quarrymen who once worked
the now abandoned limestone quarries. Llandrindod Wells, Powys, Wales, is another famous trilobite
location. The well-known Elrathia kingi trilobite is found in abundance in the Cambrian age Wheeler Shale of
Utah.[60]
Spectacularly preserved trilobite fossils, often showing soft body parts (legs, gills, antennae, etc.)
have been found in British Columbia, Canada (the Cambrian Burgess Shale and similar localities); New York
State, U.S.A. (Ordovician Walcott-Rust quarry, near Russia, and Beecher's Trilobite Bed, near Rome); China
(Lower Cambrian Maotianshan Shales near Chengjiang); Germany (the Devonian Hunsrück Slates near
Bundenbach) and, much more rarely, in trilobite-bearing strata in Utah (Wheeler Shale and other formations),
Ontario, and Manuels River, Newfoundland and Labrador.
[edit] Importance
The study of Paleozoic trilobites in the Welsh-English borders by Niles Eldredge was fundamental in
formulating and testing punctuated equilibrium as a mechanism of evolution.[61][62][63]
Identification of the 'Atlantic' and 'Pacific' trilobite faunas in North America and Europe[64] implied the
closure of the Iapetus Ocean (producing the Iapetus suture),[65] thus providing important supporting
evidence for the theory of continental drift.[66][67]
Trilobites have been important in estimating the rate of speciation during the period known as the
Cambrian Explosion because they are the most diverse group of metazoans known from the fossil record of
the early Cambrian.[68][69]
Trilobites are excellent stratigraphic markers of the Cambrian period: researchers who find trilobites
with alimentary prosopon, and a micropygium, have found Early Cambrian strata.[70] Most of the Cambrian
stratigraphy is based on the use of trilobite marker fossils.[71][72][73]
Trilobites are the state fossils of Ohio (Isotelus), Wisconsin (Calymene celebra) and Pennsylvania
(Phacops rana).
Until the early 1900s, the Ute Indians of Utah wore trilobites, which they called pachavee (little water
bug), as amulets. A hole was bored in the head and the fossil was worn on a string.[74]
[edit] See also

Paleontology portal
Arthropods portal
• Prehistoric life
• List of trilobites
• Media related to Trilobita at Wikimedia Commons
• Data related to Trilobita at Wikispecies
[edit] References
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• Gon III, Sam, A Guide to the Orders of Trilobite, http://www.trilobites.info/ . (A site with
information covering trilobites from all angles. Includes many line drawings and photographs.)
• The Virtual Fossil Museum - Class Trilobita - Including extensive photographs organized by
taxonomy and locality.
• Western Trilobite Association
• Kevin's Trilobite Gallery - a collection of photographs of trilobite fossils
• Canadian trilobite web site: photographs of trilobite fossils
• The Paleontological Society
• Chisholm, Hugh, ed (1911). "Trilobites". Encyclopædia Britannica (Eleventh ed.).
Cambridge University Press.
Retrieved from "http://en.wikipedia.org/wiki/Trilobite"
Categories: Trilobites | Fossils | Prehistoric life | Arthropods | Prehistoric arthropods | Symbols of

Ohio | Symbols of Pennsylvania | Symbols of Wisconsin
W000
Beetle

"Beetles" redirects here. For the band, see The Beatles. For the car, see Volkswagen Beetle.
This article is about the insect. For other uses, see Beetle (disambiguation).
Beetle
PreЄ
g
Pennsylvanian – Recent
Phyllobius glaucus, a species of weevil
Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Subclass: Pterygota
Infraclass: Neoptera
Superorder: Endopterygota
Coleoptera
Order:
Linnaeus, 1758
Suborders
• Adephaga
• Archostemata
• Myxophaga
• Polyphaga
See subgroups of the order Coleoptera
Beetles are insects of the order Coleoptera (pronounced /koʊliːˈɒptərə/; from Greek κολεός, koleos,
"sheath"; and πτερόν, pteron, "wing", thus "sheathed wing"), which contains more species than any other
order in the animal kingdom, constituting about 25% of all known life-forms.[1] About 40% of all described
insect species are beetles (about 400,000 species[2]), and new species are discovered frequently. Some
estimates put the total number of species, described and undescribed, at as high as 100 million, but 1 million
is a more likely figure.[3] The largest taxonomic family, the Curculionidae (the weevils or snout beetles), also
belongs to this order .
Beetles can be found in almost all habitats, but are not known to occur in the sea or in the polar
regions. They interact with their ecosystems in several ways. They often feed on plants and fungi, break
down animal and plant debris, and eat other invertebrates. Some species are prey of various animals
including birds and mammals. Certain species are agricultural pests, such as the Colorado potato beetle
Leptinotarsa decemlineata, the boll weevil Anthonomus grandis, the red flour beetle Tribolium castaneum,
and the mungbean or cowpea beetle Callosobruchus maculatus, while other species of beetles are important
controls of agricultural pests. For example, beetles in the family Coccinellidae ("ladybirds" or "ladybugs")
consume aphids, scale insects, thrips, and other plant-sucking insects that damage crops.
Contents
[hide]
• 1 Description
• 2 Development
• 3 Physiology and behaviour
• 3.2 Defence
• 3.3 Feeding
• 3.4 Adaptations to the environment
• 4 Evolutionary history and classification
• 5 Impact on humans
• 5.1 Pests
• 5.2 Beneficial organisms
• 5.3 Beetles in ancient Egypt and other cultures
• 6 Study and collection
• 7 See also
• 8 References
• 8.1 General references
• 8.2 Cited references
• 9.1 Global
• 9.2 Regional
[edit] Description
The name "Coleoptera" was given by Aristotle for the hardened shield-like forewing (coleo = sheath +
ptera = wing).[1]
A cockchafer (Melolontha melolontha, Scarabaeidae) with its elytra raised, exposing the
membranous flight wings
Other characters of this group which are believed to be monophyletic include a holometabolous life
cycle; having a prothorax that is distinct from and freely articulating with the mesothorax; the meso- and
meta-thoracic segments fusing to form a pterothorax; a depressed body shape with the legs on the ventral
surface; the coxae of legs recessed into cavities formed by heavily sclerotised thoracic sclerites; the
abdominal sternites more sclerotised than the tergites; antennae with 11 or fewer segments; and terminal
genitalic appendages retracted into the abdomen and invisible at rest.[1]
The general anatomy of a beetle is quite uniform, although specific organs and appendages may
vary greatly in appearance and function between the many families in the order. Like all insects, beetles'
bodies are divided into three sections: the head, the thorax, and the abdomen. When viewed from below, the
thorax is that part from which all three pairs of legs and both pairs of wings arise. The abdomen is everything
posterior to the thorax. When viewed from above, most beetles appear to have three clear sections, but this
is deceptive: on the beetle's upper surface, the middle "section" is a hard plate called the pronotum, which is
only the front part of the thorax; the back part of the thorax is concealed by the beetle's wings. Like all
arthropods, beetles are segmented organisms, and all three of the major sections of the body are themselves
composed of several further segments, although these are not always readily discernible. This further
segmentation is usually best seen on the abdomen.
Beetles are generally characterised by a particularly hard exoskeleton and hard forewings (elytra).
The beetle's exoskeleton is made up of numerous plates called sclerites, separated by thin sutures. This
design creates the armoured defences of the beetle while maintaining flexibility. The elytra are not used for
flight, but tend to cover the hind part of the body and protect the second pair of wings (alae). The elytra must
be raised in order to move the hind flight wings. A beetle's flight wings are crossed with veins and are folded
after landing, often along these veins, and are stored below the elytra.
In some beetles, the ability to fly has been lost. These include some ground beetles (family
Carabidae) and some "true weevils" (family Curculionidae), but also some desert and cave-dwelling species
of other families. Many of these species have the two elytra fused together, forming a solid shield over the
abdomen. In a few families, both the ability to fly and the elytra have been lost, with the best known example
being the glow-worms of the family Phengodidae, in which the females are larviform throughout their lives.
Head of Cephalota circumdata, showing the compound eyes and mouthparts
Beetles have mouthparts similar to those of grasshoppers. Of these parts, the most commonly known
are probably the mandibles, which appear as large pincers on the front of some beetles. The mandibles are a
pair of hard, often tooth-like structures that move horizontally to grasp, crush, or cut food or enemies (see
defence, below). Two pairs of finger-like appendages are found around the mouth in most beetles, serving to
move food into the mouth. These are the maxillary and labial palpi.
The eyes are compound and may display remarkable adaptability, as in the case of whirligig beetles
(family Gyrinidae), in which the eyes are split to allow a view both above and below the waterline. Other
species also have divided eyes – some longhorn beetles (family Cerambycidae) and weevils – while many
beetles have eyes that are notched to some degree. A few beetle genera also possess ocelli, which are
small, simple eyes usually situated farther back on the head (on the vertexes).
Beetles' antennae are primarily organs of smell, but may also be used to feel out a beetle's
environment physically. They may also be used in some families during mating, or among a few beetles for
defence. Antennae vary greatly in form within the Coleoptera, but are often similar within any given family. In
some cases, males and females of the same species will have different antennal forms. Antennae may be
clavate (flabellate and lamellate are sub-forms of clavate, or clubbed antennae), filiform, geniculate,
moniliform, pectinate, or serrate.
Acilius sulcatus, a diving beetle showing hind legs adapted for life in water
The legs, which are multi-segmented, end in two to five small segments called tarsi. Like many other
insect orders beetles bear claws, usually one pair, on the end of the last tarsal segment of each leg. While
most beetles use their legs for walking, legs may be variously modified and adapted for other uses. Among
aquatic families – Dytiscidae, Haliplidae, many species of Hydrophilidae and others – the legs, most notably
the last pair, are modified for swimming and often bear rows of long hairs to aid this purpose. Other beetles
have fossorial legs that are widened and often spined for digging. Species with such adaptations are found
among the scarabs, ground beetles, and clown beetles (family Histeridae). The hind legs of some beetles,
such as flea beetles (within Chrysomelidae) and flea weevils (within Curculionidae), are enlarged and
designed for jumping.
Oxygen is obtained via a tracheal system. Air enters a series of tubes along the body through
openings called spiracles, and is then taken into increasingly finer fibres. Pumping movements of the body
force the air through the system.
Beetles have haemolymph instead of blood, and the open circulatory system of the beetle is driven
by a tube-like heart attached to the top inside of the thorax.
[edit] Development
Larva of the varied carpet beetle, (Anthrenus verbasci, Dermestidae)

Larva of a longhorn beetle (Cerambycidae)
Beetles are endopterygotes with complete metamorphosis.
A single female may lay from several dozen to several thousand eggs during her lifetime. Eggs are
usually laid according to the substrate the larva will feed on upon hatching. Among others, they can be laid
loose in the substrate (e.g. flour beetle), laid in clumps on leaves (e.g. Colorado potato beetle), or individually
attached (e.g. mungbean beetle and other seed borers) or buried in the medium (e.g. carrot weevil).
The larva is usually the principal feeding stage of the beetle life cycle. Larvae tend to feed
voraciously once they emerge from their eggs. Some feed externally on plants, such as those of certain leaf
beetles, while others feed within their food sources. Examples of internal feeders are most Buprestidae and
longhorn beetles. The larvae of many beetle families are predatory like the adults (ground beetles, ladybirds,
rove beetles). The larval period varies between species but can be as long as several years.
A scarabaeiform larvae known as a Curl grub.
Beetle larvae can be differentiated from other insect larvae by their hardened, often darkened head,
the presence of chewing mouthparts, and spiracles along the sides of the body. Like adult beetles, the larvae
are varied in appearance, particularly between beetle families. Beetles whose larvae are somewhat flattened
and are highly mobile are the ground beetles, some rove beetles, and others; their larvae are described as
campodeiform. Some beetle larvae resemble hardened worms with dark head capsules and minute legs.
These are elateriform larvae, and are found in the click beetle (Elateridae) and darkling beetle
(Tenebrionidae) families. Some elateriform larvae of click beetles are known as wireworms. Beetles in the
families of the Scarabaeoidea have short, thick larvae described as scarabaeiform, but more commonly
known as grubs.
All beetle larvae go through several instars, which are the developmental stages between each
moult. In many species the larvae simply increase in size with each successive instar as more food is
consumed. In some cases, however, more dramatic changes occur. Among certain beetle families or genera,
particularly those that exhibit parasitic lifestyles, the first instar (the planidium) is highly mobile in order to
search out a host, while the following instars are more sedentary and remain on or within their host. This is
known as hypermetamorphosis; examples include the blister beetles (family Meloidae) and some rove
beetles, particularly those of the genus Aleochara.
As with all endopterygotes, beetle larvae pupate, and from this pupa emerges a fully formed, sexually
mature adult beetle, or imago. Adults have an extremely variable lifespan, from weeks to years, depending
on the species.
[edit] Physiology and behaviour

[edit] Reproduction
Punctate flower chafers (Neorrhina punctata, Scarabaeidae) mating

Beetles may display extremely intricate behaviour when mating. Pheromone communication is likely
to be important in the location of a mate.
Conflict can play a part in the mating rituals of species such as burying beetles (genus Nicrophorus)
where conflicts between males and females rage until only one of each is left, thus ensuring reproduction by
the strongest and fittest. Many male beetles are territorial and will fiercely defend their small patch of territory
from intruding males. In such species, the males may often have horns on the head and/or thorax, making
their overall body lengths greater than those of the females, unlike most insects.
Pairing is generally short but in some cases will last for several hours. During pairing sperm cells are
transferred to the female to fertilise the egg.
Parental care varies between species, ranging from the simple laying of eggs under a leaf to certain
scarab beetles, which construct underground structures complete with a supply of dung to house and feed
their young. Other beetles are leaf rollers, biting sections of leaves to cause them to curl inwards, then laying
their eggs, thus protected, inside.
[edit] Defence
Clytus arietis (Cerambycidae), a wasp mimic
Beetles may be preyed upon by other insects such as robber flies

Beetles and their larvae have a variety of strategies to avoid being attacked by predators or
parasitoids. These include camouflage, mimicry, toxicity, and active defense.
Camouflage involves the use of colouration or shape to blend into the surrounding environment. This
sort of protective coloration is common and widespread among beetle families, especially those that feed on
wood or vegetation, such as many of the leaf beetles (family Chrysomelidae) or weevils. In some of these
species, sculpturing or various coloured scales or hairs cause the beetle to resemble bird dung or other
inedible objects. Many of those that live in sandy environments blend in with the coloration of the substrate.
Another defence that often uses colour or shape to deceive potential enemies is mimicry. A number
of longhorn beetles (family Cerambycidae) bear a striking resemblance to wasps, which helps them avoid
predation even though the beetles are in fact harmless. This defence can be found to a lesser extent in other
beetle families, such as the scarab beetles. Beetles may combine their colour mimicry with behavioural
mimicry, acting like the wasps they already closely resemble. Many beetle species, including ladybirds,
blister beetles, and lycid beetles can secrete distasteful or toxic substances to make them unpalatable or
even poisonous. These same species often exhibit aposematism, where bright or contrasting colour patterns
warn away potential predators, and there are, not surprisingly, a great many beetles and other insects that
mimic these chemically protected species.
Large ground beetles and longhorn beetles may defend themselves using strong mandibles and/or
spines or horns to forcibly persuade a predator to seek out easier prey. Others, such as bombardier beetles
(within Carabidae), may spray chemicals from their abdomen to repel predators.
[edit] Feeding
Mylabris pustulata (Meloidae) feeding on the petals of Ipomoea carnea

Besides being abundant and varied, beetles are able to exploit the wide diversity of food sources
available in their many habitats. Some are omnivores, eating both plants and animals. Other beetles are
highly specialised in their diet. Many species of leaf beetles, longhorn beetles, and weevils are very host
specific, feeding on only a single species of plant. Ground beetles and rove beetles (family Staphylinidae),
among others, are primarily carnivorous and will catch and consume many other arthropods and small prey
such as earthworms and snails. While most predatory beetles are generalists, a few species have more
specific prey requirements or preferences.
Decaying organic matter is a primary diet for many species. This can range from dung, which is
consumed by coprophagous species such as certain scarab beetles (family Scarabaeidae), to dead animals,
which are eaten by necrophagous species such as the carrion beetles (family Silphidae). Some of the beetles
found within dung and carrion are in fact predatory, such as the clown beetles, preying on the larvae of
coprophagous and necrophagous insects.
[edit] Adaptations to the environment

Aquatic beetles use several techniques for retaining air beneath the water's surface. Beetles of the
family Dytiscidae hold air between the abdomen and the elytra when diving. Hydrophilidae have hairs on their
under surface that retain a layer of air against their bodies. Adult crawling water beetles use both their elytra
and their hind coxae (the basal segment of the back legs) in air retention,[4] while whirligig beetles simply
carry an air bubble down with them whenever they dive.
[edit] Evolutionary history and classification
Fossil buprestid beetle from the Eocene Messel pit, which retains its structural colour
A 2007 study based on DNA of living beetles and maps of likely beetle evolution indicated that
beetles may have originated during the Lower Permian, up to 299 million years ago.[5] In 2009, a fossil
beetle was described from the Pennsylvanian of Mazon Creek, Illinois, pushing the origin of the beetles to an
earlier date, 318 to 299 million years ago.[6]
The four extant suborders of beetle are these:
• Polyphaga is the largest suborder, containing more than 300,000 described species in more
than 170 families, including rove beetles (Staphylinidae), scarab beetles (Scarabaeidae), blister
beetles (Meloidae), stag beetles (Lucanidae) and true weevils (Curculionidae). These beetles can be
identified by the cervical sclerites (hardened parts of the head used as points of attachment for
muscles) absent in the other suborders.
• Adephaga contains about 10 families of largely predatory beetles, includes ground beetles
(Carabidae), Dytiscidae and whirligig beetles (Gyrinidae). In these beetles, the testes are tubular and
the first abdominal sternum (a plate of the exoskeleton) is divided by the hind coxae (the basal joints
of the beetle's legs).
• Archostemata contains four families of mainly wood-eating beetles, including reticulated
beetles (Cupedidae) and the telephone-pole beetle.
• Myxophaga contains about 100 described species in four families, mostly very small,
including Hydroscaphidae and the genus Sphaerius.
These suborders diverged in the Permian and Triassic. Their phylogenetic relationship is uncertain,
with the most popular hypothesis being that Polyphaga and Myxophaga are most closely related, with
Adephaga as the sister group to those two, and Archostemata as sister to the other three collectively.
There are about 450,000 species of beetles – representing about 40% of all known insects. Such a
large number of species poses special problems for classification, with some families consisting of thousands
of species and needing further division into subfamilies and tribes. This immense number of species
allegedly led evolutionary biologist J. B. S. Haldane to quip, when some theologians asked him what could be
inferred about the mind of the Creator from the works of His Creation, that God displayed "an inordinate
fondness for beetles".[7]
[edit] Impact on humans
[edit] Pests
Larvae of the Colorado potato beetle, Leptinotarsa decemlineata

Many agricultural, forestry, and household insect pests are beetles. These include the following:
• The Colorado potato beetle, Leptinotarsa decemlineata, is a notorious pest of potato plants.
Crops are destroyed and the beetle can only be treated by employing expensive pesticides, many of
which it has begun to develop resistance to. As well as potatoes, suitable hosts can be a number of
plants from the potato family (Solanaceae), such as nightshade, tomato, aubergine and capsicum.
• The boll weevil, Anthonomus grandis, has cost cotton producers in the United States billions
of dollars since it first entered that country.
• The bark beetles Hylurgopinus rufipes and Scolytus multistriatus, the elm leaf beetle,
Pyrrhalta luteola, and other beetles attack elm trees. The bark beetles are important elm pests
because they carry Dutch elm disease as they move from infected breeding sites to feed on healthy
elm trees. The spread of the fungus by the beetle has led to the devastation of elm trees in many
parts of the Northern Hemisphere, notably in Europe and North America.
Red flour beetle, Tribolium castaneum

• Flour beetles are pests of cereal silos. They feed on wheat and other grains and are adapted
to survive in very dry environments. They are a major pest in the agricultural industry and are highly
resistant to insecticides.
• The death watch beetle, Xestobium rufovillosum, (family Anobiidae) is of considerable
importance as a pest of older wooden buildings in Great Britain. It attacks hardwoods such as oak
and chestnut, always where some fungal decay has taken or is taking place. It is thought that the
actual introduction of the pest into buildings takes place at the time of construction.
• Coconut hispine beetle, Brontispa longissima, feeds on young leaves and damages
seedlings and mature coconut palms. On September 27, 2007, Philippines' Metro Manila and 26
provinces were quarantined due to having been infested with this pest (to save the $800-million
Philippine coconut industry).[8]
• The mountain pine beetle normally attacks mature or weakened lodgepole pine. It can be the
most destructive insect pest of mature pine forests. The current infestation in British Columbia is the
largest Canada has ever seen.[9]
[edit] Beneficial organisms

Coccinella septempunctata, a beneficial beetle
A number of insects are beneficial to humans, usually by controlling the populations of pests.
Both the larvae and adults of some ladybugs (family Coccinellidae) are found in aphid colonies.
Other ladybugs feed on scale insects and mealybugs. If normal food sources are scarce, they may feed on
other things, such as small caterpillars, young plant bugs, honeydew and nectar.
Ground beetles (family Carabidae) are common predators of many different insects and other
arthropods, including fly eggs, caterpillars, wireworms and others.
Plant-feeding beetles are often important beneficial insects, controlling problem weeds. Some flea
beetles of the genus Aphthona feed on Euphorbia esula (leafy spurge, Euphorbiaceae), a considerable weed
of rangeland in western North America.
Dung beetles (Coleoptera, Scarabidae) have been successfully used to reduce the populations of
pestilent flies and parasitic worms that breed in cattle dung. The beetles make the dung unavailable to
breeding pests by quickly rolling and burying it in the soil, with the added effect of improving soil fertility and
nutrient cycling. The Australian Dung Beetle Project (1965–1985), led by Dr. George Bornemissza of the
Commonwealth Scientific and Industrial Research Organisation introduced species of dung beetle to
Australia from South Africa and Europe and effectively reduced the bush fly ( Musca vetustissima) population
by 90%.
Some farmers develop beetle banks to foster and provide cover for beneficial beetles.
Some beetles of the family Dermestidae are often used in taxidermy to clean bones of remaining
flesh.
[edit] Beetles in ancient Egypt and other cultures
Ancient Egyptian scene depicting a scarab beetle

Several species of dung beetle, most notably Scarabaeus sacer (often referred to as "scarab"),
enjoyed a sacred status among the ancient Egyptians, as the creatures were likened to the major god Khepri.
Many thousands of amulets and stamp seals have been excavated that depict the scarab. In many artifacts,
the scarab is depicted pushing the sun along its course in the sky, much as scarabs push or roll balls of dung
to their brood sites. During and following the New Kingdom, scarab amulets were often placed over the heart
of the mummified deceased.
Some tribal groups, particularly in tropical parts of the world, use the colourful, iridescent elytra of
certain beetles, especially certain Scarabaeidae, in ceremonies and as adornment.
[edit] Study and collection
Beetle collection at the Melbourne Museum, Australia

The study of beetles is called coleopterology (from Coleoptera, see above, and Greek -λογία, -logia),
and its practitioners are coleopterists. Coleopterists have formed organisations to facilitate the study of
beetles. Among these is The Coleopterists Society, an international organisation based in the United States.
Such organisations may have both professionals and amateurs interested in beetles as members.
Research in this field is often published in peer-reviewed journals specific to the field of
coleopterology, though journals dealing with general entomology also publish many papers on various
aspects of beetle biology. Some of the journals specific to beetle research are:
• The Coleopterist (United Kingdom beetle fauna)
• The Coleopterists Bulletin (published by The Coleopterists Society)
• Elytron (published by the European Association of Coleopterology)
[edit] See also

• Blister beetle dermatitis
• Heteroptera, suborder of the Hemiptera (true bugs), which may resemble beetles
• Leaf litter sieve
[edit] References
[edit] General references
• Poul Beckmann, Living Jewels: The Natural Design of Beetles ISBN 3-7913-2528-0
• Arthur V. Evans, Charles Bellamy, and Lisa Charles Watson, An Inordinate Fondness for
Beetles ISBN 0-520-22323-3
• Cooter J. & Barclay M.V.L. (eds.) (2006) A Coleopterist’s Handbook. Amateur Entomological
Society. 439 pages. ISBN 0-900054-70-0
• Entomological Society of America , Beetle Larvae of the World ISBN 0-643-05506-1
• David Grimaldi, Michael S. Engel, Evolution of the Insects ISBN 0-521-82149-5
• Ross H. Arnett, Jr. and Michael C. Thomas, American Beetles (CRC Press, 2001–2002).
ISBN 0-8493-1925-0
• K. W. Harde, A Field Guide in Colour to Beetles ISBN 0-7064-1937-5 Pages 7–24
• White, R.E. 1983. Beetles. Houghton Mifflin Company, New York, NY. ISBN 0-395-91089-7
[edit] Cited references

1. ^ a b c James K. Liebherr and Joseph V. McHugh in Resh, V. H. & R. T. Cardé (Editors) 2003.
Encyclopedia of Insects. Academic Press.
2. ^ P. M. Hammond 1992. Species inventory. pp. 17–39 in Global Biodiversity, Status of the
Earth’s Living Resources, B. Groombridge, ed. Chapman and Hall, London. 585 pp.
3. ^ Arthur D. Chapman (2009) (PDF). Numbers of Living Species in Australia and the World
(2nd ed.). Department of the Environment, Water, Heritage and the Arts. ISBN 978-0-642-56861-8.
http://www.environment.gov.au/biodiversity/abrs/publications/other/species-
numbers/2009/pubs/nlsaw-2nd-complete.pdf.
4. ^ R. H. Arnett, Jr. & M. C. Thomas (2001). "Haliplidae". American Beetles, Volume 1. CRC
Press, Boca Raton, Florida. pp. 138–143. ISBN 0-8493-1925-0.
5. ^ Dave Mosher (December 26, 2007). "Modern beetles predate dinosaurs". Live Science.
http://www.livescience.com/animals/071226-tough-beetles.html. Retrieved June 24, 2010.
6. ^ Oliver Béthoux (2009). "The earliest beetle identified". Journal of Paleontology 83 (6): 931–
937. doi:10.1666/08-158.1.
7. ^ Hutchinson, G. Evelyn (1959). "Homage to Santa Rosalia or Why Are There So Many
Kinds of Animals?". The American Naturalist 93 (870): 145–159. doi:10.1086/282070.
http://links.jstor.org/sici?sici=0003-0147(195905/06)93%3A870%3C145%3AHTSROW%3E2.0.CO;2-
D.
8. ^ Amy R. Remo (September 27, 2007). "Beetles infest coconuts in Manila, 26 provinces".
Philippine Daily Inquirer. http://newsinfo.inquirer.net/breakingnews/nation/view_article.php?
article_id=91109.
9. ^ "The Mountain Pine Beetle in British Columbia". Natural Resources Canada. August 19,
2008. http://mpb.cfs.nrcan.gc.ca/biology/introduction_e.html. Retrieved June 24, 2010.

Find more about Beetle on Wikipedia's sister projects:

Wikispecies has information related to: Coleoptera

Coleoptera
[edit] Global
• Coleoptera from the Tree of Life Web Project
• List of major Beetle collections
• Beetles and coleopterologists
• (German) Käfer der Welt
• Coleop-Terra
• Beetles – Coleoptera
• Beetle larvae
• Beetle images
[edit] Regional
• Gallery of European beetles
• Poland beetles
• Identification keys to some British beetles
• North American Beetles
• Beetles of North America
• Texas beetle information
• The Beetle Ring
• Beetles of Africa
• Beetles of Mauritius
• Southeast Asian beetles
Retrieved from "http://en.wikipedia.org/wiki/Beetle"
Categories: Beetles | Insects

W000
W000
Coral

For other uses, see Coral (disambiguation).
Coral
Pillar coral, Dendrogyra cylindricus
Kingdom: Animalia
Phylum: Cnidaria
Anthozoa
Class:
Ehrenberg, 1831
Extant Subclasses and Orders
Alcyonaria
Alcyonacea
Helioporacea
Zoantharia
Antipatharia
Corallimorpharia
Scleractinia
Zoanthidea
[1][2] See Anthozoa for details
Corals are marine organisms in class Anthozoa of phylum Cnidaria typically living in compact
colonies of many identical individual "polyps." The group includes the important reef builders that inhabit
tropical oceans, which secrete calcium carbonate to form a hard skeleton.
A coral "head," which appears to be a single organism, is a colony of myriad genetically identical
polyps. Each polyp is typically only a few millimeters in diameter. Over many generations the colony secretes
a skeleton that is characteristic of the species. Individual heads grow by asexual reproduction of individual
polyps. Corals also breed sexually by spawning. Polyps of the same species release gametes
simultaneously over a period of one to several nights around a full moon.
Although corals can catch small fish and animals such as plankton using stinging cells on their
tentacles, most corals obtain the majority of their energy and nutrients from photosynthetic unicellular algae
called zooxanthellae. Such corals require sunlight and grow in clear, shallow water, typically at depths
shallower than 60 metres (200 ft). Corals can be major contributors to the physical structure of the coral reefs
that develop in tropical and subtropical waters, such as the enormous Great Barrier Reef off the coast of
Queensland, Australia. Other corals do not have associated algae and can live in much deeper water, with
the cold-water genus Lophelia surviving as deep as 3,000 metres (9,800 ft).[3] Examples live on the Darwin
Mounds located north-west of Cape Wrath, Scotland. Corals have also been found off the coast of the U.S. in
Washington state and the Aleutian Islands in Alaska.
Contents
[hide]
• 1 Taxonomy
• 2 Anatomy
• 3 Feeding
• 4 Reproduction
• 4.1 Sexual
• 4.2 Asexual
• 4.3 Colony division
• 5 Reefs
• 6 Types
• 6.1 Perforate corals
• 6.2 Hermatypic corals
• 6.3 Ahermatypic corals
• 8 Threats
• 9 Importance to humans
• 9.1 In jewelry
• 9.2 In construction
• 9.3 In climate research
• 10 See also
• 11 Gallery
[edit] Taxonomy
A Short Tentacle Plate coral in Papua New Guinea

Main articles: Anthozoa, Alcyonaria, and Zoantharia
Corals divide into two subclasses, depending on the number of tentacles or lines of symmetry, and a
series of orders corresponding to their exoskeleton, nematocyst type and mitochondrial genetic analysis.[1]
[2][4] Those with eight tentacles are called octocorallia or Alcyonaria and comprise soft corals, sea fans and
sea pens. Those with more than eight in a multiple of six are called hexacorallia or Zoantharia. This group
includes reef-building corals (Scleractinians), sea anemones and zoanthids.
[edit] Anatomy
Anatomy of a coral polyp
Initially believed to be a plant, William Herschel used a microscope to establish in the 18th Century
that Coral had the characteristic thin cell membranes of an animal.[5]
While a coral head appears to be a single organism, it is actually a group of many individual, yet
genetically identical, polyps. The polyps are multicellular organisms. Polyps are usually a few millimeters in
diameter, and are formed by a layer of outer epithelium and inner jellylike tissue known as the mesoglea.
They are radially symmetrical with tentacles surrounding a central mouth, the only opening to the stomach or
coelenteron, through which food is ingested and waste expelled.
The stomach closes at the base of the polyp, where the epithelium produces an exoskeleton called
the basal plate or calicle (L. small cup). The calicle is formed by a thickened calcareous ring (annular
thickening) with six supporting radial ridges (as shown below). These structures grow vertically and project
into the base of the polyp. When a polyp is physically stressed, its tentacles contract into the calyx so that
virtually no part is exposed above the skeletal platform. This protects the organism from predators and the
elements.[6][7]
The polyp grows by extension of vertical calices which occasionally septate to form a new, higher,
basal plate. Over many generations this extension forms the large calcareous structures of corals and
ultimately coral reefs.
Formation of the calcareous exoskeleton involves deposition of the mineral aragonite by the polyps
from calcium and carbonate ions they acquire from seawater. The rate of deposition, while varying greatly
across species and environmental conditions, can be as much as 10 g / m² of polyp / day (0.3 ounce / sq yd /
day). This is light dependent, with night-time production 90% lower than that during the middle of the day.[8]
Nematocyst discharge: A dormant nematocyst discharges response to nearby prey touching the
cnidocil, the operculum flap opens and its stinging apparatus fires the barb into the prey leaving a hollow
filament through which poisons are injected to immobilise the prey, then the tentacles manoeuvre the prey to
the mouth.
Nematocysts are stinging cells at the tips of the calices that carry poison which they rapidly release in
response to contact with another organism. The tentacles also bear a contractile band of epithelium called
the pharynx. Jellyfish and sea anemones also carry nematocysts.
The polyps interconnect by a complex and well developed system of gastrovascular canals allowing
significant sharing of nutrients and symbiotes. In soft corals these range in size from 50–500 micrometres
(0.0020–0.020 in) in diameter and allow transport of both metabolites and cellular components.[9]
Close-up of Montastrea cavernosa polyps. Tentacles are clearly visible.

Many corals as well as other cnidarian groups such as sea anemones (e.g. Aiptasia), form a
symbiotic relationship with a class of algae, zooxanthellae, of the genus Symbiodinium. Aiptasia, while
considered a pest among coral reef aquarium hobbyists, serves as a valuable model organism in the study of
cnidarian-algal symbiosis. Typically a polyp harbors one species of algae. Via photosynthesis, these provide
energy for the coral, and aid in calcification.[10] The algae benefit from a safe environment, and consume the
carbon dioxide and nitrogenous waste produced by the polyp. Due to the strain the algae can put on the
polyp, stress on the coral often drives the coral to eject the algae. Mass ejections are known as coral
bleaching, because the algae contribute to coral's brown coloration; other colors, however, are due to host
coral pigments, such as GFPs (green fluorescent protein). Ejection increases the polyp's chances of
surviving short-term stress—they can regain algae at a later time. If the stressful conditions persist, the polyp
eventually dies.[11]
[edit] Feeding
Polyps feed on a variety of small organisms, from microscopic plankton to small fish. The polyp's
tentacles immobilize or kill prey using their nematocysts. The tentacles then contract to bring the prey into the
stomach. Once digested, the stomach reopens, allowing the elimination of waste products and the beginning
of the next hunting cycle.
These poisons are usually too weak to harm humans. An exception is fire coral.
[edit] Reproduction
Corals can be both gonochoristic (unisexual) and hermaphroditic, each of which can reproduce
sexually and asexually. Reproduction also allows coral to settle new areas.
[edit] Sexual
Life cycles of broadcasters and brooders.

Corals predominantly reproduce sexually. 25% of hermatypic corals (stony corals) form single sex
(gonochoristic) colonies, while the rest are hermaphroditic.[12] About 75% of all hermatypic corals "broadcast
spawn" by releasing gametes—eggs and sperm—into the water to spread offspring. The gametes fuse during
fertilization to form a microscopic larva called a planula, typically pink and elliptical in shape. A typical coral
colony form several thousand larvae per year to overcome the odds against formation of a new colony.[13]
Planulae exhibits positive phototaxis, swimming towards light to reach surface waters where they
drift and grow before descending to seek a hard surface to which it can attach and establish a new colony.
They also exhibit positive sonotaxis, moving towards sounds that emanate from the reef and away from open
water.[14] High failure rates afflict many stages of this process, and even though millions of gametes are
released by each colony very few new colonies form. The time from spawning to settling is usually 2–3 days,
but can be up to 2 months.[15] The larva grows into a polyp and eventually becomes a coral head by asexual
budding and growth.
A male star coral, Montastraea cavernosa, releases sperm into the water.
Synchronous spawning is very typical on the coral reef and often, even when multiple species are
present, all corals spawn on the same night. This synchrony is essential so that male and female gametes
can meet. Corals must rely on environmental cues, varying from species to species, to determine the proper
time to release gametes into the water. The cues involve lunar changes, sunset time, and possibly chemical
signalling.[12] Synchronous spawning may form hybrids and is perhaps involved in coral speciation.[16] In
some places the spawn can be visually dramatic, clouding the usually clear water with gametes, typically at
night.
Corals use two methods for sexual reproduction, which differ in whether the female gametes are
released:
• Broadcasters, the majority of which mass spawn, rely heavily on environmental cues,
because they release both sperm and eggs into the water. The corals use long-term cues such as
day length, water temperature, and/or rate of temperature change. The short-term cue is most often
the lunar cycle, with sunset cuing the release.[12] About 75% of coral species are broadcasters, the
majority of which are hermatypic, or reef-building corals.[12] The positively buoyant gametes float
towards the surface where fertilization produces planula larvae. The larvae swim towards the surface
light to enter into currents, where they remain usually for two days, but can be up to three weeks, and
in one known case two months,[15] after which they settle and metamorphose into polyps and form
colonies.
• Brooders are most often ahermatypic (non-reef building) in areas of high current or wave
action. Brooders release only sperm, which is negatively buoyant, and can harbor unfertilized eggs
for weeks, lowering the need for mass synchronous spawning events, which do sometimes occur.
[12] After fertilization the corals release planula larvae which are ready to settle.[10]
[edit] Asexual
Calices (basal plates) of Orbicella annularis showing multiplication by gemmation (small central
calice) and division (large double calice).
The tabulate coral Aulopora (Devonian) showing initial budding from protocorallite.
Within a coral head the genetically identical polyps reproduce asexually, either via gemmation
(budding) or division, both shown in the photo of Orbicella annularis. Budding involves a new polyp growing
from an adult, whereas division forms two polyps each as large as the original.[13]
• Budding expands colony size. It occurs when a new corallite grows out from an adult polyp.
As the new polyp grows it produces its body parts. The distance between the new and adult polyps
grows, and with it the coenosarc (the common body of the colony; see coral anatomy). Budding can
be:
• Intra-tentacular—from its oral discs, producing same-sized polyps within the ring of
tentacles.
• Extra-tentacular—from its base, producing a smaller polyp.
• Longitudinal division begins when a polyp broadens and then divides its coelenteron. The
mouth also divides and new tentacles form. The two "new" polyps then generate their missing body
parts and exoskeleton.
• Transversal division occurs when polyps and the exoskeleton divide transversally into two
parts. This means that one has the basal disc (bottom) and the other has the oral disc (top). The two
new polyps must again generate the missing pieces.
[edit] Colony division

• Fission occurs in some corals, especially among the family Fungiidae, where the colony
splits into two or more colonies during early developmental stages.
Whole colonies can reproduce asexually through fragmentation or bailout, forming another individual
colony with the same genotype.
• Bailout occurs when a single polyp abandons the colony and settles on a different substrate
to create a new colony.
• Fragmentation, involves individuals broken from the colony during storms or other situations.
The separated individuals can start new colonies.
[edit] Reefs
Locations of coral reefs

Main article: Coral reef
The hermatypic, stony corals are often found in coral reefs, large calcium carbonate structures
generally found in shallow, tropical water. Reefs are built up from coral skeletons and held together by layers
of calcium carbonate produced by coralline algae. Reefs are extremely diverse marine ecosystems hosting
over 4,000 species of fish, massive numbers of cnidarians, mollusks, crustaceans, and many other animals.
[17]
[edit] Types
[edit] Perforate corals
Corals can be perforate or imperforate. Perforate corals have porous skeletons, which allows their
polyps to connect with each other through the skeleton. Imperforate corals have hard solid skeletons.[18]
[edit] Hermatypic corals

Further information: Scleractinia, Millepora, Tubipora, and Heliopora
Hermatypic or stony corals build reefs. With the help of zooxanthellae, they convert surplus food to
calcium carbonate forming a hard skeleton. Hermatypic species include Scleractinia, Millepora, Tubipora and
Heliopora.[19]
In the Caribbean alone 50 species of uniquely structured hard coral exist. Well known types include:
• Brain coral grow to 1.8 meters (6 ft) in width.
• Acropora and Staghorn coral grow fast and large and are important reef-builders. Staghorn
coral displays large antler-like branches and grows in areas with strong surf.
• Galaxea fascicularis or star coral is another important reef-builder.
• Pillar coral forms pillars which can grow to 3 meters (10 ft) in height.
• Leptopsommia or rock coral, appears almost everywhere in the Caribbean.[20]
[edit] Ahermatypic corals

Further information: Alcyonacea and Anthipatharia
Ahermatypic corals have no zooxanthellae and do not build reefs. They include Alcyonaceas, as well
as some Anthipatharia-species (Black coral, Cirripathes, Antipathes).[19] Ahermatypic corals such as sea
whips, sea feathers, and sea pens[20] are also known as soft corals. Unlike stony corals, they are flexible,
undulating back and forth in the current, and often are perforated, with a lacy appearance. Their skeletons
are proteinaceous, rather than calcareous. Soft corals are somewhat less plentiful (in the Caribbean, twenty
species appear) than stony corals.
Solitary rugose coral (Grewingkia) in three views; Ordovician, southeastern Indiana.

Although corals first appeared in the Cambrian period,[21] some 542 million years ago, fossils are
extremely rare until the Ordovician period, 100 million years later, when Rugose and Tabulate corals became
widespread.
Tabulate corals occur in the limestones and calcareous shales of the Ordovician and Silurian
periods, and often form low cushions or branching masses alongside Rugose corals. Their numbers began to
decline during the middle of the Silurian period and they finally became extinct at the end of the Permian
period, 250 million years ago. The skeletons of Tabulate corals are composed of a form of calcium carbonate
known as calcite.
Rugose corals became dominant by the middle of the Silurian period, and became extinct early in the
Triassic period. The Rugose corals existed in solitary and colonial forms, and are also composed of calcite.
The Scleractinian corals filled the niche vacated by the extinct Rugose and Tabulate species. Their
fossils may be found in small numbers in rocks from the Triassic period, and become common in the Jurassic
and later periods. Scleractinian skeletons are composed of a form of calcium carbonate known as aragonite.
[22] Although they are geologically younger than the Tabulate and Rugose corals, their aragonitic skeleton is
less readily preserved, and their fossil record is less complete.
Timeline of the major coral fossil record and developments from 650 m.y.a. to
present.[23][24] edit
At certain times in the geological past corals were very abundant. Like modern corals, these
ancestors built reefs, some of which now lie as great structures in sedimentary rocks.
Fossils of fellow reef-dwellers algae, sponges, and the remains of many echinoids, brachiopods,
bivalves, gastropods, and trilobites appear along with coral fossils. This makes some corals useful index
fossils, enabling geologists to date the age the rocks in which they are found.
Coral fossils are not restricted to reef remnants, and many solitary corals may be found elsewhere,
such as Cyclocyathus, which occurs in England's Gault clay formation.
A Petoskey stone is a rock and a fossil, often pebble-shaped, that is composed of a fossilized coral,
Hexagonaria percarinata. They are found predominantly in Michigan's Upper Peninsula, and the
northwestern portion of Michigan's lower peninsula.
[edit] Threats
A healthy coral reef has a striking level of biodiversity in many forms of marine life.
Corals are highly sensitive to environmental changes. Scientists have predicted that over 50% of the
world's coral reefs may be destroyed by 2030;[25] as a result most nations protect them through
environmental laws.
Seaweed/Algae can destroy a coral reef. In the Caribbean and tropical Pacific, direct contact
between ~40 to 70% of common seaweeds and coral cause bleaching and death to the coral via transfer of
lipid–soluble metabolites.[26] Seaweed and algae proliferate given adequate nutrients and limited grazing by
herbivores. Coral die if surrounding water temperature changes by more than a degree or two beyond their
normal range or if water salinity drops. In an early symptom of environmental stress, corals expel their
zooxanthellae; without their symbiotic algae, coral tissues become colorless as they reveal the white of their
calcium carbonate skeletons, an event known as coral bleaching.[27]
Many governments now prohibit removal of coral from reefs and use education to inform their
populations about reef protection and ecology. However, many other human activities damage reefs,
including runoff, mooring, fishing, diving, mining and construction.
Coral's narrow niche and the stony corals' reliance on calcium carbonate deposition makes them
susceptible to changes in water pH. The increase in atmospheric carbon dioxide has caused enough
dissolution of carbon dioxide to lower the ocean's pH, in a process known as ocean acidification. Lowered pH
reduces corals' ability to produce calcium carbonate, and at the extreme, can dissolve their skeletons.
Without deep and immediate cuts in anthropogenic CO 2, many scientists fear that acidification will severely
degrade or destroy coral ecosystems.[28]
A section through a coral, dyed to determine growth rate
[edit] Importance to humans

Local economies near major coral reefs benefit from an abundance of fish and other marine
creatures as a food source. Reefs also provide recreational scuba diving and snorkeling tourism.
Unfortunately these activities can have deleterious effects, such as accidental destruction of coral. Coral is
also useful as a protection against hurricanes and other extreme weather.
Coral reefs provide medical benefits for humans. Chemical compounds taken from corals are used in
medicine for cancer, AIDS, pain, and other uses. Corals are also commonly used for bone grafting in
humans.
Live coral is highly sought after for aquaria. Given the proper ecosystem, live coral makes a stunning
addition to any salt water aquarium. Soft corals are easier to maintain in captivity than hard corals.[29]
Isididae may be usable as living bone implants and in aquatic cultivation, because of their potential to
mimic valuable biological properties.[30]
[edit] In jewelry
Main article: Coral (precious)
Coral's many colors give it appeal for necklaces and other jewelry. Intensely red coral is prized as a
gemstone. It is sometimes called fire coral, but is not the same as fire coral. Red coral is very rare because of
overharvesting due to the great demand for perfect specimens.
[edit] In construction
Tabulate coral (a syringoporid); Boone Limestone (Lower Carboniferous) near Hiwasse, Arkansas.
Scale bar is 2.0 cm.
Ancient coral reefs on land provide lime or use as building blocks ("coral rag"). Coral rag is an
important local building material in places such as the East African coast.
[edit] In climate research

The annual growth bands in bamboo corals and others allow geologists to construct year-by-year
chronologies, a form of incremental dating, which underlie high-resolution records of past climatic and
environmental changes using geochemical techniques.[31]
Certain species form communities called microatolls, which are colonies whose top is dead and
mostly above the water line, but whose perimeter is mostly submerged and alive. Average tide level limits
their height. By analyzing the various growth morphologies, microatolls offer a low resolution record of sea
level change. Fossilized microatolls can also be dated using radioactive carbon dating. Such methods can
help to reconstruct Holocene sea levels.[32]
Deep sea bamboo corals (Isididae) may be among the first organisms to display the effects of ocean
acidification. They produce growth rings similar to those of tree and can provide a view of changes in the
condition in the deep sea over time.[33]
[edit] See also

• Bamboo coral
• Coral dermatitis
• Coral Triangle
• Organ pipe coral
• Sea Turtle Association of Japan, Kuroshima Research Station
[edit] Gallery
Further images: commons:Category:Coral reefs and commons:Category:Coral
Polyps of Eusmilia Staghorn coral,

Fungia sp. skeleton fastigiata Acropora
Brain coral, Diploria
labyrinthiformis
Brain coral
Orange cup coral, Brain coral releasing Fringing coral reef
spawning
Balanophyllia elegans eggs off the coast of Eilat, Israel.
[edit] References
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• Coral, The Reef & Marine Aquarium Magazine. ISSN 1556-5769 Coral Magazine
• Book of Coral Propagation by Anthony Calfo. ISBN 0980236509
• Coral Reefs of the World by Susan Wells
• Corals of the World: Biology and Field Guide by Surrey Redhill
• Marine Biology, An Ecological Approach, Sixth Edition by Nybakken, J.W. 2004. ISBN
0805345825
• Indo-Pacific Coral Reef Field Guide by Allen, G.R & R. Steene. 1994. ISBN 9810056877
• Coral Reef Animals of the Indo-Pacific, Animals Life from Africa to Hawai‘i (invertebrates) by
Gosliner, T., D. Behrens & G. Williams. 1996. ISBN 0930118219
• Tropical Pacific Invertebrates by Colin, P.L. & C. Arneson. 1995. ISBN 0964562502
• Corals of Australia and the Indo-Pacific by Veron, J.E.N. 1993. ISBN 0824815041
• The Evolution of Reef Communities by Fagerstrom, J.A. 1987. ISBN 0471815284
• A Reef Comes to Life. Creating an Undersea Exhibit by Segaloff, Nat, and Paul Erickson.
1991. ISBN 0531109941
• SeaWorld – Coral reef bibliography

Wikispecies has information related to: Coral
Wikimedia Commons has media related to (category):

Coral or Anthozoa
• Precht, William F. Coral Reef Restoration Handbook ISBN 0849320739
• Microdocs: What is a coral?
• NOAA CoRIS – Coral Reef Biology
• NOAA Ocean Service Education – Corals
• University of Southern Mississippi – Coral Reef Resource Guide
• Hard Corals Order:Scleractinia From Gulf of Kutch
• Coral Reproduction at the Smithsonian Ocean Portal
[hide]v · d · eCorals and coral reefs
Stony Scleractinia · Blue coral · Brain coral · Elkhorn

corals coral · Hermatypic coral · Pillar coral · Staghorn coral ·
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Coral reefs Coral reef fish · Census of Coral Reefs · The Structure
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Coral Deep water coral · Andros, Bahamas · Belize

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Coral Coral bleaching · Black band disease ·

diseases Skeletal eroding band · White band disease · White
pox disease
Coral reef protection · Project AWARE · Reef

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Society for Reef Studies
Artificial reef · Coral biology · Coral dermatitis ·

Other Coral (precious) · Coral rag · Coral sand · Coralline
algae · Environmental issues · Fire coral · Rugosa
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Retrieved from "http://en.wikipedia.org/wiki/Coral"
Categories: Anthozoa | Incremental dating | Coral reefs

W000
History of RNA biology


Numerous key discoveries in biology have emerged from studies of RNA (ribonucleic acid), including
seminal work in the fields of biochemistry, genetics, microbiology, molecular biology, molecular evolution and
structural biology. As of 2010, 30 scientists have been awarded Nobel Prizes for experimental work that
includes studies of RNA. Specific discoveries of high biological significance are discussed in this article.
For related information, see the articles on History of Molecular Biology and History of Genetics. For
background information, see the articles on RNA and nucleic acid
Contents
[hide]
• 1 1930 - 1950
• 1.1 RNA and DNA have distinct chemical properties
• 2 1951 - 1965
• 2.1 Messenger RNA (mRNA) carries genetic
information that directs protein synthesis
• 2.2 Ribosomes make proteins
• 2.3 Transfer RNA (tRNA) is the physical link
between RNA and protein
• 2.4 The genetic code is solved
• 2.5 RNA polymerase is purified
• 3 1966 - 1975
• 3.1 First complete nucleotide sequence of a
biological nucleic acid molecule
• 3.2 Evolutionary variation of homologous RNA
sequences reveals folding patterns
• 3.3 First complete genomic nucleotide sequence
• 3.4 Reverse transcriptase can copy RNA into DNA
• 3.5 RNA replicons evolve rapidly
• 3.6 Ribosomal RNA (rRNA) sequences provide a
record of the evolutionary history of all life forms
[edit] 1930 - 1950
[edit] RNA and DNA have distinct chemical properties
When first studied in the early 1900s, the chemical and biological differences between RNA and DNA
were not apparent, and they were named after the materials from which they were isolated; RNA was initially
known as "yeast nucleic acid" and DNA was "pancreas nucleic acid". Using diagnostic chemical tests,
carbohydrate chemists showed that the two nucleic acids contained different sugars, whereupon the common
name for RNA became "ribose nucleic acid". Other early biochemical studies showed that RNA was readily
broken down at high pH, while DNA was stable (although denatured) in alkali. Nucleoside composition
analysis showed first that RNA contained similar nucleobases to DNA, with uracil instead of thymine, and that
RNA contained a number of minor nucleobase components, e.g. small amounts of pseudouridine and
dimethylguanine.[1]
[edit] 1951 - 1965

[edit] Messenger RNA (mRNA) carries genetic information that directs
protein synthesis
The concept of messenger RNA emerged during the late 1950s, and is associated with Crick's
description of his "Central Dogma of Molecular Biology", which asserted that DNA led to the formation of
RNA, which in turn led to the synthesis of proteins. During the early 1960s, sophisticated genetic analysis of
mutations in the lac operon of E. coli and in the rII locus of bacteriophage T4 were instrumental in defining
the nature of both messenger RNA and the genetic code. The short-lived nature of bacterial RNAs, together
with the highly complex nature of the cellular mRNA population, made the biochemical isolation of mRNA
very challenging. This problem was overcome in the 1960s by the use of reticulocytes in vertebrates, which
produce large quantities of mRNA that are highly enriched in RNA encoding alpha- and beta-globin (the two
major protein chains of hemoglobin).[2]
[edit] Ribosomes make proteins

In the 1950s, results of labeling experiments in rat liver showed that radioactive amino acids were
found to be associated with "microsomes" (later redefined as ribosomes) very rapidly after administration,
and before they became widely incorporated into cellular proteins. Ribosomes were first visualized using
electron microscopy, and their ribonucleoprotein components were identified by biophysical methods, chiefly
sedimentation analysis within ultracentrifuges capable of generating very high accelerations (equivalent to
hundreds of thousands times gravity). Polysomes (multiple ribosomes moving along a single mRNA
molecule) were identified in the early 1960s, and their study led to an understanding of how ribosomes
proceed to read the mRNA in a 5' to 3' direction, processively generating proteins as they do so.[3]
[edit] Transfer RNA (tRNA) is the physical link between RNA and protein
Biochemical fractionation experiments showed that radioactive amino acids were rapidly
incorporated into small RNA molecules that remained soluble under conditions where larger RNA-containing
particles would precipitate. These molecules were termed soluble (sRNA) and were later renamed transfer
RNA (tRNA). Subsequent studies showed that (i) every cell has multiple species of tRNA, each of which is
associated with a single specific amino acid, (ii) that there are a matching set of enzymes responsible for
linking tRNAs with the correct amino acids, and (iii) that tRNA anticodon sequences form a specific decoding
interaction with mRNA codons.[4]
[edit] The genetic code is solved
The genetic code consists of the translation of particular nucleotide sequences in mRNA to specific
amino acid sequences in proteins (polypeptides). The ability to work out out the genetic code emerged from
the convergence of three different areas of study--(i) new methods to generate synthetic RNA molecules of
defined composition to serve as artificial mRNAs, (ii) development of in vitro translation systems that could
used to translate the synthetic mRNAs into protein, and (iii) experimental and theoretical genetic work which
established that the code was written in three letter "words" (codons). Today, our understanding of the
genetic code permits the prediction of the amino sequence of the protein products of the tens of thousands of
genes whose sequences are being determined in genome studies.[5]
[edit] RNA polymerase is purified

The biochemical purification and characterization of RNA polymerase from the bacterium Escherichia
coli enabled the understanding of the mechanisms through which RNA polymerase initiates and terminates
transcription, and how those processes are regulated to regulate gene expression (i.e. turn genes on and
off). Following the isolation of E. coli RNA polymerase, the three RNA polymerases of the eukaryotic nucleus
were identified, as well as those associated with viruses and organelles. Studies of transcription also led to
the identification of many protein factors that influence transcription, including repressors, activators and
enhancers. The availability of purified preparations of RNA polymerase permitted investigators to develop a
wide range of novel methods for studying RNA in the test tube, and led directly to many of the subsequent
key discoveries in RNA biology.[6]
[edit] 1966 - 1975
[edit] First complete nucleotide sequence of a biological nucleic acid
molecule
Although determining the sequence of proteins was becoming somewhat routine, methods for
sequencing of nucleic acids were not available until the mid-1960s. In this seminal work, a specific tRNA was
purified in substantial quantities, and then sliced into overlapping fragments using a variety of ribonucleases.
Analysis of the detailed nucleotide composition of each fragment provided the information necessary to
deduce the sequence of the tRNA. Today, the sequence analysis of much larger nucleic acid molecules is
highly-automated and enormously faster.[7]
[edit] Evolutionary variation of homologous RNA sequences reveals

folding patterns
Additional tRNA molecules were purified and sequenced. The first comparative sequence analysis
was done and revealed that the sequences varied through evolution in such a way that all of the tRNAs could
fold into very similar secondary structures (two-dimensional structures) and had identical sequences at
numerous positions (e.g. CCA at the 3' end). The radial four-arm structure of tRNA molecules is termed the
'cloverleaf structure', and results from the evolution of sequences with common ancestry and common
biological function. Since the discovery of the tRNA cloverleaf, comparative analysis of numerous other
homologous RNA molecules has led to the identification of common sequences and folding patterns.[8]
[edit] First complete genomic nucleotide sequence
The 3569 nucleotide sequence of all of the genes of the RNA bacteriophage MS2 was determined by
a large team of researchers over several years, and was reported in a series of scientific papers. These
results enabled the analysis of the first complete genome, albeit an extremely tiny one by modern standards.
Several surprising features were identified, including genes that partially overlap one another and the first
clues that different organisms might have slightly different codon usage patterns.[9]
[edit] Reverse transcriptase can copy RNA into DNA

Retroviruses were shown to have a single-stranded RNA genome and to replicate via a DNA
intermediate, the reverse of the usual DNA-to-RNA transcription pathway. They encode a RNA-dependent
DNA polymerase (reverse transcriptase) that is essential for this process. Some retroviruses can cause
diseases, including several that are associated with cancer, and HIV-1 which causes AIDS. Reverse
transcriptase has been widely used as an experimental tool for the analysis of RNA molecules in the
laboratory, in particular the conversion of RNA molecules into DNA prior to molecular cloning and/or
polymerase chain reaction (PCR).[10]
[edit] RNA replicons evolve rapidly

Biochemical and genetic analyses showed that the enzyme systems that replicate viral RNA
molecules (reverse transcriptases and RNA replicases) lack molecular proofreading (3' to 5' exonuclease)
activity, and that RNA sequences do not benefit from extensive repair systems analogous to those that exist
for maintaining and repairing DNA sequences. Consequently, RNA genomes appear to be subject to
significantly higher mutation rates than DNA genomes. For example, mutations in HIV-1 that lead to the
emergence of viral mutants that are insensitive to antiviral drugs are common, and constitute a major clinical
challenge.[11]
[edit] Ribosomal RNA (rRNA) sequences provide a record of the

evolutionary history of all life forms
Analysis of ribosomal RNA sequences from a large number of organisms demonstrated that all
extant forms of life on Earth share common structural and sequence features of the ribosomal RNA,
reflecting a common ancestry. Mapping the similarities and differences among rRNA molecules from different
sources provides clear and quantitative information about the phylogenetic (i.e. evolutionary) relationships
among organisms. Analysis of rRNA molecules led to the identification of a third major kingdom of
organisms, the archaea, in addition to the prokaryotes and eukaryotes.[12]
[edit] Non-encoded nucleotides are added to the ends of RNA

molecules
Molecular analysis of mRNA molecules showed that, following transcription, mRNAs have non-DNA-
encoded nucleotides added to both their 5' and 3' ends (guanosine caps and poly-A, respectively). Enzymes
were also identified that add and maintain the universal CCA sequence on the 3' end of tRNA molecules.
These events are among the first discovered examples of RNA processing, a complex series of reactions
that are needed to convert RNA primary transcripts into biologically active RNA molecules.[13]
[edit] 1976 - 1985
[edit] Small RNA molecules are abundant in the eukaryotic nucleus
Small nuclear RNA molecules (snRNAs) were identified in the eukaryotic nucleus using
immunological studies with autoimmune antibodies, which bind to small nuclear ribonucleoprotein complexes
(snRNPs; complexes of the snRNA and protein). Subsequent biochemical, genetic, and phylogenetic studies
established that many of these molecules play key roles in essential RNA processing reactions within the
nucleus and nucleolus, including RNA splicing, polyadenylation, and the maturation of ribosomal RNAs.[14]
[edit] RNA molecules require a specific, complex three-dimensional

structure for activity
The detailed three-dimensional structure of tRNA molecules was determined using X-ray
crystallography, and revealed highly complex, compact three dimensional structures consisting of tertiary
interactions laid upon the basic cloverleaf secondary structure. Key features of tRNA tertiary structure include
the coaxial stacking of adjacent helices and non-Watson-Crick interactions among nucleotides within the
apical loops. Additional crystallographic studies showed that a wide range of RNA molecules (including
ribozymes, riboswitches and ribosomal RNA) also fold into specific structures containing a variety of 3D
structural motifs. The ability of RNA molecules to adopt specific tertiary structures is essential for their
biological activity, and results from the single-stranded nature of RNA. In many ways, RNA folding is more
highly analogous to the folding of proteins rather than to the highly repetitive folded structure of the DNA
double helix.[4]
[edit] Genes are commonly interrupted by introns that must be removed
by RNA splicing
Analysis of mature eukaryotic messenger RNA molecules showed that they are often much smaller
than the DNA sequences that encode them. The genes were shown to be discontinuous, composed of
sequences that are not present in the final mature RNA (introns), located between sequences that are
retained in the mature RNA (exons). Introns were shown to be removed after transcription through a process
termed RNA splicing. Splicing of RNA transcripts requires a highly precise and coordinated sequence of
molecular events, consisting of (a) definition of boundaries between exons and introns, (b) RNA strand
cleavage at exactly those sites, and (c) covalent linking (ligation) of the RNA exons in the correct order. The
discovery of discontinuous genes and RNA splicing was entirely unexpected by the community of RNA
biologists, and stands as one of the most shocking findings in molecular biology research.[15]
[edit] Alternative pre-mRNA splicing generates multiple proteins from a

single gene
The great majority of protein-coding genes encoded within the nucleus of metazoan cells contain
multiple introns. In many cases, these introns were shown to be processed in more than one pattern, thus
generating a family of related mRNAs that differ, for example, by the inclusion or exclusion of particular
exons. The end result of alternative splicing is that a single gene can encode a number of different protein
isoforms that can exhibit a variety of (usually related) biological functions. Indeed, most of the proteins
encoded by the human genome are generated by alternative splicing.[16]
[edit] Discovery of catalytic RNA (ribozymes)
An experimental system was developed in which an intron-containing rRNA precursor from the
nucleus of the ciliated protozoan Tetrahymena could be spliced in vitro. Subsequent biochemical analysis
shows that this group I intron was self-splicing; that is, the precursor RNA is capable of carrying out the
complete splicing reaction in the absence of proteins. In separate work, the RNA component of the bacterial
enzyme ribonuclease P (a ribonucleoprotein complex) was shown to catalyze its tRNA-processing reaction in
the absence of proteins. These experiments represented landmarks in RNA biology, since they revealed that
RNA could play an active role in cellular processes, by catalyzing specific biochemical reactions. Before
these discoveries, it was believed that biological catalysis was solely the realm of protein enzymes.[17] [18]
[edit] RNA was likely critical for prebiotic evolution

The discovery of catalytic RNA (ribozymes) showed that RNA could both encode genetic information
(like DNA) and catalyze specific biochemical reactions (like protein enzymes). This realization led to the RNA
World Hypothesis, a proposal that RNA may have played a critical role in prebiotic evolution at a time before
the molecules with more specialized functions (DNA and proteins) came to dominate biological information
coding and catalysis. Although it is not possible for us to know the course of prebiotic evolution with any
certainty, the presence of functional RNA molecules with common ancestry in all modern-day life forms is a
strong argument that RNA was widely present at the time of the last common ancestor.[19]
[edit] Introns can be mobile genetic elements

Some self-splicing introns can spread through a population of organisms by "homing", inserting
copies of themselves into genes at sites that previously lacked an intron. Because they are self-splicing (that
is, they remove themselves at the RNA level from genes into which they have inserted), these sequences
represent transposons that are genetically silent, i.e. they do not interfere with the expression of the gene into
which they become inserted. These introns can be regarded as examples of selfish DNA. Some mobile
introns encode homing endonucleases, enzymes that initiate the homing process by specifically cleaving
double-stranded DNA at or near the intron-insertion site of alleles lacking an intron. Mobile introns are
frequently members of either the group I or group II families of self-splicing introns.[20]
[edit] Spliceosomes mediate nuclear pre-mRNA splicing

Introns are removed from nuclear pre-mRNAs by splicesomes, large ribonucleoprotein complexes
made up of snRNA and protein molecules whose composition and molecular interactions change during the
course of the RNA splicing reactions. Spliceosomes assemble on and around splice sites (the boundaries
between introns and exons in the unspliced pre-mRNA) in mRNA precursors and use RNA-RNA interactions
to identify critical nucleotide sequences and, probably, to catalyze the splicing reactions. Nuclear pre-mRNA
introns and spliceosome-associated snRNAs show similar structural features to self-splicing group II introns.
In addition, the splicing pathway of nuclear pre-mRNA introns and group II introns shares a similar reaction
pathway. These similarities have led to the hypothesis that these molecules may share a common ancestor.
[21]
[edit] 1986 - 2000

[edit] RNA sequences can be edited within cells
Messenger RNA precursors from a wide range of organisms can be edited before being translated
into protein. In this process, non-encoded nucleotides may be inserted into specific sites in the RNA, and
encoded nucleotides may be removed or replaced. RNA editing was first discovered within the mitochondria
of kinetoplastid protozoans, where it has been shown to be extensive.[22] For example, some protein-coding
genes encode fewer than 50% of the nucleotides found within the mature, translated mRNA. Other RNA
editing events are found in mammals, plants, bacteria and viruses. These latter editing events involve fewer
nucleotide modifications, insertions and deletions than the events within kinetoplast DNA, but still have high
biological significance for gene expression and its regulation.[23]
[edit] Telomerase uses a built-in RNA template to maintain chromosome

ends
Telomerase is an enzyme that is present in all eukaryotic nuclei which serves to maintain the ends of
the linear DNA in the linear chromosomes of the eukaryotic nucleus, through the addition of terminal
sequences that are lost in each round of DNA replication. Before telomerase was identified, its activity was
predicted on the basis of a molecular understanding of DNA replication, which indicated that the DNA
polymerases known at that time could not replicate the 3' end of a linear chromosome, due to the absence of
a template strand. Telomerase was shown to be a ribonucleoprotein enzyme that contains an RNA
component that serves as a template strand, and a protein component that has reverse transcriptase activity
and adds nucleotides to the chromosome ends using the internal RNA template.[24]
[edit] Ribosomal RNA catalyzes peptide bond formation

For years, scientists had worked to identify which protein(s) within the ribosome were responsible for
peptidyl transferase function during translation, because the covalent linking of amino acids represents one
of the most central chemical reactions in all of biology. Careful biochemical studies showed that extensively-
deproteinized large ribosomal subunits could still catalyze peptide bond formation, thereby implying that the
sought-after activity might lie within ribosomal RNA rather than ribosomal proteins. Structural biologists,
using X-ray crystallography, localized the peptidyl transferase center of the ribosome to a highly-conserved
region of the large subunit ribosomal RNA (rRNA) that is located at the place within the ribosome where the
amino-acid-bearing ends of tRNA bind, and where no proteins are present. These studies led to the
conclusion that the ribosome is a ribozyme. The rRNA sequences that make up the ribosomal active site
represent some of the most highly conserved sequences in the biological world. Together, these
observations indicate that peptide bond formation catalyzed by RNA was a feature of the last common
ancestor of all known forms of life.[25]
[edit] Combinatorial selection of RNA molecules enables in vitro

evolution
Experimental methods were invented that allowed investigators to use large, diverse populations of
RNA molecules to carry out in vitro molecular experiments that utilized powerful selective replication
strategies used by geneticists, and which amount to evolution in the test tube. These experiments have been
described using different names, the most common of which are "combinatorial selection", "in vitro selection",
and SELEX (for Systematic Evolution of Ligands by Exponential Enrichment). These experiments have been
used for isolating RNA molecules with a wide range of properties, from binding to particular proteins, to
catalyzing particular reactions, to binding low molecular weight organic ligands. They have equal applicability
to elucidating interactions and mechanisms that are known properties of naturally-occurring RNA molecules
to isolating RNA molecules with biochemical properties that are not known in nature. In developing in vitro
selection technology for RNA, laboratory systems for synthesizing complex populations of RNA molecules
were established, and used in conjunction with the selection of molecules with user-specified biochemical
activities, and in vitro schemes for RNA replication. These steps can be viewed as (a) mutation, (b) selection,
and (c) replication. Together, then, these three processes enable in vitro molecular evolution.[26]
[edit] 2001 - present
[edit] Many mobile DNA elements use an RNA intermediate
Transposable genetic elements (transposons) are found which can replicate via transcription into an
RNA intermediate which is subsequently converted to DNA by reverse transcriptase. These sequences,
many of which are likely related to retroviruses, constitute much of the DNA of the eukaryotic nucleus,
especially so in plants. Genomic sequencing shows that retrotransposons make up 36% of the human
genome and over half of the genome of major cereal crops (wheat and maize).[27]
[edit] Riboswitches bind cellular metabolites and control gene

expression
Segments of RNA, typically embedded within the 5'-untranslated region of a vast number of bacterial
mRNA molecules, have a profound effect on gene expression through a previously-undiscovered mechanism
that does not involve the participation of proteins. In many cases, riboswitches change their folded structure
in response to environmental conditions (e.g. ambient temperature or concentrations of specific metabolites),
and the structural change controls the translation or stability of the mRNA in which the riboswitch is
embedded. In this way, gene expression can be dramatically regulated at the post-transcriptional level.[28]
[edit] Small RNA molecules regulate gene expression by post-

transcriptional gene silencing
Another previously unknown mechanism by which RNA molecules are involved in genetic regulation
was discovered in the 1990s. Small RNA molecules termed microRNA (miRNA) and small interfering RNA
(siRNA) are abundant in eukaryotic cells and exert post-transcriptional control over mRNA expression. They
function by binding to specific sites within the mRNA and inducing cleavage of the mRNA via a specific
silencing-associated RNA degradation pathway.[29]
[edit] Noncoding RNA controls epigenetic phenomena

In addition to their well-established roles in translation and splicing, members of noncoding RNA
(ncRNA) families have recently been found to function in genome defense and chromosome inactivation. For
example, piwi-interacting RNAs (piRNAs) prevent genome instability in germ line cells, while Xist (X-inactive-
specific-transcript) is essential for X-chromosome inactivation in mammals.[30]
[edit] Nobel Laureates in RNA biology

See also: List of RNA biologists
Name Dates Institution Awards
1989 Nobel Prize

Altman, Sidney 1939- Yale University
in Chemistry
California Institute of 1975 Nobel Prize

Baltimore, David 1938-
Technology in Physiology or Medicine
Barré-Sinoussi, 2008 Nobel Prize
1947- Pasteur Institute
Françoise in Physiology or Medicine
Blackburn, University of California, 2009 Nobel Prize

1948-
Elizabeth San Francisco in Physiology or Medicine
2002 Nobel Prize

Brenner, Sydney 1927- Salk Institute
in Physiology or Medicine
University of Colorado, 1989 Nobel Prize

Cech, Thomas 1947-
Boulder in Chemistry
1916- 1962 Nobel Prize

Crick, Francis Salk Institute
2004 in Physiology or Medicine
CNR Institute of 1975 Nobel Prize

Dulbecco, Renato 1914-
Biomedical Technologies (Italy) in Physiology or Medicine
2006 Nobel Prize

Fire, Andrew 1959- Stanford University
Gilbert, Walter 1932- Harvard University 1980 Nobel Prize

in Chemistry
Johns Hopkins 2009 Nobel Prize

Greider, Carol 1961-
University in Physiology or Medicine

Holley, Robert Cornell University
1965 Nobel Prize

Jacob, François 1920 Pasteur Institute
Khorana, H. Massachusetts 1968 Nobel Prize

1922-
Gobind Institute of Technology in Physiology or Medicine
Medical Research 1982 Nobel Prize

Klug, Aaron 1926-
Council (UK) in Chemistry
2006 Nobel Prize

Kornberg, Roger 1947- Stanford University
in Chemistry
University of 2006 Nobel Prize

Mello, Craig 1960-
Massachusetts Medical School in Physiology or Medicine
Monod, Jacques Pasteur Institute
2008 Nobel Prize

Montagnier, Luc 1932- Pasteur Institute
Nirenberg, 1927- National Institutes of 1968 Nobel Prize

Marshall 2010 Health (USA) in Physiology or Medicine

Ochoa, Severo New York University
1934- University of 1975 Nobel Prize

Temin, Howard
1994 Wisconsin, Madison in Physiology or Medicine
Ramakrishnan, Medical Research 2009 Nobel Prize

1952-
Venkatraman Council (UK) in Chemistry
1993 Nobel Prize

Roberts, Richard 1943- New England Biolabs
Sharp, Philip 1944- Massachusetts 1993 Nobel Prize

Institute of Technology in Physiology or Medicine
2009 Nobel Prize

Steitz, Thomas 1940- Yale University
in Chemistry
2009 Nobel Prize

Szostak, Jack 1952- Harvard University
1907- University of 1957 Nobel Prize

Todd, Alexander
1997 Cambridge in Chemistry
Cold Spring Harbor 1962 Nobel Prize

Watson, James 1928-
Laboratory in Physiology or Medicine
Weizmann Institute of 2009 Nobel Prize

Yonath, Ada 1939-
Science in Chemistry
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siRNAs". Cell 136 (4): 642. doi:10.1016/j.cell.2009.01.035. PMID 19239886. edit
30.^ Bonasio, R.; Tu, S.; Reinberg, D. (2010). "Molecular Signals of Epigenetic States". Science
330 (6004): 612. doi:10.1126/science.1191078. PMID 21030644. edit
Retrieved from "http://en.wikipedia.org/wiki/History_of_RNA_biology"
Categories: RNA | Non-coding RNA | History of science

W000
Stephen Jay Gould


This article is about the paleontologist and science writer. For the science fiction writer, see Steven
Gould.
Stephen Jay Gould
September 10, 1941
Born
Bayside, New York, United States
May 20, 2002(2002-05-20) (aged 60)

Died
Manhattan, New York, United States
Nationality American
Fields Paleontology, Evolutionary biology, History of Science
Harvard University,
Institutions American Museum of Natural History,
New York University
Alma mater Antioch College, Columbia University
Linnean Society of London's Darwin-Wallace Medal (2008)

Notable awards Paleontological Society Medal (2002)
Charles Schuchert Award (1975)
Signature
Stephen Jay Gould (September 10, 1941 – May 20, 2002) was an American paleontologist,
evolutionary biologist and historian of science. He was also one of the most influential and widely read writers
of popular science of his generation.[1] Gould spent most of his career teaching at Harvard University and
working at the American Museum of Natural History in New York. In the latter years of his life, Gould also
taught biology and evolution at New York University near his home in SoHo.
Gould's greatest contribution to science was the theory of punctuated equilibrium which he
developed with Niles Eldredge in 1972.[2] The theory proposes that most evolution is marked by long periods
of evolutionary stability, which is punctuated by rare instances of branching evolution. The theory was
contrasted against phyletic gradualism, the popular idea that evolutionary change is marked by a pattern of
smooth and continuous change in the fossil record.
Most of Gould's empirical research was based on the land snail genera Poecilozonites and Cerion.
He also contributed to evolutionary developmental biology, and has received wide praise for his book
Ontogeny and Phylogeny. In evolutionary theory he opposed strict selectionism, sociobiology as applied to
humans, and evolutionary psychology. He campaigned against creationism and proposed that science and
religion should be considered two distinct fields, or "magisteria", whose authorities do not overlap.[3]
Many of Gould's Natural History essays were reprinted in collected volumes, such as Ever Since
Darwin and The Panda's Thumb, while his popular treatises included books such as The Mismeasure of
Man, Wonderful Life and Full House.
Contents
[hide]
• 1 Biography
• 2 Scientific career
• 2.1 Punctuated equilibrium
• 2.2 Evolutionary developmental biology
• 2.3 Selectionism and sociobiology
• 2.3.1 Against "Sociobiology"
• 2.3.2 Spandrels and the Panglossian
Paradigm
• 2.4 Evolutionary progress
• 2.5 Cladistics
• 2.6 Technical work on land snails
• 2.7 Influence
• 2.8 The Structure of Evolutionary Theory
• 3 As a public figure
• 4 Controversies
• 4.1 Opposition to sociobiology and evolutionary
psychology
• 4.2 Cambrian fauna
• 4.3 Mismeasure of Man
• 5 Non-overlapping magisteria
[edit] Biography
A life size cast of the Tyrannosaurus rex.

Gould was born and raised in the community of Bayside, a quiet suburb located in the Queens
borough of New York City. His father Leonard was a court stenographer, and his mother Eleanor was an
artist. When Gould was five years old, his father took him to the Hall of Dinosaurs in the American Museum of
Natural History, where he first encountered Tyrannosaurus rex. "I had no idea there were such things—I was
awestruck," Gould once recalled.[4] It was in that moment that he decided to become a paleontologist.
Raised in a secular Jewish home, Gould did not formally practice religion and preferred to be called
an agnostic.[3] Though he "had been brought up by a Marxist father," he has stated that his father's politics
were "very different" from his own.[5] In describing his own political views he has said they "tend to the left of
center."[6] According to Gould the most influential political books he read were C. Wright Mills' The Power
Elite and the political writings of Noam Chomsky.[6]
While attending Antioch College in the early 1960s, Gould was active in the civil rights movement
and often campaigned for social justice. When he attended the University of Leeds as a visiting
undergraduate, he organized weekly demonstrations outside a Bradford dance hall which refused to admit
Blacks. Gould continued these demonstrations until the policy was revoked.[7] Throughout his career and
writings he spoke out against cultural oppression in all its forms, especially what he saw as pseudoscience
used in the service of racism and sexism.[8]
Gould was twice married. His first marriage was to artist Deborah Lee on October 3, 1965. Gould met
Lee while they were students together at Antioch College.[4] They had two sons, Jesse and Ethan. His
second marriage was in 1995 to artist and sculptor Rhonda Roland Shearer who is the mother of two
children, Jade and London Allen, stepchildren of Gould.[9]
In July 1982, Gould was diagnosed with peritoneal mesothelioma, a deadly form of cancer affecting
the abdominal lining and frequently found in people who have been exposed to asbestos. After a difficult two-
year recovery, Gould published a column for Discover magazine, titled "The Median Isn't the Message",
which discusses his reaction to discovering that mesothelioma patients had a median lifespan of only eight
months after diagnosis.[10] He then describes the true significance behind this number, and his relief upon
realizing that statistical averages are just useful abstractions, and do not encompass the full range of
variation.
The median is the halfway point, which means that 50% of patients will die before 8 months, but the
other half will live longer, potentially much longer. He then needed to determine where his personal
characteristics placed him within this range. Considering that the cancer was detected early, the fact he was
young, optimistic, and had the best treatments available, Gould figured that he should be in the favorable half
of the upper statistical range. After an experimental treatment of radiation, chemotherapy, and surgery, Gould
made a full recovery, and his column became a source of comfort for many cancer patients.
Gould was also an advocate for medical marijuana. During this bout with cancer, he smoked the
illegal drug to alleviate the nausea associated with his medical treatments. According to Gould, his use of
marijuana had a "most important effect" on his eventual recovery.[11] In 1998 he testified in the case of Jim
Wakeford, a Canadian medical-marijuana user and activist.
His scientific essays for Natural History frequently refer to his nonscientific interests and pastimes. As
a boy he collected baseball cards and remained a fiercely avid baseball fan throughout his life. As an adult
he was fond of science fiction movies but often lamented about their mediocrity (not just in their presentation
of science, but in their storytelling as well).[12] His other interests included singing in the Boston Cecilia, and
he was a great aficionado of Gilbert and Sullivan operettas. He collected rare antiquarian books and
textbooks. He often traveled to Europe, and spoke French, German, Russian, and Italian. He admired
Renaissance architecture. When discussing the Judeo-Christian tradition, he usually referred to it simply as
"Moses". He sometimes alluded ruefully to his tendency to put on weight.[13]
Gould died on May 20, 2002 from a metastatic adenocarcinoma of the lung, a form of cancer which
had spread to his brain.[14] This cancer was unrelated to his abdominal cancer, from which he had fully
recovered twenty years earlier. He died in his home "in a bed set up in the library of his SoHo loft, surrounded
by his wife Rhonda, his mother Eleanor, and the many books he loved."[15]
[edit] Scientific career

Gould began his higher education at Antioch College, graduating with double major in geology and
philosophy in 1963.[16] During this time, he also studied abroad at the University of Leeds in the United
Kingdom.[17] After completing his graduate work at Columbia University in 1967 under the guidance of
Norman Newell, he was immediately hired by Harvard University where he worked until the end of his life
(1967–2002). In 1973, Harvard promoted him to Professor of Geology and Curator of Invertebrate
Paleontology at the institution's Museum of Comparative Zoology.
In 1982, Harvard awarded him with the title of Alexander Agassiz Professor of Zoology. The following
year, in 1983, he was awarded fellowship into the American Association for the Advancement of Science,
where he later served as president (1999–2001). The AAAS news release cited his "numerous contributions
to both scientific progress and the public understanding of science." He also served as president of the
Paleontological Society (1985–1986) and the Society for the Study of Evolution (1990–1991).
In 1989 Gould was elected into the body of the National Academy of Sciences. Through 1996–2002
Gould was Vincent Astor Visiting Research Professor of Biology at New York University. In 2001 the
American Humanist Association named him the Humanist of the Year for his lifetime of work. In 2008, he was
posthumously awarded the Darwin-Wallace Medal, along with 12 other recipients. Until 2008, this medal had
been awarded every 50 years by the Linnean Society of London.[18]
[edit] Punctuated equilibrium

Early in his career, Gould and Niles Eldredge developed the theory of punctuated equilibrium, in
which evolutionary change occurs relatively rapidly, alternating with longer periods of relative evolutionary
stability.[2] According to Gould, punctuated equilibrium revised a key pillar "in the central logic of Darwinian
theory."[5] Some evolutionary biologists have argued that while punctuated equilibrium was "of great interest
to biology,"[19] it merely modified neo-Darwinism in a manner that was fully compatible with what had been
known before.[20] Others however emphasized its theoretical novelty, and argued that evolutionary stasis
had been "unexpected by most evolutionary biologists" and "had a major impact on paleontology and
evolutionary biology."[21]
Some critics jokingly referred to the theory as "evolution by jerks,"[22] which elicited Gould to
respond in kind by describing gradualism as "evolution by creeps."[23]
[edit] Evolutionary developmental biology

Gould made significant contributions to evolutionary developmental biology,[24] especially in his
work Ontogeny and Phylogeny.[16] In this book he emphasized the process of heterochrony, which
encompasses two distinct processes: pedomorphosis and terminal additions. Pedomorphosis is the process
where ontogeny is slowed down and the organism does not reach the end of its development. Terminal
addition is the process by which an organism adds to its development by speeding and shortening earlier
stages in the developmental process. Gould's influence in the field of evolutionary developmental biology
continues to be seen, such areas as the evolution of feathers.[25]
[edit] Selectionism and sociobiology

Gould championed biological constraints such as the limitations of developmental pathways on
evolutionary outcomes, as well as other non-selectionist forces in evolution. In particular, he considered
many higher functions of the human brain to be the unintended side consequence or by-product of natural
selection, rather than direct adaptations. To describe such co-opted features he coined the term exaptation
with Elisabeth Vrba.[26] Gould believed this understanding undermines an essential premise of human
sociobiology and evolutionary psychology.
[edit] Against "Sociobiology"

In 1975, E. O. Wilson introduced his analysis of human behavior based on a sociobiological
framework.[27] In response, Gould, Richard Lewontin and others from the Boston area wrote the
subsequently well referenced letter to The New York Review of Books titled "Against 'Sociobiology'". This
open letter criticised Wilson's notion of a "deterministic view of human society and human action."[28]
But Gould did not rule out sociobiological explanations for many aspects of animal behavior, writing:
"Sociobiologists have broadened their range of selective stories by invoking concepts of inclusive fitness and
kin selection to solve (successfully I think) the vexatious problem of altruism—previously the greatest
stumbling block to a Darwinian theory of social behavior. . . . Here sociobiology has had and will continue to
have success. And here I wish it well. For it represents an extension of basic Darwinism to a realm where it
should apply."[29]
[edit] Spandrels and the Panglossian Paradigm

A spandrel from the Holy Trinity Church in Fulnek, Czech Republic.
With Richard Lewontin, Gould wrote an influential 1979 paper entitled "The Spandrels of San Marco
and the Panglossian Paradigm",[30] which introduced the architectural term "spandrel" into evolutionary
biology. In architecture, a spandrel is a curved area of masonry which exists between arches supporting a
dome. Spandrels, also called pendentives in this context, are found particularly in gothic churches.
When visiting Venice in 1978, Gould noted that the spandrels of the San Marco cathedral, while quite
beautiful, were not spaces planned by the architect. Rather the spaces arise as "necessary architectural
byproducts of mounting a dome on rounded arches." Gould and Lewontin thus defined spandrels in
evolutionary biology to mean any biological feature of an organism that arises as a necessary side
consequence of other features, which is not directly selected for by natural selection. Examples include the
"masculinized genitalia in female hyenas, exaptive use of an umbilicus as a brooding chamber by snails, the
shoulder hump of the giant Irish deer, and several key features of human mentality."[31]
In Voltaire's Candide, Dr. Pangloss is portrayed as a clueless scholar who, despite the evidence,
says that "all is for the best in this best of all possible worlds." Gould and Lewontin asserted that it is
Panglossian for evolutionary biologists to view all traits as atomized things that had been naturally selected
for, and criticised biologists for not granting theoretical space to other causes, such as phyletic and
developmental constraints. The relative frequency of spandrels, so defined, versus adaptive features in
nature, remains a controversial topic in evolutionary biology.[32] An illustrative example of Gould's approach
can be found in Elisabeth Lloyd's case study of the female orgasm as a by-product of shared developmental
pathways.[33] Gould also wrote on this topic in his essay "Male Nipples and Clitoral Ripples",[34] prompted
by Lloyd's earlier work.
[edit] Evolutionary progress
Gould favored the argument that evolution has no inherent drive towards long-term progress.
Uncritical commentaries often portray evolution as a ladder of progress, leading towards bigger, faster, and
smarter organisms, the assumption being that evolution is somehow driving organisms to get more complex
and ultimately more like humankind. Gould argued that evolution's drive was not towards complexity, but
towards diversification. Because life is constrained to begin with a simple starting point, any diversity
resulting from this left wall will be perceived to move in the direction of higher complexity. But life, Gould
argued, can easily adapt towards simplification, as is often the case with parasites.[35]
In a review of Full House, Richard Dawkins approved of Gould's general argument, but suggested
that he saw evidence of a "tendency for lineages to improve cumulatively their adaptive fit to their particular
way of life, by increasing the numbers of features which combine together in adaptive complexes. ... By this
definition, adaptive evolution is not just incidentally progressive, it is deeply, dyed-in-the wool, indispensably
progressive."[36]
[edit] Cladistics
Gould never embraced cladistics as a method of investigating evolutionary lineages and process,
possibly because he was concerned that such investigations would lead to neglect of the details in historical
biology, which he considered all-important. In the early 1990s this led him into a debate with Derek Briggs,
who had begun to apply quantitative cladistic techniques to the Burgess Shale fossils, about the methods to
be used in interpreting these fossils.[37] Around this time cladistics rapidly became the dominant method of
classification in evolutionary biology. Cheap but increasingly powerful personal computers made it possible
to process large quantities of data about organisms and their characteristics. Around the same time the
development of effective polymerase chain reaction techniques made it possible to apply cladistic methods of
analysis to biochemical features as well.[38]
[edit] Technical work on land snails

Most of Gould's empirical research pertained to land snails. He focused his early work on the
Bermudian genus Poecilozonites, while his later work concentrated on the West Indian genus Cerion.
According to Gould "Cerion is the land snail of maximal diversity in form throughout the entire world. There
are 600 described species of this single genus. In fact, they're not really species, they all interbreed, but the
names exist to express a real phenomenon which is this incredible morphological diversity. Some are shaped
like golf balls, some are shaped like pencils.…Now my main subject is the evolution of form, and the problem
of how it is that you can get this diversity amid so little genetic difference, so far as we can tell, is a very
interesting one. And if we could solve this we'd learn something general about the evolution of form."[39]
Given Cerion's extensive geographic diversity, Gould later lamented that if Christopher Columbus
had only cataloged a single Cerion it would have ended the scholarly debate over which island Columbus
had first set foot on America.[40]
[edit] Influence
Gould is one of the most frequently cited scientists in the field of evolutionary theory. His 1979
"spandrels" paper has been cited more than 3,000 times.[41] In Palaeobiology—the flagship journal of his own
speciality—only Charles Darwin and G.G. Simpson have been cited more often.[42] Gould was also a
considerably respected historian of science. Historian Ronald Numbers has been quoted as saying: "I can't
say much about Gould's strengths as a scientist, but for a long time I've regarded him as the second most
influential historian of science (next to Thomas Kuhn)."[43]
[edit] The Structure of Evolutionary Theory
Shortly before his death, Gould published a long treatise recapitulating his version of modern
evolutionary theory: The Structure of Evolutionary Theory (2002).
[edit] As a public figure

Gould became widely known through his popular science essays in Natural History magazine and his
best-selling books on evolution. Many of his essays were reprinted in collected volumes, such as Ever Since
Darwin and The Panda's Thumb, while his popular treatises included books such as The Mismeasure of
Man, Wonderful Life and Full House.
A passionate advocate of evolutionary theory, Gould wrote prolifically on the subject, trying to
communicate his understanding of contemporary evolutionary biology to a wide audience. A recurring theme
in his writings is the history and development of evolutionary, and pre-evolutionary, thought. He was also an
enthusiastic baseball fan and made frequent references to the sport in his essays. Many of his baseball
essays were anthologized in his posthumously published book Triumph and Tragedy in Mudville (2003).[44]
Although a proud Darwinist, his emphasis was less gradualist and reductionist than most neo-
Darwinists. He fiercely opposed many aspects of sociobiology and its intellectual descendant evolutionary
psychology. He devoted considerable time to fighting against creationism (and the related constructs
Creation science and Intelligent design). Most notably, Gould provided expert testimony against the equal-
time creationism law in McLean v. Arkansas. Gould later developed the term "non-overlapping magisteria"
(NOMA) to describe how, in his view, science and religion could not comment on each other's realm. Gould
went on to develop this idea in some detail, particularly in the books Rocks of Ages (1999) and The
Hedgehog, the Fox, and the Magister's Pox (2003). In a 1982 essay for Natural History Gould wrote:
Our failure to discern a universal good does not record any lack of insight or ingenuity, but
merely demonstrates that nature contains no moral messages framed in human terms. Morality
is a subject for philosophers, theologians, students of the humanities, indeed for all thinking
people. The answers will not be read passively from nature; they do not, and cannot, arise from
the data of science. The factual state of the world does not teach us how we, with our powers for
good and evil, should alter or preserve it in the most ethical manner.[45]
The anti-evolution petition A Scientific Dissent From Darwinism spawned the National Center for
Science Education's anti-petition Project Steve, which is named in Gould's honor.
Gould also became a noted public face of science, often appearing on television. In 1984 Gould
received his own NOVA special on PBS.[46] Other appearances included interviews on CNN's Crossfire,
NBC's The Today Show, and regular appearances on the Charlie Rose show. Gould was also a guest in all
seven episodes of the Dutch talk-series A Glorious Accident, which he appeared with his good friend Oliver
Sacks.[47]
Gould was featured prominently as a guest in Ken Burns' PBS documentary Baseball, as well as
PBS's highly produced Evolution series. Gould was also on the Board of Advisers to the influential Children's
Television Workshop television show, 3-2-1 Contact, where he made frequent guest appearances.
In 1997 he voiced a cartoon version of himself on the television series The Simpsons. In the episode
"Lisa the Skeptic", Lisa finds a skeleton that many people believe is an apocalyptic angel. Lisa contacts
Gould and asks him to test the skeleton's DNA. However the fossil is discovered to be a marketing gimmick
for a new mall.[48] During production the only phrase Gould objected to was a line in the script that
introduced him as the "world's most brilliant paleontologist."[49] In 2002 the show paid tribute to Gould after
his death, dedicating the season 13 finale to his memory. Gould had died 2 days before the episode aired.
[edit] Controversies
Gould received many accolades for his scholarly work and popular expositions of natural history,[14]
[50] but was not immune from criticism by those in the biological community who felt his public presentations
were, for various reasons, out of step with mainstream evolutionary theory.[51] The public debates between
Gould's proponents and detractors have been so quarrelsome that they have been dubbed "The Darwin
Wars" by several commentators.[52][53][54][55]
John Maynard Smith, an eminent British evolutionary biologist, was among Gould's strongest critics.
Maynard Smith thought that Gould misjudged the vital role of adaptation in biology, and was also critical of
Gould's acceptance of species selection as a major component of biological evolution.[56] In a review of
Daniel Dennett's book Darwin's Dangerous Idea, Maynard Smith wrote that Gould "is giving non-biologists a
largely false picture of the state of evolutionary theory."[57] But Maynard Smith has not been consistently
negative, writing in a review of The Panda's Thumb that "Stephen Gould is the best writer of popular science
now active. . . . Often he infuriates me, but I hope he will go right on writing essays like these."[58] Maynard
Smith was also among those who welcomed Gould's reinvigoration of evolutionary paleontology.[20]
One reason for such criticism was that Gould appeared to be presenting his ideas as a revolutionary
way of understanding evolution, and argued for the importance of mechanisms other than natural selection,
mechanisms which he believed had been ignored by many professional evolutionists. As a result, many non-
specialists sometimes inferred from his early writings that Darwinian explanations had been proven to be
unscientific (which Gould never tried to imply). Along with many other researchers in the field, Gould's works
were sometimes deliberately taken out of context by creationists as a "proof" that scientists no longer
understood how organisms evolved.[59] Gould himself corrected some of these misinterpretations and
distortions of his writings in later works.[60]
Gould and Dawkins also disagreed over the importance of gene selection in evolution. Dawkins
argued that evolution is best understood as competition among genes (or replicators), while Gould advocated
the importance of multi-level selection, including selection amongst genes, cell lineages, organisms, demes,
species, and clades.[55] Criticism of Gould and his theory of punctuated equilibrium can be found in chapter
9 of Dawkins' The Blind Watchmaker and chapter 10 of Dennett's Darwin's Dangerous Idea. Dawkins
subsequently offered a concession via an endnote in a new edition of his book The Selfish Gene, where he
states:
p.86 Progressive evolution may be not so much a steady upward climb as a series of discrete
steps from stable plateau to stable plateau
This paragraph is a fair summary of one way of expressing the now well-known theory of
punctuated equilibrium. I am ashamed to say that, when I wrote my conjecture, I, like many
biologists in England at the time, was totally ignorant of that theory, although it had been
published three years earlier. I have since, for instance in The Blind Watchmaker, become
somewhat petulant - perhaps too much so - over the way the theory of punctuated equilibrium
has been oversold. If this has hurt anybody's feelings, I regret it. They may like to note that, at
least in 1976, my heart was in the right place.[61]
[edit] Opposition to sociobiology and evolutionary psychology

Gould also had a long-running public feud with E. O. Wilson and other evolutionary biologists over
human sociobiology and its later descendant evolutionary psychology (which Gould, Lewontin, and Maynard
Smith opposed, but which Richard Dawkins, Daniel Dennett, and Steven Pinker advocated).[62] These
debates reached their climax in the 1970s, and included strong opposition from groups like the Sociobiology
Study Group and Science for the People.[63] Pinker accuses Gould, Lewontin and other opponents of
evolutionary psychology of being "radical scientists," whose stance on human nature is influenced by politics
rather than science.[64] Gould stated that he made "no attribution of motive in Wilson's or anyone else's
case" but cautioned that all human beings are influenced, especially unconsciously, by our personal
expectations and biases. He wrote:
I grew up in a family with a tradition of participation in campaigns for social justice, and I was
active, as a student, in the civil rights movement at a time of great excitement and success in the
early 1960s. Scholars are often wary of citing such commitments. … [but] it is dangerous for a
scholar even to imagine that he might attain complete neutrality, for then one stops being
vigilant about personal preferences and their influences—and then one truly falls victim to the
dictates of prejudice. Objectivity must be operationally defined as fair treatment of data, not
absence of preference.[65]
Gould's primary criticism held that human sociobiological explanations lacked evidential support, and
argued that adaptive behaviors are frequently assumed to be genetic for no other reason than their supposed
universality, or their adaptive nature. Gould emphasized that adaptive behaviors can be passed on through
culture as well, and either hypothesis is equally plausible.[66] Gould did not deny the relevance of biology to
human nature, but reframed the debate as "biological potentiality vs. biological determinism." Gould stated
that the human brain allows for a wide range of behaviors. Its flexibility "permits us to be aggressive or
peaceful, dominant or submissive, spiteful or generous… Violence, sexism, and general nastiness are
biological since they represent one subset of a possible range of behaviors. But peacefulness, equality, and
kindness are just as biological—and we may see their influence increase if we can create social structures
that permit them to flourish."[66]
[edit] Cambrian fauna
Gould's interpretation of the Cambrian Burgess Shale fossils in his book Wonderful Life emphasized
the striking morphological disparity (or "weirdness") of the Burgess Shale fauna, and the role of chance in
determining which members of this fauna survived and flourished. He used the Cambrian fauna as an
example of the role of contingency in the broader pattern of evolution.
Gould's view was criticized by Simon Conway Morris in his 1998 book The Crucible Of Creation.[67]
Conway Morris stressed those members of the Cambrian fauna that resemble modern taxa. He also
promoted convergent evolution as a mechanism producing similar forms in similar environmental
circumstances, and argued in a subsequent book that the appearance of human-like animals is likely.
Paleontologists Derek Briggs and Richard Fortey have also argued that much of the Cambrian fauna may be
regarded as stem groups of living taxa,[68] though this is still a subject of intense research and debate, and
the relationship of many Cambrian taxa to modern phyla has not been established in the eyes of many
palaeontologists.
Paleontologist Richard Fortey noted that prior to the release of Wonderful Life, Conway Morris
shared many of Gould's sentiments and views. It was only after publication of Wonderful Life that Conway
Morris revised his interpretation and adopted a more progressive stance towards the history of life.[69]
[edit] Mismeasure of Man

Main article: The Mismeasure of Man
Gould was the author of The Mismeasure of Man (1981), a history and inquiry of psychometrics and
intelligence testing. Gould investigated the methods of nineteenth century craniometry, as well as the history
of psychological testing. Gould claimed that both theories developed from an unfounded belief in biological
determinism, the view that "social and economic differences between human groups—primarily races,
classes, and sexes—arise from inherited, inborn distinctions and that society, in this sense, is an accurate
reflection of biology."[70]
It was reprinted in 1996 with the addition of a new foreword and a critical review of The Bell Curve.
The Mismeasure of Man has generated perhaps the greatest controversy of all of Gould's books. It has
received both widespread praise[71] and extensive criticism (by a number of psychologists),[72] which
included claims of misrepresentation.[73]
[edit] Non-overlapping magisteria

Main article: Non-overlapping magisteria
In his book Rocks of Ages (1999), Gould put forward what he described as "a blessedly simple and
entirely conventional resolution to...the supposed conflict between science and religion."[74] He defines the
term magisterium as "a domain where one form of teaching holds the appropriate tools for meaningful
discourse and resolution."[74] The non-overlapping magisteria (NOMA) principle therefore divides the
magisterium of science to cover "the empirical realm: what the Universe is made of (fact) and why does it
work in this way (theory). The magisterium of religion extends over questions of ultimate meaning and moral
value. These two magisteria do not overlap, nor do they encompass all inquiry."[74] He suggests that "NOMA
enjoys strong and fully explicit support, even from the primary cultural stereotypes of hard-line traditionalism"
and that NOMA is "a sound position of general consensus, established by long struggle among people of
goodwill in both magisteria."[74] This view has not been without criticism, however. In his book The God
Delusion, Richard Dawkins argues that this division is not quite as simple as it seems, as few religions exist
without miracles impinging on the scientific magisterium.
[edit] Gould's publications
[edit] Articles
During his lifetime, Stephen Jay Gould's publications were numerous. One review of his publications
between 1965 and 2000 noted 479 peer-reviewed papers, 22 books, 300 essays, and 101 major book
reviews by him.[75] A select number of his papers are listed online.
[edit] Books
The following is a list of books either written or edited by Stephen Jay Gould, including those
published posthumously, after his death in 2002. While some books have been republished at later dates, by
multiple publishers, the list below comprises the original publisher and publishing date.
• 1977. Ontogeny and Phylogeny, Cambridge MA: Belknap Press of Harvard University Press,
ISBN 0-674-63940-5 online preview
• 1977. Ever Since Darwin, New York: W. W. Norton, ISBN 978-0-393-06425-4
• 1980. The Panda's Thumb, New York: W. W. Norton, ISBN 0-393-01380-4
• 1980. Gould, Stephen Jay (1980-12), The Evolution of Gryphaea, New York: Arno Press,
ISBN 0-405-12751-0, http://books.google.com/?id=k4ykb5el47kC&printsec=frontcover&dq=
%22'The+Evolution+of+Gryphaea%22&q
• 1981. The Mismeasure of Man, New York: W. W. Norton, ISBN 978-0-393-31425-0
• 1983. Hen's Teeth and Horse's Toes, New York: W. W. Norton, ISBN 978-0-393-01716-8
• 1985. The Flamingo's Smile, New York: W. W. Norton, ISBN 0-393-02228-5
• 1987. Time's Arrow, Time's Cycle, Cambridge MA: Harvard Univ. Press, ISBN 0-674-89198-
8 online preview
• 1987. An Urchin in the Storm: Essays about Books and Ideas, N.Y.: W. W. Norton, ISBN 0-
393-02492-X
• 1989. Wonderful Life: The Burgess Shale and the Nature of History , New York: W. W.
Norton, ISBN 0-393-02705-8 . 347 pp.
• 1991. Bully for Brontosaurus, New York: W. W. Norton, ISBN 978-0-393-02961-1 . 540 pp.
• 1992. Finders, Keepers: Eight Collectors, New York: W. W. Norton, ISBN 978-0-393-03054-
9
• 1993. Eight Little Piggies, New York: W. W. Norton, ISBN 0-393-03416-X
• 1993. The Book of Life. Preface, pp. 6–21. New York: W. W. Norton (S. J. Gould general
editor, 10 contributors). ISBN 0-393-05003-3 review citing original publishing date
• 1995. Dinosaur in a Haystack, New York: Harmony Books, ISBN 0-517-70393-9
• 1996. Full House: The Spread of Excellence From Plato to Darwin , New York: Harmony
Books, ISBN 0-517-70394-7
• 1997. Questioning the Millennium: A Rationalist's Guide to a Precisely Arbitrary Countdown ,
New York: Harmony Books, ISBN 0-609-60541-0
• 1998. Leonardo's Mountain of Clams and the Diet of Worms, N.Y.: Harmony Books, ISBN 0-
609-60141-5
• 1999. Rocks of Ages: Science and Religion in the Fullness of Life, New York: Ballantine
Books, ISBN 0-345-43009-3
• 2000. The Lying Stones of Marrakech, New York: Harmony Books, ISBN 0-609-60142-3
• 2000. Crossing Over: Where Art and Science Meet, New York: Three Rivers Press, ISBN 0-
609-80586-X
• 2002. The Structure of Evolutionary Theory, Cambridge MA: Belknap Press of Harvard
University Press, ISBN 978-0-674-00613-3 online preview
• 2002. I Have Landed: The End of a Beginning in Natural History , New York: Harmony Books,
ISBN 0-609-60143-1
• 2003. Triumph and Tragedy in Mudville: A Lifelong Passion for Baseball, New York: W. W.
Norton, ISBN 0-393-05755-0
• 2003. The Hedgehog, the Fox, and the Magister's Pox, New York: Harmony Books, ISBN 0-
609-60140-7
• 2007. Punctuated Equilibrium, Cambridge MA: Belknap Press of Harvard University Press,
ISBN 0-674-02444-3 Book review
[edit] Notes and references

1. ^ Shermer, Michael (2002), "This View of Science", Social Studies of Science 32 (4): 489–
525, http://www.stephenjaygould.org/library/shermer_sjgould.pdf.
2. ^ a b Eldredge, Niles, and S. J. Gould (1972). "Punctuated equilibria: an alternative to phyletic
gradualism." In T.J.M. Schopf, ed., Models in Paleobiology. San Francisco: Freeman, Cooper and
Company, pp. 82-115.
3. ^ a b Gould, S. J. (1997). "Nonoverlapping magisteria". Natural History 106 (March): 16-22.
4. ^ a b Green, Michelle (1986). "Stephen Jay Gould: driven by a hunger to learn and to write".
People 25 (2 June): 109-114.
5. ^ a b Gould, S. J. (2002). The Structure of Evolutionary Theory. Cambridge: Belknap Press of
Harvard University Press. ISBN 0-674-00613-5
6. ^ a b Gould, S. J. (1981). "Official Transcript for Gould’s deposition in McLean v. Arkansas".
(Nov. 27). Under oath Gould stated: "My political views tend to the left of center. Q. Could you be
more specific about your political views? A. I don't know how to be. I am not a joiner, so I am not a
member of any organization. So I have always resisted labeling. But if you read my other book, The
Mismeasure of Man, which is not included because it is not about evolution, you will get a sense of
my political views". p. 153.
7. ^ Gasper, Phil (2002). "Stephen Jay Gould: Dialectical Biologist". International Socialist
Review 24 (July–August).
8. ^ Lewontin, Richard and Richard Levins (2002). "Stephen Jay Gould—what does it mean to
be a radical?" Monthly Review 54 (Nov. 1). "The public intellectual and political life of Steve Gould
was extraordinary, if not unique. First, he was an evolutionary biologist and historian of science
whose intellectual work had a major impact on our views of the process of evolution. Second, he
was, by far, the most widely known and influential expositor of science who has ever written for a lay
public. Third, he was a consistent political activist in support of socialism and in opposition to all
forms of colonialism and oppression. The figure he most closely resembled in these respects was the
British biologist of the 1930s, J. B. S. Haldane, a founder of the modern genetical theory of evolution,
a wonderful essayist on science for the general public, and an idiosyncratic Marxist and columnist for
the Daily Worker who finally split with the Communist Party over its demand that scientific claims
follow Party doctrine."
9. ^ Carol Kaesuk Yoon (2002). "Stephen Jay Gould, 60, Is Dead; Enlivened Evolutionary
Theory." New York Times May 21, 2002.
10.^ Gould, S. J. (1985). "The Median Isn't the Message". Discover 6 (June): 40-42.
11.^ Bakalar, James and Lester Grinspoon (1997). Marihuana, the Forbidden Medicine. New
Haven: Yale University Press, pp. 39-41.
12.^ Gould, S. J. (1993). "Dinomania". New York Review of Books 40 (August 12): 51-56.
13.^ Gould, S. J. (1983). Hen's Teeth and Horse's Toes. New York: W. W. Norton & Company.
ISBN 0-393-31103-1.
14.^ a b Harvard News Office (2002). "Paleontologist, author Gould dies at 60". The Harvard
Gazette. (May 20). Retrieved on 2009-6-4.
15.^ Krementz, Jill (2002). "Jill Krementz Photo Journal". New York Social Diary. Retrieved on
2009-6-4.
16.^ a b Allen, Warren (2008). "The Structure of Gould". In Warren Allen et al. Stephen Jay
Gould: Reflections on His View of Life. Oxford: Oxford University Press, p. 24, 59.
17.^ Masha, Etkin (2002). "A Tribute to Stephen Jay Gould '63". Antiochian (Winter ed.).
Retrieved on 2009-6-4.
18.^ Linnean Society of London (2008). "The Darwin-Wallace Medal". Retrieved on 2009-6-4.
19.^ Dawkins, Richard (1999). The Extended Phenotype. Oxfordshire: Oxford University Press.
p. 101. ISBN 0-19-288051-9.
20.^ a b Maynard Smith, John (1984), "Paleontology at the high table", Nature 309 (5967): 401–
402, doi:10.1038/309401a0.
21.^ Mayr, Ernst (1992). "Speciational Evolution or Punctuated Equilibria". In Steven Peterson
and Albert Somit. The Dynamics of Evolution. Ithaca: Cornell University Press, pp. 21-48. ISBN 0-
8014-9763-9.
22.^ Turner, John (1984). "Why we need evolution by jerks." New Scientist 101 (Feb. 9): 34-35.
23.^ Gould, S. J. and Steven Rose, ed. (2007). The Richness of Life: The Essential Stephen Jay
Gould. New York: W. W. Norton & Co., p. 6.
24.^ Thomas, R.D.K. (2009). "Gould, Stephen Jay (1941–2002)". in M. Ruse and J. Travis (eds).
Evolution: The First Four Billion Years. Cambridge MA: Belknap Press. pp. 611-615.
25.^ Prum, R.O., & Brush, A.H. (March 2003). "Which Came First, the Feather or the Bird?"
Scientific American, vol.288, no.3, pp.84-93
26.^ Gould, S. J.; Vrba, E. (1982), "Exaptation—a missing term in the science of form",
Paleobiology 8 (1): 4–15,
http://evolutionanddesign.googlepages.com/Gould__Vrba_1982_Exaptation.pdf.
27.^ Wilson, E. O. (1975). Sociobiology: The New Synthesis. Cambridge MA: Harvard University
Press.
28.^ Allen, Elizabeth, et al. (1975). "Against 'Sociobiology'". [letter] New York Review of Books
22 (Nov. 13): 182, 184-186.
29.^ Gould, S. J. (1980). "Sociobiology and the Theory of Natural Selection". In G. W. Barlow
and J. Silverberg, eds., Sociobiology: Beyond Nature/Nurture? Boulder CO: Westview Press, pp.
257-269.
30.^ Gould, S. J. and Richard Lewontin (1979). "The spandrels of San Marco and the
Panglossian paradigm: a critique of the adaptationist programme". Proc. R. Soc. Lond., B, Biol. Sci.
205 (1161): 581–98. DOI PMID; for background see Gould's "The Pattern of Life's History" in John
Brockman The Third Culture. New York: Simon & Schuster. 1996, pp. 52-64. ISBN 0-684-82344-6.
31.^ Gould, S. J. (1997). "The exaptive excellence of spandrels as a term and prototype". Proc.
Natl. Acad. Sci. U.S.A. 94 (20): 10750–5. DOI PMID
32.^ Maynard Smith, John (1995). "Genes, Memes, & Minds". The New York Review of Books
42 (Nov. 30): 46–48. "By and large, I think their [Spandrels] paper had a healthy effect. . . . Their
critique forced us to clean up our act and to provide evidence for our stories. But adaptationism
remains the core of biological thinking." A similar appraisal is reflected by Ernst Mayr in his 1983
paper "How to Carry Out the Adaptationist Program?" The American Naturalist 121 (3): 324–334; and
George C. Williams, Natural Selection: Domains, Levels, and Challenges. New York: Oxford
University Press. 1992.
33.^ Lloyd, E.A. (2005). The Case of The Female Orgasm: Bias in the science of evolution.
Cambridge MA: Harvard University Press.
34.^ Gould, S.J. (1992). "Male Nipples and Clitoral Ripples". In Bully for Brontosaurus: Further
Reflections in Natural History. New York: W. W. Norton. pp. 124-138.
35.^ Gould, S. J. (1996). Full House: The Spread of Excellence From Plato to Darwin. New
York: Harmony Books.
36.^ Dawkins, Richard; Gould, Stephen Jay (1997), "Human chauvinism", Evolution 51 (3):
1015–1020, doi:10.2307/2411179, http://www.simonyi.ox.ac.uk/dawkins/WorldOfDawkins-
archive/Dawkins/Work/Reviews/1997-06fullhouse.shtml.
37.^ Gould, S. J. (1991). "The disparity of the Burgess Shale arthropod fauna and the limits of
cladistic analysis". Paleobiology 17 (October): 411-423.
38.^ Baron, Christian and J. T. Høeg (2005). "Gould, Scharm and the Paleontologocal
Perspective in Evolutionary Biology". In S. Koenemann and R.A. Jenner, Crustacea and Arthropod
Relationships. CRC Press. pp. 3–14. ISBN 0-8493-3498-5.
39.^ Wolpert, Lewis and Alison Richards (1998). A Passion For Science. Oxford: Oxford
University Press, pp. 139-152. ISBN 0-19-854212-7
40.^ Gould, S. J. (1996). "A Cerion for Christopher". Natural History 105 (Oct.): 22-29, 78—79.
41.^ Google Scholar. http://scholar.google.com. Retrieved on 2009-8-22.
42.^ Prothero, Donald (2000). "Evolution Revolution: Paleontology, History, Biography". Skeptic
Festschrift lecture for Stephen Jay Gould. October 7, 2000.
43.^ Shermer, Michael (2002), "This View of Science", Social Studies of Science 32 (4): 518,
http://www.stephenjaygould.org/library/shermer_sjgould.pdf.
44.^ Gould, S. J. (2003). Triumph and Tragedy in Mudville. New York: W. W. Norton & Co. See
his essays: "The Streak of Streaks", "Thcience Studies", and "Baseball's reliquary: the oddly possible
hybrid of shrine and university"
45.^ Gould, S. J. (1982). "Nonmoral Nature". Natural History 91 (Feb.): 19–26.
46.^ PBS (1984). "Stephen Jay Gould: This View of Life". NOVA. December 18.
47.^ Sacks, Oliver (2007). Forward. In Steven Rose, ed. The Richness of Life. New York: W. W.
Norton & Company, p. xi. Video
48.^ Fox. The Simpsons. "Lisa the Skeptic", November 23, 1997. Audio here.
49.^ Scully, Mike (2006). The Simpsons. Season 9 DVD Commentary for "Lisa the Skeptic".
DVD. 20th Century Fox.
50.^ Shermer, Michael (2002). "This View of Science". Social Studies of Science 32 (4): 518.
Awards include a National Book Award for The Panda’s Thumb, a National Book Critics
Circle Award for The Mismeasure of Man, the Phi Beta Kappa Book Award for Hen’s
Teeth and Horse’s Toes, and a Pulitzer Prize Finalist for Wonderful Life, on which Gould
commented `close but, as they say, no cigar’. Forty-four honorary degrees and 66 major
fellowships, medals, and awards bear witness to the depth and scope of his
accomplishments in both the sciences and humanities: Member of the National
Academy of Sciences, President and Fellow of AAAS, MacArthur Foundation ‘genius’
Fellowship (in the first group of awardees), Humanist Laureate from the Academy of
Humanism, Fellow of the Linnean Society of London, Fellow of the Royal Society of
Edinburgh, Fellow of the American Academy of Arts and Sciences, Fellow of the
European Union of Geosciences, Associate of the Muséum National D’Histoire Naturelle
Paris, the Schuchert Award for excellence in paleontological research, Scientist of the
Year from Discover magazine, the Silver Medal from the Zoological Society of London,
the Gold Medal for Service to Zoology from the Linnean Society of London, the
Edinburgh Medal from the City of Edinburgh, the Britannica Award and Gold Medal for
dissemination of public knowledge, Public Service Award from the Geological Society of
America, Anthropology in Media Award from the American Anthropological Association,
Distinguished Service Award from the National Association of Biology Teachers,
Distinguished Scientist Award from UCLA, the Randi Award for Skeptic of the Year from
the Skeptics Society, and a Festschrift in his honour at Caltech.
51.^ Leda Cosmides and John Tooby (1997) write:

John Maynard Smith, one of the world's leading evolutionary biologists, recently
summarized in the NYRB the sharply conflicting assessments of Stephen Jay Gould:
"Because of the excellence of his essays, he has come to be seen by non-biologists as
the preeminent evolutionary theorist. In contrast, the evolutionary biologists with whom I
have discussed his work tend to see him as a man whose ideas are so confused as to
be hardly worth bothering with, but as one who should not be publicly criticized because
he is at least on our side against the creationists." (NYRB, Nov. 30th 1995, p. 46). No
one can take any pleasure in the evident pain Gould is experiencing now that his actual
standing within the community of professional evolutionary biologists is finally becoming
more widely known. . . But as Maynard Smith points out, more is at stake. Gould "is
giving non-biologists a largely false picture of the state of evolutionary theory"—or as
Ernst Mayr says of Gould and his small group of allies—they "quite conspicuously
misrepresent the views of [biology's] leading spokesmen." Indeed, although Gould
characterizes his critics as "anonymous" and "a tiny coterie," nearly every major
evolutionary biologist of our era has weighed in a vain attempt to correct the tangle of
confusions that the higher profile Gould has inundated the intellectual world with.* The
point is not that Gould is the object of some criticism—so properly are we all—it is that his
reputation as a credible and balanced authority about evolutionary biology is non-
existent among those who are in a professional position to know. *These include Ernst
Mayr, John Maynard Smith, George Williams, Bill Hamilton, Richard Dawkins, E.O.
Wilson, Tim Clutton-Brock, Paul Harvey, Brian Charlesworth, Jerry Coyne, Robert
Trivers, John Alcock, Randy Thornhill, and many others.
It should be noted that Ernst Mayr in this quotation is not speaking of Gould in particular, and does
not mention him by name, but is speaking generally of the critics of the Neo-Darwinian Synthesis.
Some of the names Tooby and Cosmides cite are also questionable. For example, Mayr, Williams,
Hamilton, Dawkins, Wilson, Coyne, and Trivers have shown great respect for Gould as a scientist. In
reference to Maynard Smith's comments, Gould writes "Darwinian Fundamentalism" New York
Review of Books 44 (June 12, 1997): 34-37:
A false fact can be refuted, a false argument exposed; but how can one respond
to a purely ad hominem attack? This harder, and altogether more discouraging,
task may best be achieved by exposing internal inconsistency and unfairness of
rhetoric. . . . It seems futile to reply to an attack so empty of content, and based
only on comments by anonymous critics . . . Instead of responding to Maynard
Smith's attack against my integrity and scholarship, citing people unknown and
with arguments unmentioned, let me, instead, merely remind him of the blatant
inconsistency between his admirable past and lamentable present. Some sixteen
years ago he wrote a highly critical but wonderfully supportive review of my early
book of essays, The Panda's Thumb, stating: "I hope it will be obvious that my
wish to argue with Gould is a compliment, not a criticism." He then attended my
series of Tanner Lectures at Cambridge in 1984 and wrote in a report for Nature,
and under the remarkable title "Paleontology at the High Table", the kindest and
most supportive critical commentary I have ever received. He argued that the
work of a small group of American paleobiologists had brought the entire subject
back to theoretical centrality within the evolutionary sciences. . . . So we face the
enigma of a man who has written numerous articles, amounting to tens of
thousands of words, about my work—always strongly and incisively critical, always
richly informed (and always, I might add, enormously appreciated by me). But
now Maynard Smith needs to canvass unnamed colleagues to find out that my
ideas are "hardly worth bothering with." He really ought to be asking himself why
he has been bothering about my work so intensely, and for so many years.
52.^ Brown, Andrew (1999). The Darwin Wars: The Scientific Battle for the Soul of Man.
London: Simon & Schuster. ISBN 0-8050-7137-7
53.^ Rose, Steven (2002). "Obituaries: Stephen Jay Gould". The Guardian (May 22): 20.
54.^ Blume, Harvey (2002). "The Origin of Specious". The American Prospect (September 22):
41–43.
55.^ a b Sterelny, Kim (2007), Dawkins vs. Gould: Survival of the Fittest, Cambridge, U.K.: Icon
Books, ISBN 1-84046-780-0 Also ISBN 978-1-84046-780-2
56.^ Maynard Smith, John (1981). "Did Darwin get it right?" The London Review of Books 3 (11):
10-11; Also reprinted in Did Darwin Get it Right? New York: Chapman and Hall, 1989, pp. 148-156.
57.^ Maynard Smith, John (1995). "Genes, Memes, & Minds". The New York Review of Books
42 (Nov. 30): 46–48.
58.^ Maynard Smith, John (1981). "Review of The Panda's Thumb" The London Review of
Books pp. 17–30; Reprinted as "Tinkering" in his Did Darwin Get It Right? New York: Chapman and
Hall. 1989, pp. 94, 97.
59.^ Wright, Robert (1999). "The Accidental Creationist: Why Stephen J. Gould is bad for
evolution". The New Yorker 75 (Dec. 13): 56-65.
60.^ Gould, S. J. (1981). "Evolution as fact and theory". Discover 2 (May): 34-37.
61.^ Dawkins, Richard (1989). The Selfish Gene. Oxford: Oxford University Press. (Endnotes to
chapter 5, p.287) ISBN 0-19-286092-5 The endnote online
62.^ Gould, S. J. (1997). "Evolution: The pleasures of pluralism". The New York Review of
Books 44 (June 26): 47–52.
63.^ Wilson, E. O. (2006). Naturalist New York: Island Press, p.337 ISBN 1-59726-088-6.
64.^ Pinker, Steven (2002), The Blank Slate: The Modern Denial of Human Nature, New York:
Penguin Books, ISBN 0142003344
65.^ Gould S. J. (1996). The Mismeasure of Man: Revised and Expanded Edition . New York: W.
W. Norton & Co., p. 36. ISBN 0-14-025824-8
66.^ a b Gould, S. J. (1992). "Biological potentiality vs. biological determinism". In Ever Since
Darwin. New York: W. W. Norton & Co., pp. 251-259.
67.^ Conway Morris, S.; Gould, S. J. (1998), "Showdown on the Burgess Shale", Natural History
107: 48–55, http://www.stephenjaygould.org/library/naturalhistory_cambrian.html.
68.^ Briggs, Derek; Fortey, Richard (2005), "Wonderful Strife: systematics, stem groups, and the
phylogenetic signal of the Cambrian radiation", Paleobiology 31 (2): 94–112, doi:10.1666/0094-
8373(2005)031[0094:WSSSGA]2.0.CO;2,
http://www.colorado.edu/geolsci/courses/GEOL3410/BriggsFortey05_CambrianRadiation.pdf.
Abstract
69.^ Fortey, Richard (1998). "Shock Lobsters". London Review of Books 20 (Oct. 1).
70.^ Gould, S. J. (1981). The Mismeasure of Man. New York: W.W. Norton & Co. p. 20.
71.^ In 1981 The Mismeasure of Man won the National Book Critics Circle Award for non-fiction.
It was voted as the 17th greatest science book of all time by Discover magazine vol. 27 (8 Dec.
2006); 9th best skeptic book by The Skeptics Society (Frank Diller, "Scientists' Nightstand" American
Scientist); and ranked 24th place for the best non-fiction book by the Modern Library.
72.^ Blinkhorn, Steve (1982). "What Skulduggery?" Nature 296 (April 8): 506.
73.^ Jensen, Arthur (1982), "The Debunking of Scientific Fossils and Straw Persons",
Contemporary Education 1 (2): 121–135, http://www.debunker.com/texts/jensen.html.
74.^ a b c d Gould, S. J. (2002). Rocks of Ages: Science and Religion in the Fullness of Life. New
York: Ballantine Books.
75.^ Shermer, Michael (2002), p.496

Wikiquote has a collection of quotations related to: Stephen Jay Gould
• The Unofficial Stephen Jay Gould Archive

• Excerpts from Gould Lectures at Stanford University
• Richard C. Lewontin sums up Gould's career in an obituary
• "Darwinian Fundamentalism" - Gould's response to Daniel Dennett and other critics
• McLean v. Arkansas Creationism Trial - Plaintiff's transcript of Gould's testimony
• Stephen Jay Gould Charlie Rose interviews
[hide]v · d · eBooks by Stephen Jay Gould

An Urchin in the Storm · The Mismeasure of Man · Time's
General Arrow, Time's Cycle · Wonderful Life · Full House · Questioning the
Millennium · Rocks of Ages · The Hedgehog, the Fox, and the
Magister's Pox
Ever Since Darwin · The Panda's Thumb · Hen's Teeth and

Essay Horse's Toes · The Flamingo's Smile · Bully for Brontosaurus ·
collections Eight Little Piggies · Dinosaur in a Haystack · Leonardo's Mountain
in Natural History of Clams and the Diet of Worms · The Lying Stones of Marrakech ·
I Have Landed
Technical Ontogeny and Phylogeny · The Structure of Evolutionary

Theory
Persondata
Name Gould, Stephen Jay
Alternative names
Short description American paleontologist, evolutionary biologist, and historian of science
Date of birth September 10, 1941

Place of birth New York City, New York
Date of death May 20, 2002
Place of death Manhattan, New York City, New York

Retrieved from "http://en.wikipedia.org/wiki/Stephen_Jay_Gould"
Categories: 1941 births | 2002 deaths | American agnostics | American essayists | American
paleontologists | American science writers | American socialists | American voice actors | Antioch College
alumni | Cancer deaths in New York | Columbia University alumni | Deaths from lung cancer | Developmental
biologists | Evolutionary biologists | Fellows of the American Academy of Arts and Sciences | Fellows of the
American Association for the Advancement of Science | Harvard University faculty | Historians of science |
Human evolution theorists | American Jews | Jewish agnostics | Jewish American scientists | Jewish
American writers | Jewish skeptics | MacArthur Fellows | Members of the United States National Academy of
Sciences | New York University faculty | People from Queens | Race and intelligence controversy | People
associated with the American Museum of Natural History
W000
Chimpanzee
"Panina" redirects here. For the Russian surname Panina, see Panin.
Chimpanzees[1]
Common Chimpanzee (Pan troglodytes)
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominidae
Subfamily: Homininae
Tribe: Hominini
Subtribe: Panina
Pan
Genus:
Oken, 1816
Type species
Pan troglodytes (Common Chimpanzee)

Pan paniscus (Bonobo)
Species
Pan troglodytes
Pan paniscus
Distribution of Pan troglodytes (Common Chimpanzee) and Pan paniscus (Bonobo, in red).
Chimpanzee, sometimes colloquially chimp, is the common name for the two extant species of ape in
the genus Pan. The Congo River forms the boundary between the native habitat of the two species:[2]
• Common Chimpanzee, Pan troglodytes (West and Central Africa)
• Bonobo, Pan paniscus (forests of the Democratic Republic of the Congo)
Chimpanzees are members of the Hominidae family, along with gorillas, humans, and orangutans.
Chimpanzees split from human evolution about 6 million years ago and the two chimpanzee species are the
closest living relatives to humans, all being members of the Hominini tribe (along with extinct species of
Hominina subtribe). Chimpanzees are the only known members of the Panina subtribe. The two Pan species
split only about one million years ago.
Contents
[hide]
• 1.1 Evolutionary relationship
• 1.2 Fossils
• 2 Anatomy and physiology
• 3 Behaviors
• 3.1 Social structure
• 3.2 Intelligence
• 3.2.1 Tool use
• 3.2.2 Empathy
• 3.2.3 Communication
• 3.2.4 Studies of language
• 3.2.5 Memory
• 3.2.6 Laughter in apes
• 3.3 Aggression
• 4 Interactions with humans
• 4.1 History
• 4.2 Studies
• 5 In popular culture
• 5.1 Portrayals in science fiction
• 6 See also
Evolutionary relationship
Further information: History of hominoid taxonomy
The taxonomic relationships of Hominoidea

The genus Pan is considered to be part of the subfamily Homininae to which humans also belong.
These two species are the closest living evolutionary relatives to humans, sharing a common ancestor with
humans six million years ago.[3] Research by Mary-Claire King in 1973 found 99% identical DNA between
human beings and chimpanzees,[4] although research since has modified that finding to about 94%[5]
commonality, with some of the difference occurring in non-coding DNA. It has been proposed that
troglodytes and paniscus belong with sapiens in the genus Homo, rather than in Pan. One of the arguments
for this is that other species have been reclassified to belong to the same genus on the basis of less genetic
similarity than that between humans and chimpanzees.
Fossils
A lot of human fossils have been found, but chimpanzee fossils were not described until 2005.
Existing chimpanzee populations in West and Central Africa do not overlap with the major human fossil sites
in East Africa. However, chimpanzee fossils have now been reported from Kenya. This would indicate that
both humans and members of the Pan clade were present in the East African Rift Valley during the Middle
Pleistocene.[6]
Anatomy and physiology

The male common chimp is up to 1.7 metres (5.6 ft) high when standing, and weighs as much as
70 kilograms (150 lb); the female is somewhat smaller. The common chimp’s long arms, when extended,
have a span one and a half times as long as the body’s height and a chimpanzee's arms are longer than its
legs.[7] The bonobo is a little shorter and thinner than the common chimpanzee but has longer limbs. Both
species use their long, powerful arms for climbing in trees. On the ground, chimpanzees usually walk on all
fours using their knuckles for support with their hands clenched, a form of locomotion called knuckle-walking.
Chimpanzee feet are better suited for walking than are those of the orangutan because the chimp’s soles are
broader and the toes shorter. Both the common chimpanzee and bonobo can walk upright on two legs when
carrying objects with their hands and arms. The Bonobo has proportionately longer upper limbs and tends to
walk upright more often than the Common Chimpanzee. The coat is dark; the face, fingers, palms of the
hands, and soles of the feet are hairless; and the chimp has no tail. The exposed skin of the face, hands and
feet varies from pink to very dark in both species, but is generally lighter in younger individuals, darkening as
maturity is reached. A University of Chicago Medical Centre study has found significant genetic differences
between chimpanzee populations.[8] A bony shelf over the eyes gives the forehead a receding appearance,
and the nose is flat. Although the jaws protrude, the lips are thrust out only when a chimp pouts. The brain of
a chimpanzee is about half the size of the human brain.[9]
Chimpanzee testicles are unusually large for their body size, with a combined weight of about
4 ounces (110 g) compared to a gorilla's 1 ounce (28 g) or a human's 1.5 ounces (43 g). This is generally
attributed to sperm competition due to the polyandrous nature of chimpanzee mating behavior.[10]
Chimpanzees reach puberty at an age of between 8 and 10 years and rarely live past the age of 40 in the
wild, but have been known to reach the age of more than 60 in captivity.
Behaviors
Bonobo
Anatomical differences between the Common Chimpanzee and the Bonobo are slight, but in sexual
and social behaviour there are marked differences. The Common Chimpanzee has an omnivorous diet, a
troop hunting culture based on beta males led by an alpha male, and highly complex social relationships. The
Bonobo, on the other hand, has a mostly frugivorous diet and an egalitarian, nonviolent, matriarchal, sexually
receptive behaviour.[11] Bonobos are well known to have frequent sex, with bisexuality the norm for both
males and females, and also to use sex to help prevent and resolve conflicts. Different groups of
chimpanzees also have different cultural behaviour with preferences for types of tools.[12] The Common
Chimpanzee tends to display higher levels of aggression than the Bonobo.[13]
Social structure
Chimpanzees live in large multi-male and multi-female social groups called communities. Within a
community there is a definite social hierarchy which is dictated by the position of an individual and the
influence the individual has on others. Chimpanzees live in a leaner hierarchy in which more than one
individual may be dominant enough to dominate other members of lower rank. Typically there is a dominant
male referred to as the Alpha male. The Alpha male is the highest-ranking male who controls the group and
maintains order during any disputes. In chimpanzee society the 'dominant male' does not always have to be
the largest or strongest male but rather the most manipulative and political male who can influence the
goings on within a group. Male chimpanzees typically attain dominance through cultivating allies who will
provide support for that individual in case of future ambitions for power. It's within a male chimpanzee's
character to display in an attempt to show strength and recognition from others which may be fundamental to
holding on to status. The alpha male will regularly display by making their normally slim coats puffed up to
increase view size and charge to look as threatening and as powerful as possible to intimidate other
members in an attempt to hold on to power and maintain authority. Lower-ranking chimpanzees will show
respect by making submissive gestures in body language or reaching out their hand while grunting. Female
chimpanzees will show deference to the alpha male by presenting their hind-quarters.
Female chimpanzees also have a hierarchy which is influenced by the position of a female individual
within a group. In some chimpanzee communities, the young females may inherit high status from a high-
ranking mother. The females will also form allies to dominate lower-ranking females. In contrast to males who
have a main purpose of acquiring dominant status for access to mating privileges and sometimes violent
domination of subordinates, females acquire dominant status for access to resources such as food. High-
ranking females will often get first access to resources. In general, both genders acquire dominant status to
improve social standing within a group.
Its often the females who choose the alpha male. For a male chimpanzee to win the alpha status he
must gain acceptance from the females in the community as they are the ones who actually dictate the way
the lifestyles are set up (the females are the ones who ensure the survival of the next generation; they have
to make sure that their group is going to places that supply them with enough food). There are cases where a
group of dominant females will oust an alpha male who is not to their preference and rather back up the other
male who they see potential of leading the group as a successful alpha male.
Intelligence
Further information: Primate cognition
Diagram of brain. Topography of the main groups of foci in the motor field of Chimpanzee
Chimpanzees make tools and use them to acquire foods and for social displays; they have
sophisticated hunting strategies requiring cooperation, influence and rank; they are status conscious,
manipulative and capable of deception; they can learn to use symbols and understand aspects of human
language including some relational syntax, concepts of number and numerical sequence;[14] and they are
capable of spontaneous planning for a future state or event.[15]
Tool use
One of the most significant discoveries was in October 1960 when Jane Goodall observed the use of
tools among chimpanzees. Recent research indicates that chimpanzee stone tool use dates to at least 4,300
years ago.[16] Chimpanzee tool usage includes digging into termite mounds with a large stick tool, and then
using a small stick that has been altered to "fish" the termites out.[17] A recent study revealed the use of
such advanced tools as spears, with which Common Chimpanzees in Senegal sharpen with their teeth and
use to spear Senegal Bushbabies out of small holes in trees.[18][19] Before the discovery of tool use in
chimps, it was believed that humans were the only species to make and use tools, but several other tool-
using species are now known.[20][21]
Empathy
Chimpanzee mother and baby

Recent studies have shown that chimpanzees engage in apparently altruistic behaviour within
groups,[22][23] but are indifferent to the welfare of unrelated group members.[24]
Evidence for "chimpanzee spirituality" includes display of mourning, "incipient romantic love", "rain
dance", appreciation of natural beauty such as a sunset over a lake, curiosity and respect towards wildlife
(such as the python, which is neither a threat nor a food source to chimpanzees), empathy toward other
species (such as feeding turtles) and even "animism" or "pretend play" in chimps cradling and grooming
rocks or sticks.[25]
Communication
Chimps communicate in a manner similar to human non-verbal communication, using vocalizations,
hand gestures, and facial expressions. Research into the chimpanzee brain has revealed that chimp
communication activates an area of the chimp brain that is in the same position as Broca's area, the
language center in the human brain.[26]
Studies of language
Main article: Great ape language
Side profile of a Chimpanzee
Scientists have long been fascinated with the studies of language, believing it to be a unique human
cognitive ability. To test this hypothesis, scientists have attempted to teach human language to several
species of great apes. One early attempt by Allen and Beatrice Gardner in the 1960s involved spending 51
months teaching American Sign Language to a chimpanzee named Washoe. The Gardners reported that
Washoe learned 151 signs, and that she had spontaneously taught them to other chimpanzees.[27] Over a
longer period of time, Washoe learned over 800 signs.[28]
There is ongoing debate among some scientists, notably Noam Chomsky and David Premack, about
non-human great apes' ability to learn language. Since the early reports on Washoe, numerous other studies
have been conducted with varying levels of success,[29] including one involving a chimpanzee named, in
parody, Nim Chimpsky, trained by Herbert Terrace of Columbia University. Although his initial reports were
quite positive, in November 1979, Terrace and his team re-evaluated the videotapes of Nim with his trainers,
analyzing them frame by frame for signs as well as for exact context (what was happening both before and
after Nim’s signs). In the re-analysis, Terrace concluded that Nim’s utterances could be explained merely as
prompting on the part of the experimenters, as well as mistakes in reporting the data. “Much of the apes’
behavior is pure drill,” he said. “Language still stands as an important definition of the human species.” In this
reversal, Terrace now argued that Nim’s use of ASL was not like human language acquisition. Nim never
initiated conversations himself, rarely introduced new words, and simply imitated what the humans did. Nim’s
sentences also did not grow in length, unlike human children whose vocabulary and sentence length show a
strong positive correlation.[30]
Memory
A 30-year study at Kyoto University’s Primate Research Institute has shown that chimps are able to
learn to recognize the numbers 1-9 and their values. The chimps further show an aptitude for photographic
memory, demonstrated in experiments in which the jumbled digits 1-9 are flashed onto a computer screen for
less than a quarter of a second, after which the chimp, Ayumu, is able to correctly and quickly point to the
positions where they appeared in ascending order. The same experiment was failed by world memory
champion Ben Pridmore on most attempts.[31]
Laughter in apes
Young chimpanzees playing

Laughter might not be confined or unique to humans. The differences between chimpanzee and
human laughter may be the result of adaptations that have evolved to enable human speech. Self-awareness
of one's situation as seen in the mirror test, or the ability to identify with another's predicament (see mirror
neurons), are prerequisites for laughter, so animals may be laughing in the same way that humans do.
Chimpanzees, gorillas, and orangutans show laughterlike vocalizations in response to physical
contact, such as wrestling, play chasing, or tickling. This is documented in wild and captive chimpanzees.
Common Chimpanzee laughter is not readily recognizable to humans as such, because it is generated by
alternating inhalations and exhalations that sound more like breathing and panting. There are instances in
which non-human primates have been reported to have expressed joy. One study analyzed and recorded
sounds made by human babies and Bonobos when tickled. It found that although the Bonobo's laugh was a
higher frequency, the laugh followed a pattern similar to that of human babies and included similar facial
expressions. Humans and chimpanzees share similar ticklish areas of the body, such as the armpits and
belly. The enjoyment of tickling in chimpanzees does not diminish with age.[32]
See also: Laughter in animals
Aggression
Male chimpanzees in Mahale National Park, Tanzania

Adult Common Chimpanzees, particularly males, can be very aggressive. They are highly territorial
and are known to kill other chimps.[33] Chimpanzees also engage in targeted hunting of lower order primates
such as the red colobus[34] and bush babies,[35][36] and use the meat from these kills as a "social tool"
within their community.[37] In February 2009, after an incident in which a pet chimp named Travis attacked
and mutilated a woman in Stamford, Connecticut, the U.S. House of Representatives approved a primate pet
ban in the United States.[38]
Interactions with humans

History
Gregoire: 62-year-old chimpanzee

Africans have had contact with chimpanzees for millennia. Chimpanzees have been kept as pets for
centuries in a few African villages, especially in the Democratic Republic of Congo. In Virunga National Park
in the east of the country the park authorities regularly confiscate chimpanzees from people who are keeping
them as pets.[39] The first recorded contact of Europeans with chimps took place in present-day Angola
during the 17th century. The diary of Portuguese explorer Duarte Pacheco Pereira (1506), preserved in the
Portuguese National Archive (Torre do Tombo), is probably the first European document to acknowledge that
chimpanzees built their own rudimentary tools.
The first use of the name "chimpanzee", however, did not occur until 1738. The name is derived from
a Tshiluba language term "kivili-chimpenze", which is the local name for the animal and translates loosely as
"mockman" or possibly just "ape". The colloquialism " chimp" was most likely coined some time in the late
1870s.[40] Biologists applied Pan as the genus name of the animal. Chimps as well as other apes had also
been purported to have been known to Western writers in ancient times, but mainly as myths and legends on
the edge of European and Arab societal consciousness, mainly through fragmented and sketchy accounts of
European adventurers. Apes are mentioned variously by Aristotle, as well as the English Bible, where they
are described as having been collected by Solomon. (1 Kings 10:22. However the Hebrew word, qőf, may
mean a monkey.) Apes are mentioned in the Qur'an (7:166), where God tells Israelites who transgressed
Shabbat "Be ye apes".
Hugo Rheinhold's Affe mit Schädel ("Ape with skull") is an example of how chimps were viewed at
the end of the 19th century.
The first of these early transcontinental chimpanzees came from Angola and were presented as a gift
to Frederick Henry, Prince of Orange in 1640, and were followed by a few of its brethren over the next
several years. Scientists described these first chimpanzees as "pygmies", and noted the animals' distinct
similarities to humans. The next two decades would see a number of the creatures imported into Europe,
mainly acquired by various zoological gardens as entertainment for visitors.
Darwin's theory of natural selection (published in 1859) spurred scientific interest in chimpanzees, as
in much of life science, leading eventually to numerous studies of the animals in the wild and captivity. The
observers of chimpanzees at the time were mainly interested in behaviour as it related to that of humans.
This was less strictly and disinterestedly scientific than it might sound, with much attention being focused on
whether or not the animals had traits that could be considered 'good'; the intelligence of chimpanzees was
often significantly exaggerated, as immortalized in Hugo Rheinhold's Affe mit Schädel (see image, left). By
the end of the 19th century chimpanzees remained very much a mystery to humans, with very little factual
scientific information available.
The 20th century saw a new age of scientific research into chimpanzee behaviour. Before 1960,
almost nothing was known about chimpanzee behaviour in their natural habitat. In July of that year, Jane
Goodall set out to Tanzania's Gombe forest to live among the chimpanzees, where she primarily studied the
members of the Kasakela chimpanzee community. Her discovery that chimpanzees made and used tools
was groundbreaking, as humans were previously believed to be the only species to do so. The most
progressive early studies on chimpanzees were spearheaded primarily by Wolfgang Köhler and Robert
Yerkes, both of whom were renowned psychologists. Both men and their colleagues established laboratory
studies of chimpanzees focused specifically on learning about the intellectual abilities of chimpanzees,
particularly problem-solving. This typically involved basic, practical tests on laboratory chimpanzees, which
required a fairly high intellectual capacity (such as how to solve the problem of acquiring an out-of-reach
banana). Notably, Yerkes also made extensive observations of chimpanzees in the wild which added
tremendously to the scientific understanding of chimpanzees and their behaviour. Yerkes studied
chimpanzees until World War II, while Köhler concluded five years of study and published his famous
Mentality of Apes in 1925 (which is coincidentally when Yerkes began his analyses), eventually concluding
that "chimpanzees manifest intelligent behaviour of the general kind familiar in human beings ... a type of
behaviour which counts as specifically human" (1925).[41]
Chimpanzee at the Los Angeles Zoo
The August 2008 issue of the American Journal of Primatology reported results of a year-long study
of chimpanzees in Tanzania’s Mahale Mountains National Park which produced evidence that chimpanzees
are becoming sick from viral infectious diseases they have likely contracted from humans. Molecular,
microscopic and epidemiological investigations demonstrated that the chimpanzees living at Mahale
Mountains National Park have been suffering from a respiratory disease that is likely caused by a variant of a
human paramyxovirus.[42]
Studies
As of November 2007, there were 1,300 chimpanzees housed in 10 U.S. laboratories (out of 3,000
great apes living in captivity there), either wild-caught, or acquired from circuses, animal trainers, or zoos.[43]
Most of the labs either conduct or make the chimps available for invasive research,[44] defined as
"inoculation with an infectious agent, surgery or biopsy conducted for the sake of research and not for the
sake of the chimpanzee, and/or drug testing".[45] Two federally-funded laboratories use chimps: Yerkes
National Primate Research Laboratory at Emory University in Atlanta, Georgia, and the Southwest National
Primate Center in San Antonio, Texas.[46] Five hundred chimps have been retired from laboratory use in the
U.S. and live in sanctuaries in the U.S. or Canada.[44]
Enos the space chimp before being inserted into the Mercury-Atlas 5 capsule in 1961.
Chimpanzees used in biomedical research tend to be used repeatedly over decades, rather than
used and killed as with most laboratory animals. Some individual chimps currently in U.S. laboratories have
been used in experiments for over 40 years.[47] According to Project R&R, a campaign to release chimps
held in U.S. labs—run by the New England Anti-Vivisection Society in conjunction with Jane Goodall and
other primate researchers—the oldest known chimp in a U.S. lab is Wenka, who was born in a laboratory in
Florida on May 21, 1954.[48] She was removed from her mother on the day of birth to be used in a vision
experiment that lasted 17 months, then sold as a pet to a family in North Carolina. She was returned to the
Yerkes National Primate Research Center in 1957 when she became too big to handle. Since then, she has
given birth six times, and has been used in research into alcohol use, oral contraceptives, ageing, and
cognitive studies.[49]
With the publication of the chimpanzee genome, there are reportedly plans to increase the use of
chimps in labs, with some scientists arguing that the federal moratorium on breeding chimps for research
should be lifted.[46][50] A five-year moratorium was imposed by the U.S. National Institutes of Health (NIH) in
1996, because too many chimps had been bred for HIV research, and it has been extended annually since
2001.[46]
Other researchers argue that chimps are unique animals and either should not be used in research,
or should be treated differently. Pascal Gagneux, an evolutionary biologist and primate expert at the
University of California, San Diego, argues that, given chimpanzees' sense of self, tool use, and genetic
similarity to human beings, studies using chimps should follow the ethical guidelines that are used for human
subjects unable to give consent.[46] Also, a recent study suggests that chimpanzees which are retired from
labs exhibit a form of posttraumatic stress disorder.[51] Stuart Zola, director of the Yerkes National Primate
Research Laboratory, disagrees. He told National Geographic: "I don't think we should make a distinction
between our obligation to treat humanely any species, whether it's a rat or a monkey or a chimpanzee. No
matter how much we may wish it, chimps are not human."[46]
An increasing number of governments are enacting a Great Ape research ban forbidding the use of
chimpanzees and other great apes in research or toxicology testing.[52] As of 2006, Austria, New Zealand,
the Netherlands, Sweden, and the UK had introduced such bans.[53]
In popular culture
See also: List of fictional apes and Category:Famous apes
Chimpanzees have been commonly stereotyped in popular culture, where they are most often cast in
standardized roles[54] as childlike companions, sidekicks or clowns.[55] They are especially suited for the
latter role on account of their prominent facial features, long limbs and fast movements, which humans often
find amusing.[55] Accordingly, entertainment acts featuring chimpanzees dressed up as humans have been
traditional staples of circuses and stage shows.[55]
In the age of television, a new genre of chimp act emerged in the United States: series whose cast
consisted entirely of chimpanzees dressed as humans and "speaking" lines dubbed by human actors.[54]
These shows, examples of which include Lancelot Link, Secret Chimp in the 1970s or The Chimp Channel in
the 1990s, relied on the novelty of their ape cast to make their timeworn, low comedy gags funny.[54] Their
chimpanzee "actors" were as interchangeable as the apes in a circus act, being amusing as chimpanzees
and not as individuals.[54] Animal rights group, PETA, has urged advertisers against the use of chimpanzees
in television and commercials, citing animal abuse.[56]
When chimpanzees appear in other TV shows, they generally do so as comic relief sidekicks to
humans. In that role, for instance, J. Fred Muggs appeared with Today Show host Dave Garroway in the
1950s, Judy on Daktari in the 1960s or Darwin on The Wild Thornberrys in the 1990s.[54] In contrast to the
fictional depictions of other animals, such as dogs (as in Lassie), dolphins (Flipper), horses (The Black
Stallion) or even other great apes (King Kong), chimpanzee characters and actions are rarely relevant to the
plot.[54]
Portrayals in science fiction

The rare depictions of chimpanzees as individuals rather than stock characters, and as central rather
than incidental to the plot[54] are generally found in works of science fiction. Robert A. Heinlein's short story
"Jerry Was a Man" (1947) centers on a genetically enhanced chimpanzee suing for better treatment. The
1972 film Conquest of the Planet of the Apes, set in the near future, portrays a revolt of enslaved apes led by
the only talking chimpanzee, Caesar, against their human masters.[54] Another short story "The Pope of the
Chimps" by Robert Silverberg, set in the present day, shows the development of the first signs of religiosity in
a group of chimpanzees, much to the surprise of the humans observing them. David Brin's Uplift novels
present a future in which humans have "uplifted" chimpanzees (and certain other species) with human-level
sapience.
See also
Mammals portal
• Chimp Haven
• Chimpanzee genome project
• Great ape personhood
• List of apes
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42.^ Newswise: Researchers Find Human Virus in Chimpanzees Retrieved on June 5, 2008.
43.^ "End chimpanzee research: overview". Project R&R, New England Anti-Vivisection Society.
2005-12-11. http://www.releasechimps.org/mission/end-chimpanzee-research. Retrieved 2008-03-
24.
44.^ a b "Chimpanzee lab and sanctuary map". The Humane Society of the United States.
http://www.hsus.org/animals_in_research/chimps_deserve_better/research/chimpanzee-lab-and-
sanctuary-map.html. Retrieved 2008-03-24.
45.^ "Chimpanzee Research: Overview of Research Uses and Costs". Humane Society of the
United States. Archived from the original on 2008-03-07.
http://web.archive.org/web/20080307055406/http://www.hsus.org/animals_in_research/chimps_dese
rve_better/research/overview_of_research_uses_and.html. Retrieved 2008-03-24.
46.^ a b c d e Lovgren, Stefan. Should Labs Treat Chimps More Like Humans?, National
Geographic News, September 6, 2005.
47.^ Chimps Deserve Better, Humane Society of the United States.
48.^ A former Yerkes lab worker. "Release & Restitution for Chimpanzees in U.S. Laboratories »
Wenka". Releasechimps.org. http://www.releasechimps.org/chimpanzees/their-stories/wenka/.
49.^ Wenka, Project R&R, New England Anti-Vivisection Society.
50.^ Langley, Gill. Next of Kin: A Report on the Use of Primates in Experiments, British Union for
the Abolition of Vivisection, p. 15, citing VandeBerg, JL et al. "A unique biomedical resource at risk",
Nature 437:30-32.
51.^ Bradshaw, G.A. et al. Building an Inner Sanctuary: Complex PTSD in Chimpanzees. 9.
Journal of Trauma and Dissociation. pp. 9–34.
http://www.releasechimps.org/pdfs/ExecSumTraumaFINAL.pdf.
52.^ Guldberg, Helen. The great ape debate, Spiked online, March 29, 2001. Retrieved August
12, 2007.
53.^ Langley, Gill. Next of Kin: A Report on the Use of Primates in Experiments, British Union for
the Abolition of Vivisection, p. 12.
54.^ a b c d e f g h Van Riper, A. Bowdoin (2002). Science in popular culture: a reference guide .
Westport: Greenwood Press. p. 19. ISBN 0–313–31822–0.
55.^ a b c Van Riper, op.cit., p. 18.
56.^ "Animal Actors | PETA.org". Nomoremonkeybusiness.com.
http://www.nomoremonkeybusiness.com/. Retrieved 2011-01-28.
General references
• Pickrell, John. (September 24, 2002). "Humans, Chimps Not as Closely Related as
Thought?". National Geographic.
Further reading
• Hawks, John. "How Strong Is a Chimpanzee?" Slate, February 25, 2009.
External links
Wikispecies has information related to: Chimpanzee
• Media related to Pan at Wikimedia Commons

• Chimpanzee: Wildlife summary African Wildlife Foundation
• Stanford, Craig B. The Predatory Behavior and Ecology of Wild Chimpanzees university of
Southern California. 2002(?)
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W000
Diatom

For a molecule of two atoms, see Diatomic molecule.
Diatoms
Marine diatoms.
Domain: Eukaryota
Kingdom: Chromalveolata
Phylum: Heterokontophyta
Bacillariophyceae
Class:
Haeckel 1878
Orders
• Centrales
• Pennales
A diatom. Numbered ticks are 10 microns apart.
Diatoms[1] are a major group of algae, and are one of the most common types of phytoplankton.
Most diatoms are unicellular, although they can exist as colonies in the shape of filaments or ribbons (e.g.
Fragillaria), fans (e.g. Meridion), zigzags (e.g. Tabellaria), or stellate colonies (e.g. Asterionella). Diatoms are
producers within the food chain. A characteristic feature of diatom cells is that they are encased within a
unique cell wall made of silica (hydrated silicon dioxide) called a frustule. These frustules show a wide
diversity in form, but usually consist of two asymmetrical sides with a split between them, hence the group
name. Fossil evidence suggests that they originated during, or before, the early Jurassic Period. Diatom
communities are a popular tool for monitoring environmental conditions, past and present, and are commonly
used in studies of water quality.
Contents
[hide]
• 1 General biology
• 3 Ecology
• 4 Life-Cycle
• 6 Fossil record
• 7 Collection
• 8 EST sequencing
• 9 Genome sequencing
• 10 Nanotechnology research
• 11 See also
• 12 References
[edit] General biology
There are more than 200 genera of living diatoms, and it is estimated that there are approximately
100,000 extant species.[2][3][4] Diatoms are a widespread group and can be found in the oceans, in
freshwater, in soils and on damp surfaces. Most live pelagically in open water, although some live as surface
films at the water-sediment interface (benthic), or even under damp atmospheric conditions. They are
especially important in oceans, where they are estimated to contribute up to 45% of the total oceanic primary
production.[5] Spatial distribution of marine phytoplankton species is restricted both horizontally and
vertically.[6] Diatoms occur in all oceans from the poles to the tropics; polar and subpolar regions contain
relatively few species compared with temperate biota. Although tropical regions exhibit the greatest number
of species, more abundant populations are found in polar to temperate regions.[7] Usually microscopic, some
species of diatoms can reach up to 2 millimetres in length.
Several species of fresh-water diatoms.
Diatoms belong to a large group called the heterokonts, including both autotrophs (e.g. golden algae,
kelp) and heterotrophs (e.g. water moulds). Their yellowish-brown chloroplasts are typical of heterokonts,
with four membranes and containing pigments such as the carotenoid fucoxanthin. Individuals usually lack
flagella, but they are present in gametes and have the usual heterokont structure, except they lack the hairs
(mastigonemes) characteristic in other groups. Most diatoms are non-motile, although some move via
flagellation. As their relatively dense cell walls cause them to readily sink, planktonic forms in open water
usually rely on turbulent mixing of the upper layers by the wind to keep them suspended in sunlit surface
waters. Some species actively regulate their buoyancy with intracellular lipids to counter sinking.
Diatom cells are contained within a unique silicate (silicic acid) cell wall comprising two separate
valves (or shells). The biogenic silica that the cell wall is composed of is synthesised intracellularly by the
polymerisation of silicic acid monomers. This material is then extruded to the cell exterior and added to the
wall. Diatom cell walls are also called frustules or tests, and their two valves typically overlap one over the
other like the two halves of a petri dish. In most species, when a diatom divides to produce two daughter
cells, each cell keeps one of the two halves and grows a smaller half within it. As a result, after each division
cycle the average size of diatom cells in the population gets smaller. Once such cells reach a certain
minimum size, rather than simply divide vegetatively, they reverse this decline by forming an auxospore. This
expands in size to give rise to a much larger cell, which then returns to size-diminishing divisions. Auxospore
production is almost always linked to meiosis and sexual reproduction.
Decomposition and decay of diatoms leads to organic and inorganic (in the form of silicates)
sediment, the inorganic component of which can lead to a method of analyzing past marine environments by
corings of ocean floors or bay muds, since the inorganic matter is embedded in deposition of clays and silts
and forms a permanent geological record of such marine strata.
The study of diatoms is a branch of phycology, and phycologists specializing in diatoms are called
diatomists.
Selections from Ernst Haeckel's 1904 Kunstformen der Natur (Artforms of Nature), showing pennate
(left) and centric (right) frustules.
Diatomaceous earth as viewed under bright field illumination on a light microscope. Diatomaceous
earth is a soft, siliceous, sedimentary rock made up of the cell walls of diatoms and readily crumbles to a fine
powder. This sample consists of a mixture of centric (radially symmetric) and pennate (bilaterally symmetric)
diatoms. This image of diatomaceous earth particles in water is at a scale of 6.236 pixels/μm, the entire
image covers a region of approximately 1.13 by 0.69 mm.
The classification of heterokonts is still unsettled, and they may be treated as a division (or phylum),
kingdom, or something in-between. Accordingly, groups like the diatoms may be ranked anywhere from class
(usually called Diatomophyceae) to division (usually called Bacillariophyta), with corresponding changes in
the ranks of their subgroups.
Diatoms are traditionally divided into two orders:
• centric diatoms (Centrales), which are radially symmetric
• pennate diatoms (Pennales), which are bilaterally symmetric. The former are paraphyletic to
the latter.
A more recent classification[3] divides the diatoms into three classes:
• centric diatoms (Coscinodiscophyceae)
• pennate diatoms
• without a raphe (Fragilariophyceae)
• with a raphe (Bacillariophyceae)
It is probable there will be further revisions as understanding of their relationships increases.[8]
Diatoms generally range in size from ca. 2-200μm,[2] and are composed of a cell wall comprising
silica.[7] This siliceous wall can be highly patterned with a variety of pores, ribs, minute spines, marginal
ridges and elevations; all of which can be utilised to delineate genera and species. The cell itself consists of
two halves, each containing an essentially flat plate, or valve and marginal connecting, or girdle band. One
half, the hypotheca, is slightly smaller than the other half, the epitheca. Diatom morphology varies, typically
though the shape of the cell is circular, although, some cells may be triangular, square, or elliptical.
Cells are solitary or united into colonies of various kinds, which may be linked by siliceous structures;
mucilage pads, or stalks; mucilage tubes; amorphous masses of mucilage and threads of polysaccharide
(chitin), which are secreted through strutted processes. Major pigments of diatoms are chlorophylls a and c,
beta-carotene, fucoxanthin, diatoxanthin and diadinoxanthin.[2] Diatoms are primarily photosynthetic. A few,
however, are obligate heterotrophs, while others can live heterotrophically in the absence of light, provided
an appropriate organic carbon source is available. Storage products are chrysolaminarin and lipids.[7]
Round & Crawford (1990)[3] and Hoek et al. (1995)[9] provide more comprehensive coverage of
diatom taxonomy.
[edit] Ecology
A budget of the ocean's silicon cycle[10]
Planktonic diatoms in freshwater and marine environments typically exhibit a "boom and bust" (or
"bloom and bust") lifestyle. When conditions in the upper mixed layer (nutrients and light) are favourable ( e.g.
at the start of spring) their competitive edge[11] allows them to quickly dominate phytoplankton communities
("boom" or "bloom"). As such they are often classed as opportunistic r-strategists (i.e. those organisms
whose ecology is defined by a high growth rate, r).
When conditions turn unfavourable, usually upon depletion of nutrients, diatom cells typically
increase in sinking rate and exit the upper mixed layer ("bust"). This sinking is induced by either a loss of
buoyancy control, the synthesis of mucilage that sticks diatoms cells together, or the production of heavy
resting spores. Sinking out of the upper mixed layer removes diatoms from conditions unfavourable to
growth, including grazer populations and higher temperatures (which would otherwise increase cell
metabolism). Cells reaching deeper water or the shallow seafloor can then rest until conditions become more
favourable again. In the open ocean, many sinking cells are lost to the deep, but refuge populations can
persist near the thermocline.
Ultimately, diatom cells in these resting populations re-enter the upper mixed layer when vertical
mixing entrains them. In most circumstances, this mixing also replenishes nutrients in the upper mixed layer,
setting the scene for the next round of diatom blooms. In the open ocean (away from areas of continuous
upwelling[12]), this cycle of bloom, bust, then return to pre-bloom conditions typically occurs over an annual
cycle, with diatoms only being prevalent during the spring and early summer. In some locations, however, an
autumn bloom may occur, caused by the breakdown of summer stratification and the entrainment of nutrients
while light levels are still sufficient for growth. Since vertical mixing is increasing, and light levels are falling as
winter approaches, these blooms are smaller and shorter-lived than their spring equivalents.
In the open ocean, the condition that typically causes diatom (spring) blooms to end is a lack of
silicon. Unlike other nutrients, this is only a major requirement of diatoms so it is not regenerated in the
plankton ecosystem as efficiently as, for instance, nitrogen or phosphorus nutrients. This can be seen in
maps of surface nutrient concentrations - as nutrients decline along gradients, silicon is usually the first to be
exhausted (followed normally by nitrogen then phosphorus).
Because of this bloom-and-bust cycle, diatoms are believed to play a disproportionately important
role in the export of carbon from oceanic surface waters[12][13] (see also the biological pump). Significantly,
they also play a key role in the regulation of the biogeochemical cycle of silicon in the modern ocean.[10][14]
Egge & Aksnes (1992)[15] figure.

The use of silicon by diatoms is believed by many researchers to be the key to their ecological
success. In a now classic study, Egge & Aksnes (1992)[15] found that diatom dominance of mesocosm
communities was directly related to the availability of silicic acid — when concentrations were greater than 2
mmol m−3, they found that diatoms typically represented more than 70% of the phytoplankton community.
Raven (1983)[16] noted that, relative to organic cell walls, silica frustules require less energy to synthesize
(approximately 8% of a comparable organic wall), potentially a significant saving on the overall cell energy
budget. Other researchers[17] have suggested that the biogenic silica in diatom cell walls acts as an effective
pH buffering agent, facilitating the conversion of bicarbonate to dissolved CO2 (which is more readily
assimilated). Notwithstanding the possible advantages conferred by silicon, diatoms typically have higher
growth rates than other algae of a corresponding size.[11]
Diatoms occur in virtually every environment that contains water. This includes not only oceans,
seas, lakes and streams, but also soil.
[edit] Life-Cycle
Sexual reproduction of a centric diatom (oogamy)

Sexual reproduction of a pinnate diatom (morphological isogamy, physiological anisogamy)
Diatoms are non-motile; however, sperm found in some species can be flagellated, though motility is
usually limited to a gliding motion.[7] Reproduction among these organisms is primarily asexual by binary
fission, with each daughter cell receiving one of the parent cell's two frustules (or theca). This is used by each
daughter cell as the larger frustule (or epitheca) into which a second, small frustule (or hypotheca) is
constructed.
This form of division results in a size reduction of the offspring and therefore the average cell size of
a diatom population decreases, until the cells are about one-third their maximum size.[2] It has been
observed, however, the ability of certain taxa to divide without causing a reduction in cell size.[18]
Nonetheless, in order to restore the cell size of a diatom population for those that do endure size reduction,
sexual reproduction and auxospore formation must occur.[2] Vegetative cells of diatoms are diploid (2N) and
so meiosis can take place, producing male and female gametes which then fuse to form the zygote. The
zygote sheds its silica theca and grows into a large sphere covered by an organic membrane, the auxospore.
A new diatom cell of maximum size, the initial cell, forms within the auxospore thus beginning a new
generation. Resting spores may also be formed as a response to unfavourable environmental conditions with
germination occurring when conditions improve.[7]
In centric diatoms, the small male gametes have one flagellum while the female gametes are large
and non-motile (oogamous). Conversely, in pinnate diatoms both gametes lack flagella (isoogamous).[2]
Certain araphid species have been documented as anisogamous and are, therefore, considered to represent
a transitional stage between centric and pinnate diatoms.[18]

Heterokont chloroplasts appear to be derived from those of red algae, rather than directly from
prokaryotes as occurred in plants. This suggests they had a more recent origin than many other algae.
However, fossil evidence is scant, and it is really only with the evolution of the diatoms themselves that the
heterokonts make a serious impression on the fossil record.
The earliest known fossil diatoms date from the early Jurassic (~185 Ma),[19] although molecular
clock[19] and sedimentary[20] evidence suggests an earlier origin. It has been suggested that their origin
may be related to the end-Permian mass extinction (~250 Ma), after which many marine niches were
opened.[21] The gap between this event and the time that fossil diatoms first appear may indicate a period
when diatoms were unsilicified and their evolution was cryptic.[22] Since the advent of silicification, diatoms
have made a significant impression on the fossil record, with major deposits of fossil diatoms found as far
back as the early Cretaceous, and some rocks (diatomaceous earth, diatomite, kieselguhr) being composed
almost entirely of them.
Although the diatoms may have existed since the Triassic, the timing of their ascendancy and "take-
over" of the silicon cycle is more recent. Prior to the Phanerozoic (before 544 Ma), it is believed that microbial
or inorganic processes weakly regulated the ocean's silicon cycle.[23][24][25] Subsequently, the cycle
appears dominated (and more strongly regulated) by the radiolarians and siliceous sponges, the former as
zooplankton, the latter as sedentary filter feeders primarily on the continental shelves.[26] Within the last 100
My, it is thought that the silicon cycle has come under even tighter control, and that this derives from the
ecological ascendancy of the diatoms.
However, the precise timing of the "take-over" is unclear, and different authors have conflicting
interpretations of the fossil record. Some evidence, such as the displacement of siliceous sponges from the
shelves,[27] suggests that this takeover began in the Cretaceous (146 Ma to 65 Ma), while evidence from
radiolarians suggests "take-over" did not begin until the Cenozoic (65 Ma to present).[28] The expansion of
grassland biomes and the evolutionary radiation of grasses during the Miocene is believed to have increased
the flux of soluble silicon to the oceans, and it has been argued that this has promoted the diatoms during the
Cenozoic era.[29][30] However, work on the variation of diatom diversity during the Cenozoic suggests
instead that diatom success is decoupled from the evolution of grasses, and that diatoms were most diverse
prior to the diversification of grasses.[31] Nevertheless, regardless of the details of the "take-over" timing, it is
clear that this most recent revolution has installed much tighter biological control over the biogeochemical
cycle of silicon.
The fossil record of diatoms has largely been established through the recovery of their siliceous
frustules in marine and non-marine sediments. Although diatoms have both a marine and non-marine
stratigraphic record, diatom biostratigraphy, which is based on time-constrained evolutionary originations and
extinctions of unique taxa, is only well developed and widely applicable in marine systems. The duration of
diatom species ranges have been documented through the study of ocean cores and rock sequences
exposed on land.[32] Where diatom biozones are well established and calibrated to the geomagnetic polarity
time scale (e.g., Southern Ocean, North Pacific, eastern equatorial Pacific), diatom-based age estimates may
be resolved to within <100,000 years, although typical age resolution for Cenozoic diatom assemblages is
several hundred thousand years.
The Cretaceous record of diatoms is limited, but recent studies reveal a progressive diversification of
diatom types. The Cretaceous-Tertiary extinction event, which in the oceans dramatically affected organisms
with calcareous skeletons, appears to have had relatively little impact on diatom evolution.[33]
Although no mass extinctions of marine diatoms have been observed during the Cenozoic, times of
relatively rapid evolutionary turnover in marine diatom assemblages occurred near the Paleocene–Eocene
boundary[34] and at the Eocene–Oligocene boundary.[35] Further turnover of assemblages took place at
various times between the middle Miocene and late Pliocene,[36] in response to progressive cooling of polar
regions and the development of more endemic diatom assemblages. A global trend toward more delicate
diatom frustules has been noted from the Oligocene to the Quaternary.[32] This coincides with an
increasingly more vigorous circulation of the ocean’s surface and deep waters brought about by increasing
latitudinal thermal gradients at the onset of major ice sheet expansion on Antarctica and progressive cooling
through the Neogene and Quaternary towards a bipolar glaciated world. This drove the diatoms into uptaking
silica more competitively (i.e., to use less silica in formation of their frustules). Increased mixing of the oceans
renews silica and other nutrients necessary for diatom growth in surface waters, especially in regions of
coastal and oceanic upwelling.
[edit] Collection
Living diatoms are often found clinging in great numbers to filamentous algae, or forming gelatinous
masses on various submerged plants. Cladophora is frequently covered with Cocconeis, an elliptically
shaped diatom; Vaucheria is often covered with small forms. Diatoms are frequently present as a brown,
slippery coating on submerged stones and sticks, and may be seen to "stream" with river current.
The surface mud of a pond, ditch, or lagoon will almost always yield some diatoms. They can be
made to emerge by filling a jar with water and mud, wrapping it in black paper and letting direct sunlight fall
on the surface of the water. Within a day, the diatoms will come to the top in a scum and can be isolated.
Since diatoms form an important part of the food of molluscs, tunicates, and fishes, the alimentary
tracts of these animals often yield forms that are not easily secured in other ways. Marine diatoms can be
collected by direct water sampling, though benthic forms can be secured by scraping barnacles, oyster
shells, and other shells.
This section uses text from Methods in Plant Histology.[37]
[edit] EST sequencing

The first insights into the properties of the P. tricornutum gene repertoire was described using 1,000
ESTs.[38] Subsequently, the number of ESTs was extended to 12,000 and the Diatom EST Database was
constructed for functional analyses.[39] These sequences have been used to make a comparative analysis
between P. tricornutum and the putative complete proteomes from the green alga Chlamydomonas
reinhardtii, the red alga Cyanidioschyzon merolae, and T. pseudonana.[40] The diatom EST database now
consists in over 200,000 ESTs from P. tricornutum (16 libraries) and T. pseudonana (7 libraries) cells grown
in a range of different conditions, many of which corresponding to different abiotic stresses (available at
http://www.biologie.ens.fr/diatomics/EST3/).[41]
[edit] Genome sequencing

The entire genomes of the centric diatom, Thalassiosira pseudonana (32.4 Mb),[42] and the pennate
diatom, Phaeodactylum tricornutum (27.4 Mb),[43] have been sequenced. Comparisons of the two fully
sequenced diatom genomes finds that the P. tricornutum genome includes fewer genes (10,402 opposed to
11,776) than T. pseudonana and no major synteny (gene order) could be detected between the two
genomes. T. pseudonana genes show an average of ~1.52 introns per gene as opposed to 0.79 in P.
tricornutum, suggesting recent widespread intron gain in the centric diatom.[43][44] Despite relatively recent
evolutionary divergence (90 million years), the extent of molecular divergence between centrics and
pennates indicates rapid evolutionary rates within the Bacillariophyceae compared to other eukaryotic
groups.[43] Comparative genomics also established that a specific class of transposable elements, the
Diatom Copia-like retrotransposons (or CoDis), has been significantly amplified in the P. tricornutum genome
with respect to T. pseudonana, constituting 5.8 and 1% of the respective genomes.[45]
Importantly, diatom genomics brought much information about the extent and dynamics of the
endosymbiotic gene transfer (EGT) process. Comparison of the T. pseudonana proteins with homologs in
other organisms suggested that hundreds have their closest homologs in the Plantae lineage. EGT towards
diatom genomes can be illustrated by the fact that the T. pseudonana genome encodes six proteins which
are most closely related to genes encoded by the Guillardia theta (cryptomonad) nucleomorph genome. Four
of these genes are also found in red algal plastid genomes, thus demonstrating successive EGT from red
algal plastid to red algal nucleus (nucleomorph) to heterokont host nucleus.[42] More recent phylogenomic
analyses of diatom proteomes provided evidence for a prasinophyte-like endosymbiont in the common
ancestor of chromalveolates as supported by the fact the 70% of diatom genes of Plantae origin are of green
lineage provenance and that such genes are also found in the genome of other stramenopiles. Therefore, it
was proposed that chromalveolates are the product of serial secondary endosymbiosis first with a green
algae, followed by a second one with a red algae that conserved the genomic footprints of the previous but
displaced the green plastid.[46] However, phylogenomic analyses of diatom proteomes and chromalveolate
evolutionary history will likely take advantage of complementary genomic data from under-sequenced
lineages such as red algae.
In addition to EGT, horizontal gene transfer (HGT) can occur independently of an endosymbiotic
event. The publication of the P. tricornutum genome reported that at least 587 P. tricornutum genes appear to
be most closely related to bacterial genes, accounting for more than 5% of the P. tricornutum proteome.
About half of these are also found in the T. pseudonana genome, attesting their ancient incorporation in the
diatom lineage.[43]
[edit] Nanotechnology research

The deposition of silica by diatoms may also prove to be of utility to nanotechnology.[47] Diatom cells
repeatedly and reliably manufacture valves of various shapes and sizes, potentially allowing diatoms to
manufacture micro- or nano-scale structures which may be of use in a range of devices, including: optical
systems; semiconductor nanolithography; and even using diatom valves as vehicles for drug delivery. Using
an appropriate artificial selection procedure, diatoms that produce valves of particular shapes and sizes
could be evolved in the laboratory, and then used in chemostat cultures to mass produce nanoscale
components.[48] It has also been proposed that diatoms could be used as a component of solar cells, by
substituting photosensitive titanium dioxide for the silicon dioxide normally used in the creation of cell walls.
[49]
[edit] See also
• Algae
• Biological pump
• Diatomaceous earth
• Phytoplankton
• Plankton
[edit] References
1. ^ diá-tom-os "cut in half" (= dichó-tom-os) — diá "through" or "apart" and the root of tém-n-ō "I
cut". Alternation between e and o in verb root is ablaut.
2. ^ a b c d e f Hasle, G.R.; Syvertsen,E.E. (1997). Marine Diatoms. In: Tomas, C.R. (1997).
Identifying Marine Diatoms and Dinoflagellates. Academic Press. pp. 5–385.
3. ^ a b c Round, F. E. and Crawford, R. M. (1990). The Diatoms. Biology and Morphology of the
Genera, Cambridge University Press, UK.
4. ^ Canter-Lund, H. and Lund, J.W.G. (1995). Freshwater Algae, Biopress Limited. ISBN 0
948737 25 5.
5. ^ Mann, D. G. (1999). The species concept in diatoms. Phycologia 38, 437-495.
6. ^ Lipps, J.H. (1970). "Plankton Evolution". Evolution 24 (1): 1–22. doi:10.2307/2406711.
7. ^ a b c d e Horner, R.A. (2002). A Taxonomic Guide to Some Common Marine Phytoplankton .
BiopressLtd. pp. 25–30. ISBN 0948737654.
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phycology, Cambridge University Press, UK.
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measurement, community and species growth rates. J. Plankton Res. 12, 1117-1151.
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equatorial Pacific upwelling. Nature 391, 270-273.
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evolutionary and geological significance. Mar Biol. 84, 239-251.
14.^ Yool, A. and Tyrrell, T. (2003). Role of diatoms in regulating the ocean's silicon cycle.
Global Biogeochemical Cycles 17, 1103, doi:10.1029/2002GB002018.
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competition. Mar Ecol. Prog. Ser. 83, 281-289.
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17.^ Milligan, A. J. and Morel, F. M. M. (2002). A proton buffering role for silica in diatoms.
Science 297, 1848-1850.
18.^ a b Drebes, G. (1977). "Sexuality". Botanical Monographs 13: 250–283.
19.^ a b Kooistra, W. H. C. F. and Medlin, L. K. (1996). Evolution of the diatoms
(Bacillariophyta) : IV. A reconstruction of their age from small subunit rRNA coding regions and the
fossil record. Mol. Phylogenet. Evol. 6, 391-407.
20.^ Schieber, J., Krinsley, D. and Riciputi, L. (2000). Diagenetic origin of quartz silt in
mudstones and implications for silica cycling. Nature 406, 981-985.
21.^ Medlin, L. K., Kooistra, W. H. C. F., Gersonde, R., Sims, P. A. and Wellbrock, U. (1997). Is
the origin of the diatoms related to the end-Permian mass extinction? Nova Hedwegia 65, 1-11.
22.^ Raven, J. A. and Waite, A. M. (2004). The evolution of silicification in diatoms: inescapable
sinking and sinking as escape? New Phytologist 162, 45-61.
23.^ Siever, R. (1991). Silica in the oceans: biological-geological interplay. In: Schneider, S. H.,
Boston, P. H. (eds.), Scientists On Gaia, The MIT Press, Cambridge MA, USA, pp. 287-295.
24.^ Kidder, D. L. and Erwin, D. H. (2001). Secular distribution of biogenic silica through the
Phanerozoic: Comparison of silica-replaced fossils and bedded cherts at the series level. J. Geol.
109, 509-522.
25.^ Grenne, T. and Slack, J. F. (2003). Paleozoic and Mesozoic silica-rich seawater: evidence
from hematitic chert (jasper) deposits. Geology 31, 319-322.
26.^ Racki, G. and Cordey, F. (2000). Radiolarian palaeoecology and radiolarites: is the present
the key to the past? Earth-Science Reviews 52, 83-120.
27.^ Maldonado, M., Carmona, M. C., Uriz, J. M. and Cruzado, A. (1999). Decline in Mesozoic
reef-building sponges explained by silicate limitation. Nature 401, 785-788.
28.^ Harper, H. E. and Knoll, A. H. (1975). Silica, diatoms, and Cenozoic radiolarian evolution.
Geology 3, 175-177.
29.^ Falkowski, P.G.; et al. (2004). "The evolution of modern eukaryotic phytoplankton". Science
305 (5682): 354–60. doi:10.1126/science.1095964. PMID 15256663.
30.^ Kidder, D.L.; Gierlowski-Kordesch, E.H. (2005). "Impact of grassland radiation on the
nonmarine silica cycle and Miocene diatomite". PALAIOS 20: 198–206. doi:10.2110/palo.2003.p03-
108.
31.^ Rabosky, D.L.; Sorhannus, U. (2009). "Diversity dynamics of marine planktonic diatoms
across the Cenozoic". Nature 457 (7226): 183–6. doi:10.1038/nature07435. PMID 19129846.
32.^ a b Scherer, R.P., Gladenkov, A.Yu., and Barron, J.A. (2007). Methods and applications of
Cenozoic marine diatom biostratigraphy. “Paleontological Society Papers” 13, 61-83
33.^ Harwood, D.M., Nikolaev, V.A., and Winter, D.M. (2007). Cretaceous record of diatom
evolution, radiation, and expansion. “Paleontological Society Papers” 13, 33-59
34.^ Strelnikova, N. I. (1990). Evolution of diatoms during the Cretaceous and Paleogene
periods. In: Simola, H. (ed.), “Proceedings of the Tenth International Diatom Symposium”, Koeltz
Scientific Books, Koenigstein, Germany, pp. 195-204
35.^ Baldauf, J.G. (1993). Middle Eocene through early Miocene diatom floral turnover. In:
Prothero D., Berggren, W.H., (eds.), “Eocene-Oligocene climatic and biotic evolution”, Princeton
University Press, Princeton, NJ, USA, pp 310-326
36.^ Barron, J.A. (2003). Appearance and extinction of planktonic diatoms during the past 18
m.y. in the Pacific and Southern oceans. “Diatom Research” 18, 203-224
37.^ Chamberlain, C. J. (1901) Methods in Plant Histology, University of Chicago Press, USA
38.^ Scala, S.; Carels, N., Falciatore, A., Chiusano, M.L. and Bowler, C. (July 2002). "Genome
properties of the diatom Phaeodactylum tricornutum". Plant Physiol. 129 (3): 993–1002.
doi:10.1104/pp.010713. PMID 12114555. PMC 166495.
http://www.plantphysiol.org/cgi/content/full/129/3/993.
39.^ Maheswari, U., Montsant, A., Goll, J., Krishnasamy, S., Rajyashri, K.R., Patell, V.M. and
Bowler, C. (2005). The Diatom EST Database. Nucleic Acids Research 33, 344–347.
40.^ Montsant, A.; Jabbari, K., Maheswari, U. and Bowler, C. (February 2005). "Comparative
genomics of the pennate diatom Phaeodactylum tricornutum". Plant Physiol. 137 (2): 500–13.
doi:10.1104/pp.104.052829. PMID 15665249.
41.^ Maheswari U, Mock T, Armbrust EV, Bowler C: Update of the Diatom EST Database: a new
tool for digital transcriptomics. Nucleic Acids Res 2008.
42.^ a b Armbrust et al. (2004). The genome of the diatom Thalassiosira pseudonana: ecology,
evolution, and metabolism. Science 306, 79-86.
43.^ a b c d Bowler, C.; et al. (2008). "The Phaeodactylum genome reveals the evolutionary
history of diatom genomes". Nature 456 (7219): 239–244. doi:10.1038/nature07410.
PMID 18923393.
44.^ Roy SW, Penny D. A very high fraction of unique intron positions in the intron-rich diatom
Thalassiosira pseudonana indicates widespread intron gain. Mol Biol Evol. 2007 Jul;24(7):1447-57.
Epub 2007 Mar 8. PubMed PMID: 17350938.
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Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC
Genomics. 2009 Dec 22;10:624.
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footprints of a cryptic plastid endosymbiosis in diatoms. Science 2009, 324:1724-1726.
47.^ Bradbury, J. (2004). Nature's Nanotechnologists: Unveiling the Secrets of Diatoms. PLoS
Biology 2, 1512-1515.
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Biotechnology 21: 325–328. doi:10.1016/S0167-7799(03)00169-0.
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http://www.eetimes.com/showArticle.jhtml?articleID=216500176. Retrieved 13 April 2009.

Wikispecies has information related to: Diatoms
Wikimedia Commons has media related to: Diatoms
• Computer simulations of pattern formation in diatoms

• Catalogue of Diatom Names, California Academy of Sciences
• Diatom Genome, Joint Genome Institute
• Diatom EST database, École Normale Supérieure
• Plankton*Net, taxonomic database including images of diatom species
• Life History and Ecology of Diatoms, University of California Museum of Paleontology
• Diatoms: 'Nature's Marbles', Eureka site, University of Bergen
• Diatom life history and ecology, Microfossil Image Recovery and Circulation for Learning and
Education (MIRACLE), University College London
• Diatom page, Royal Botanic Garden Edinburgh
• Geometry and Pattern in Nature 3: The holes in radiolarian and diatom tests
• Art Deco Diatoms, Wim van Egmond
• Diatom QuickFacts, Monterey Bay Aquarium Research Institute
• Diatoms and other algae image database Academy of Natural Sciences in Philadelphia
(ANSP)
• Now, energy from single celled algae Deccan Herald
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Charles Darwin
Charles Robert Darwin

Charles Robert Darwin, aged 45 in 1854, by then working towards publication of On the Origin of
Species.
Born 12 February 1809(1809-02-12)
Mount House, Shrewsbury, Shropshire, England
19 April 1882(1882-04-19) (aged 73)

Died
Down House, Downe, Kent, England
Residence England
Citizenship British
Nationality British
Fields Naturalist
Institutions Geological Society of London
University of Edinburgh
Alma mater
University of Cambridge
John Stevens Henslow

Academic advisors
Adam Sedgwick
The Voyage of the Beagle

Known for On The Origin of Species
Natural selection
Influences Alexander von Humboldt

John Herschel
Charles Lyell
Joseph Dalton Hooker

Thomas Henry Huxley
Influenced
George John Romanes
Ernst Haeckel
Royal Medal (1853)

Notable awards Wollaston Medal (1859)
Copley Medal (1864)
Signature
Charles Robert Darwin FRS (12 February 1809 – 19 April 1882) was an English naturalist.[I] He
established that all species of life have descended over time from common ancestry, and proposed the
scientific theory that this branching pattern of evolution resulted from a process that he called natural
selection.
He published his theory with compelling evidence for evolution in his 1859 book On the Origin of
Species.[1][2] The scientific community and much of the general public came to accept evolution as a fact in
his lifetime.[3] However, it was not until the emergence of the modern evolutionary synthesis from the 1930s
to the 1950s that a broad consensus developed that natural selection was the basic mechanism of evolution.
[4] In modified form, Darwin's scientific discovery is the unifying theory of the life sciences, explaining the
diversity of life.[5][6]
Darwin's early interest in nature led him to neglect his medical education at the University of
Edinburgh; instead, he helped to investigate marine invertebrates. Studies at the University of Cambridge
encouraged his passion for natural science.[7] His five-year voyage on HMS Beagle established him as an
eminent geologist whose observations and theories supported Charles Lyell's uniformitarian ideas, and
publication of his journal of the voyage made him famous as a popular author.[8]
Puzzled by the geographical distribution of wildlife and fossils he collected on the voyage, Darwin
investigated the transmutation of species and conceived his theory of natural selection in 1838.[9] Although
he discussed his ideas with several naturalists, he needed time for extensive research and his geological
work had priority.[10] He was writing up his theory in 1858 when Alfred Russel Wallace sent him an essay
which described the same idea, prompting immediate joint publication of both of their theories.[11] Darwin's
work established evolutionary descent with modification as the dominant scientific explanation of
diversification in nature.[3] In 1871, he examined human evolution and sexual selection in The Descent of
Man, and Selection in Relation to Sex, followed by The Expression of the Emotions in Man and Animals. His
research on plants was published in a series of books, and in his final book, he examined earthworms and
their effect on soil.[12]
In recognition of Darwin's pre-eminence as a scientist, he was one of only five nineteenth-century
non-royal personages from the United Kingdom to be honoured by a state funeral,[13] and was buried in
Westminster Abbey, close to John Herschel and Isaac Newton.[14]
Contents
[hide]
• 1 Life of Darwin
• 1.1 Childhood and education
• 1.2 Voyage of the Beagle
• 1.3 Inception of Darwin's evolutionary theory
• 1.4 Overwork, illness, and marriage
• 1.5 Preparing the theory of natural selection for
publication
• 1.6 Publication of the theory of natural selection
• 1.7 Responses to the publication
• 1.8 Descent of Man, sexual selection, and botany
• 2 Darwin's children
• 3 Religious views
• 4 Political interpretations
• 4.1 Eugenics
• 4.2 Social Darwinism
• 5 Commemoration
• 6 Works
• 7 See also
• 8 Notes
• 9 Citations
Life of Darwin
Childhood and education
See also: Charles Darwin's education and Darwin-Wedgwood family
The seven-year-old Charles Darwin in 1816.

Charles Robert Darwin was born in Shrewsbury, Shropshire, England on 12 February 1809 at his
family home, the Mount.[15] He was the fifth of six children of wealthy society doctor and financier Robert
Darwin, and Susannah Darwin (née Wedgwood). He was the grandson of Erasmus Darwin on his father's
side, and of Josiah Wedgwood on his mother's side. Both families were largely Unitarian, though the
Wedgwoods were adopting Anglicanism. Robert Darwin, himself quietly a freethinker, had baby Charles
baptised in the Anglican Church, but Charles and his siblings attended the Unitarian chapel with their mother.
The eight-year-old Charles already had a taste for natural history and collecting when he joined the day
school run by its preacher in 1817. That July, his mother died. From September 1818, he joined his older
brother Erasmus attending the nearby Anglican Shrewsbury School as a boarder.[16]
Darwin spent the summer of 1825 as an apprentice doctor, helping his father treat the poor of
Shropshire, before going to the University of Edinburgh Medical School with his brother Erasmus in October
1825. He found lectures dull and surgery distressing, so neglected his studies. He learned taxidermy from
John Edmonstone, a freed black slave who had accompanied Charles Waterton in the South American
rainforest, and often sat with this "very pleasant and intelligent man".[17]
In Darwin's second year he joined the Plinian Society, a student natural history group whose debates
strayed into radical materialism. He assisted Robert Edmund Grant's investigations of the anatomy and life
cycle of marine invertebrates in the Firth of Forth, and on 27 March 1827 presented at the Plinian his own
discovery that black spores found in oyster shells were the eggs of a skate leech. One day, Grant praised
Lamarck's evolutionary ideas. Darwin was astonished, but had recently read the similar ideas of his
grandfather Erasmus and remained indifferent.[18] Darwin was rather bored by Robert Jameson's natural
history course which covered geology including the debate between Neptunism and Plutonism. He learned
classification of plants, and assisted with work on the collections of the University Museum, one of the largest
museums in Europe at the time.[19]
This neglect of medical studies annoyed his father, who shrewdly sent him to Christ's College,
Cambridge, for a Bachelor of Arts degree as the first step towards becoming an Anglican parson. As Darwin
was unqualified for the Tripos, he joined the ordinary degree course in January 1828.[20] He preferred riding
and shooting to studying. His cousin William Darwin Fox introduced him to the popular craze for beetle
collecting which Darwin pursued zealously, getting some of his finds published in Stevens' Illustrations of
British entomology. He became a close friend and follower of botany professor John Stevens Henslow and
met other leading naturalists who saw scientific work as religious natural theology, becoming known to these
dons as "the man who walks with Henslow". When his own exams drew near, Darwin focused on his studies
and was delighted by the language and logic of William Paley's Evidences of Christianity.[21] In his final
examination in January 1831 Darwin did well, coming tenth out of 178 candidates for the ordinary degree.[22]
Darwin had to stay at Cambridge until June. He studied Paley's Natural Theology which made an
argument for divine design in nature, explaining adaptation as God acting through laws of nature.[23] He
read John Herschel's new book which described the highest aim of natural philosophy as understanding such
laws through inductive reasoning based on observation, and Alexander von Humboldt's Personal Narrative of
scientific travels. Inspired with "a burning zeal" to contribute, Darwin planned to visit Tenerife with some
classmates after graduation to study natural history in the tropics. In preparation, he joined Adam Sedgwick's
geology course, then went with him in the summer for a fortnight to map strata in Wales.[24] After a week
with student friends at Barmouth, he returned home to find a letter from Henslow proposing Darwin as a
suitable (if unfinished) gentleman naturalist for a self-funded place with captain Robert FitzRoy, more as a
companion than a mere collector, on HMS Beagle which was to leave in four weeks on an expedition to chart
the coastline of South America.[25] His father objected to the planned two-year voyage, regarding it as a
waste of time, but was persuaded by his brother-in-law, Josiah Wedgwood, to agree to his son's participation.
[26]
Voyage of the Beagle
For more details on this topic, see Second voyage of HMS Beagle.
The voyage of the Beagle

Beginning on the 27th of December, 1831, the voyage lasted almost five years and, as FitzRoy had
intended, Darwin spent most of that time on land investigating geology and making natural history
collections, while the Beagle surveyed and charted coasts.[3][27] He kept careful notes of his observations
and theoretical speculations, and at intervals during the voyage his specimens were sent to Cambridge
together with letters including a copy of his journal for his family.[28] He had some expertise in geology,
beetle collecting and dissecting marine invertebrates, but in all other areas was a novice and ably collected
specimens for expert appraisal.[29] Despite repeatedly suffering badly from seasickness while at sea, most
of his zoology notes are about marine invertebrates, starting with plankton collected in a calm spell.[27][30]
On their first stop ashore at St. Jago, Darwin found that a white band high in the volcanic rock cliffs
included seashells. FitzRoy had given him the first volume of Charles Lyell's Principles of Geology which set
out uniformitarian concepts of land slowly rising or falling over immense periods,[II] and Darwin saw things
Lyell's way, theorising and thinking of writing a book on geology.[31] In Brazil, Darwin was delighted by the
tropical forest,[32] but detested the sight of slavery.[33]
At Punta Alta in Patagonia he made a major find of fossil bones of huge extinct mammals in cliffs
beside modern seashells, indicating recent extinction with no signs of change in climate or catastrophe. He
identified the little known Megatherium by a tooth and its association with bony armour which had at first
seemed to him like a giant version of the armour on local armadillos. The finds brought great interest when
they reached England.[34][35] On rides with gauchos into the interior to explore geology and collect more
fossils he gained social, political and anthropological insights into both native and colonial people at a time of
revolution, and learnt that two types of rhea had separate but overlapping territories.[36][37] Further south he
saw stepped plains of shingle and seashells as raised beaches showing a series of elevations. He read
Lyell's second volume and accepted its view of "centres of creation" of species, but his discoveries and
theorising challenged Lyell's ideas of smooth continuity and of extinction of species.[38][39]
As HMS Beagle surveyed the coasts of South America, Darwin theorised about geology and
extinction of giant mammals.
Three Fuegians on board, who had been seized during the first Beagle voyage and had spent a year
in England, were taken back to Tierra del Fuego as missionaries. Darwin found them friendly and civilised,
yet their relatives seemed "miserable, degraded savages", as different as wild from domesticated animals.
[40] To Darwin the difference showed cultural advances, not racial inferiority. Unlike his scientist friends, he
now thought there was no unbridgeable gap between humans and animals.[41] A year on, the mission had
been abandoned. The Fuegian they had named Jemmy Button lived like the other natives, had a wife, and
had no wish to return to England.[42]
Darwin experienced an earthquake in Chile and saw signs that the land had just been raised,
including mussel-beds stranded above high tide. High in the Andes he saw seashells, and several fossil trees
that had grown on a sand beach. He theorised that as the land rose, oceanic islands sank, and coral reefs
round them grew to form atolls.[43][44]
On the geologically new Galápagos Islands Darwin looked for evidence attaching wildlife to an older
"centre of creation", and found mockingbirds allied to those in Chile but differing from island to island. He
heard that slight variations in the shape of tortoise shells showed which island they came from, but failed to
collect them, even after eating tortoises taken on board as food.[45][46] In Australia, the marsupial rat-
kangaroo and the platypus seemed so unusual that Darwin thought it was almost as though two distinct
Creators had been at work.[47] He found the Aborigines "good-humoured & pleasant", and noted their
depletion by European settlement.[48]
The Beagle investigated how the atolls of the Cocos (Keeling) Islands had formed, and the survey
supported Darwin's theorising.[44] FitzRoy began writing the official Narrative of the Beagle voyages, and
after reading Darwin's diary he proposed incorporating it into the account.[49] Darwin's Journal was
eventually rewritten as a separate third volume, on natural history.[50]
In Cape Town Darwin and FitzRoy met John Herschel, who had recently written to Lyell praising his
uniformitarianism as opening bold speculation on "that mystery of mysteries, the replacement of extinct
species by others" as "a natural in contradistinction to a miraculous process".[51] When organising his notes
as the ship sailed home, Darwin wrote that if his growing suspicions about the mockingbirds, the tortoises
and the Falkland Islands Fox were correct, "such facts undermine the stability of Species", then cautiously
added "would" before "undermine".[52] He later wrote that such facts "seemed to me to throw some light on
the origin of species".[53]
Inception of Darwin's evolutionary theory

For more details on this topic, see Inception of Darwin's theory.
While still a young man, Charles Darwin joined the scientific elite
When the Beagle reached Falmouth, Cornwall, on 2 October 1836, Darwin was already a celebrity in
scientific circles as in December 1835 Henslow had fostered his former pupil's reputation by giving selected
naturalists a pamphlet of Darwin's geological letters.[54] Darwin visited his home in Shrewsbury and saw
relatives, then hurried to Cambridge to see Henslow, who advised on finding naturalists available to
catalogue the collections and agreed to take on the botanical specimens. Darwin's father organised
investments, enabling his son to be a self-funded gentleman scientist, and an excited Darwin went round the
London institutions being fêted and seeking experts to describe the collections. Zoologists had a huge
backlog of work, and there was a danger of specimens just being left in storage.[55]
Charles Lyell eagerly met Darwin for the first time on 29 October and soon introduced him to the up-
and-coming anatomist Richard Owen, who had the facilities of the Royal College of Surgeons to work on the
fossil bones collected by Darwin. Owen's surprising results included other gigantic extinct ground sloths as
well as the Megatherium, a near complete skeleton of the unknown Scelidotherium and a hippopotamus-
sized rodent-like skull named Toxodon resembling a giant capybara. The armour fragments were actually
from Glyptodon, a huge armadillo-like creature as Darwin had initially thought.[56][35] These extinct
creatures were related to living species in South America.[57]
In mid-December Darwin took lodgings in Cambridge to organise work on his collections and rewrite
his Journal.[58] He wrote his first paper, showing that the South American landmass was slowly rising, and
with Lyell's enthusiastic backing read it to the Geological Society of London on 4 January 1837. On the same
day, he presented his mammal and bird specimens to the Zoological Society. The ornithologist John Gould
soon announced that the Galapagos birds that Darwin had thought a mixture of blackbirds, "gros-beaks" and
finches, were, in fact, twelve separate species of finches. On 17 February Darwin was elected to the Council
of the Geological Society, and Lyell's presidential address presented Owen's findings on Darwin's fossils,
stressing geographical continuity of species as supporting his uniformitarian ideas.[59]
Early in March, Darwin moved to London to be near this work, joining Lyell's social circle of scientists
and experts such as Charles Babbage,[60] who described God as a programmer of laws. Darwin stayed with
his freethinking brother Erasmus, part of this Whig circle and close friend of writer Harriet Martineau who
promoted Malthusianism underlying the controversial Whig Poor Law reforms to stop welfare from causing
overpopulation and more poverty. As a Unitarian she welcomed the radical implications of transmutation of
species, promoted by Grant and younger surgeons influenced by Geoffroy. Transmutation was anathema to
Anglicans defending social order,[61] but reputable scientists openly discussed the subject and there was
wide interest in John Herschel's letter praising Lyell's approach as a way to find a natural cause of the origin
of new species.[51]
Gould met Darwin and told him that the Galápagos mockingbirds from different islands were
separate species, not just varieties, and what Darwin had thought was a "wren" was also in the finch group.
Darwin had not labelled the finches by island, but from the notes of others on the Beagle, including FitzRoy,
he allocated species to islands.[62] The two rheas were also distinct species, and on 14 March Darwin
announced how their distribution changed going southwards.[63]
In mid-July 1837 Darwin started his "B" notebook on Transmutation of Species, and on page 36
wrote "I think" above his first evolutionary tree.
By mid-March, Darwin was speculating in his Red Notebook on the possibility that "one species does
change into another" to explain the geographical distribution of living species such as the rheas, and extinct
ones such as the strange Macrauchenia which resembled a giant guanaco. His thoughts on lifespan, asexual
reproduction and sexual reproduction developed in his "B" notebook around mid-July on to variation in
offspring "to adapt & alter the race to changing world" explaining the Galápagos tortoises, mockingbirds and
rheas. He sketched branching descent, then a genealogical branching of a single evolutionary tree, in which
"It is absurd to talk of one animal being higher than another", discarding Lamarck's independent lineages
progressing to higher forms.[64]
Overwork, illness, and marriage

See also: Charles Darwin's health
While developing this intensive study of transmutation, Darwin became mired in more work. Still
rewriting his Journal, he took on editing and publishing the expert reports on his collections, and with
Henslow's help obtained a Treasury grant of £1,000 to sponsor this multi-volume Zoology of the Voyage of
H.M.S. Beagle, a sum equivalent to about £75,000 in 2009.[65] He stretched the funding to include his
planned books on geology, and agreed unrealistic dates with the publisher.[66] As the Victorian era began,
Darwin pressed on with writing his Journal, and in August 1837 began correcting printer's proofs.[67]
Darwin's health suffered from the pressure. On 20 September he had "an uncomfortable palpitation
of the heart", so his doctors urged him to "knock off all work" and live in the country for a few weeks. After
visiting Shrewsbury he joined his Wedgwood relatives at Maer Hall, Staffordshire, but found them too eager
for tales of his travels to give him much rest. His charming, intelligent, and cultured cousin Emma
Wedgwood, nine months older than Darwin, was nursing his invalid aunt. His uncle Jos pointed out an area
of ground where cinders had disappeared under loam and suggested that this might have been the work of
earthworms, inspiring "a new & important theory" on their role in soil formation which Darwin presented at the
Geological Society on 1 November.[68]
William Whewell pushed Darwin to take on the duties of Secretary of the Geological Society. After
initially declining the work, he accepted the post in March 1838.[69] Despite the grind of writing and editing
the Beagle reports, Darwin made remarkable progress on transmutation, taking every opportunity to question
expert naturalists and, unconventionally, people with practical experience such as farmers and pigeon
fanciers.[3][70] Over time his research drew on information from his relatives and children, the family butler,
neighbours, colonists and former shipmates.[71] He included mankind in his speculations from the outset,
and on seeing an orangutan in the zoo on 28 March 1838 noted its child-like behaviour.[72]
The strain took a toll, and by June he was being laid up for days on end with stomach problems,
headaches and heart symptoms. For the rest of his life, he was repeatedly incapacitated with episodes of
stomach pains, vomiting, severe boils, palpitations, trembling and other symptoms, particularly during times
of stress such as attending meetings or making social visits. The cause of Darwin's illness remained
unknown, and attempts at treatment had little success.[73]
On 23 June he took a break and went "geologising" in Scotland. He visited Glen Roy in glorious
weather to see the parallel "roads" cut into the hillsides at three heights. He later published his view that
these were marine raised beaches, but then had to accept that they were shorelines of a proglacial lake.[74]
Fully recuperated, he returned to Shrewsbury in July. Used to jotting down daily notes on animal
breeding, he scrawled rambling thoughts about career and prospects on two scraps of paper, one with
columns headed "Marry" and "Not Marry". Advantages included "constant companion and a friend in old
age ... better than a dog anyhow", against points such as "less money for books" and "terrible loss of
time."[75] Having decided in favour, he discussed it with his father, then went to visit Emma on 29 July. He
did not get around to proposing, but against his father's advice he mentioned his ideas on transmutation.[76]
Continuing his research in London, Darwin's wide reading now included the sixth edition of Malthus's
An Essay on the Principle of Population
In October 1838, that is, fifteen months after I had begun my systematic enquiry, I happened to
read for amusement Malthus on Population, and being well prepared to appreciate the struggle
for existence which everywhere goes on from long-continued observation of the habits of
animals and plants, it at once struck me that under these circumstances favourable variations
would tend to be preserved, and unfavourable ones to be destroyed. The result of this would be
the formation of new species. Here, then, I had at last got a theory by which to work...[77]
Malthus asserted that unless human population is kept in check, it increases in a geometrical
progression and soon exceeds food supply in what is known as a Malthusian catastrophe.[3] Darwin was well
prepared to see at once that this also applied to de Candolle's "warring of the species" of plants and the
struggle for existence among wildlife, explaining how numbers of a species kept roughly stable. As species
always breed beyond available resources, favourable variations would make organisms better at surviving
and passing the variations on to their offspring, while unfavourable variations would be lost. This would result
in the formation of new species.[3][78] On 28 September 1838 he noted this insight, describing it as a kind of
wedging, forcing adapted structures into gaps in the economy of nature as weaker structures were thrust out.
[3] By mid December he saw a similarity between farmers picking the best breeding stock and a Malthusian
Nature selecting from chance variants so that "every part of newly acquired structure is fully practical and
perfected",[79] thinking this comparison "a beautiful part of my theory".[80]
Darwin chose to marry his cousin, Emma Wedgwood.
On 11 November, he returned to Maer and proposed to Emma, once more telling her his ideas. She
accepted, then in exchanges of loving letters she showed how she valued his openness in sharing their
differences, also expressing her strong Unitarian beliefs and concerns that his honest doubts might separate
them in the afterlife.[81] While he was house-hunting in London, bouts of illness continued and Emma wrote
urging him to get some rest, almost prophetically remarking "So don't be ill any more my dear Charley till I
can be with you to nurse you." He found what they called "Macaw Cottage" (because of its gaudy interiors) in
Gower Street, then moved his "museum" in over Christmas. On 24 January 1839 Darwin was elected a
Fellow of the Royal Society.[82]
On 29 January Darwin and Emma Wedgwood were married at Maer in an Anglican ceremony
arranged to suit the Unitarians, then immediately caught the train to London and their new home.[83]
Preparing the theory of natural selection for publication

For more details on this topic, see Development of Darwin's theory.
Darwin now had the framework of his theory of natural selection "by which to work",[84] as his "prime
hobby".[85] His research included animal husbandry and extensive experiments with plants, finding evidence
that species were not fixed and investigating many detailed ideas to refine and substantiate his theory.[3] For
fifteen years this work was in the background to his main occupation of writing on geology and publishing
expert reports on the Beagle collections.[86]
When FitzRoy's Narrative was published in May 1839, Darwin's Journal and Remarks was such a
success as the third volume that later that year it was published on its own.[87] Early in 1842, Darwin wrote
about his ideas to Charles Lyell, who noted that his ally "denies seeing a beginning to each crop of species".
[88]
Darwin's book The Structure and Distribution of Coral Reefs on his theory of atoll formation was
published in May 1842 after more than three years of work, and he then wrote his first "pencil sketch" of his
theory of natural selection.[89] To escape the pressures of London, the family moved to rural Down House in
September.[90] On 11 January 1844 Darwin mentioned his theorising to the botanist Joseph Dalton Hooker,
writing with melodramatic humour "it is like confessing a murder".[91][92] Hooker replied "There may in my
opinion have been a series of productions on different spots, & also a gradual change of species. I shall be
delighted to hear how you think that this change may have taken place, as no presently conceived opinions
satisfy me on the subject."[93]
Darwin's "sandwalk" at Down House was his usual "Thinking Path".[94]
By July, Darwin had expanded his "sketch" into a 230-page "Essay", to be expanded with his
research results if he died prematurely.[95] In November the anonymously published sensational best-seller
Vestiges of the Natural History of Creation brought wide interest in transmutation. Darwin scorned its
amateurish geology and zoology, but carefully reviewed his own arguments. Controversy erupted, and it
continued to sell well despite contemptuous dismissal by scientists.[96][97]
Darwin completed his third geological book in 1846. He now renewed a fascination and expertise in
marine invertebrates, dating back to his student days with Grant, by dissecting and classifying the barnacles
he had collected on the voyage, enjoying observing beautiful structures and thinking about comparisons with
allied structures.[98] In 1847, Hooker read the "Essay" and sent notes that provided Darwin with the calm
critical feedback that he needed, but would not commit himself and questioned Darwin's opposition to
continuing acts of creation.[99]
In an attempt to improve his chronic ill health, Darwin went in 1849 to Dr. James Gully's Malvern spa
and was surprised to find some benefit from hydrotherapy.[100] Then in 1851 his treasured daughter Annie
fell ill, reawakening his fears that his illness might be hereditary, and after a long series of crises she died.
[101]
In eight years of work on barnacles (Cirripedia), Darwin's theory helped him to find "homologies"
showing that slightly changed body parts served different functions to meet new conditions, and in some
genera he found minute males parasitic on hermaphrodites, showing an intermediate stage in evolution of
distinct sexes.[102] In 1853 it earned him the Royal Society's Royal Medal, and it made his reputation as a
biologist.[103] He resumed work on his theory of species in 1854, and in November realised that divergence
in the character of descendants could be explained by them becoming adapted to "diversified places in the
economy of nature".[104]
Publication of the theory of natural selection

For more details on this topic, see Publication of Darwin's theory.
Darwin was forced into swift publication of his theory of natural selection.
By the start of 1856, Darwin was investigating whether eggs and seeds could survive travel across
seawater to spread species across oceans. Hooker increasingly doubted the traditional view that species
were fixed, but their young friend Thomas Henry Huxley was firmly against evolution. Lyell was intrigued by
Darwin's speculations without realising their extent. When he read a paper by Alfred Russel Wallace on the
Introduction of species, he saw similarities with Darwin's thoughts and urged him to publish to establish
precedence. Though Darwin saw no threat, he began work on a short paper. Finding answers to difficult
questions held him up repeatedly, and he expanded his plans to a "big book on species" titled Natural
Selection. He continued his researches, obtaining information and specimens from naturalists worldwide
including Wallace who was working in Borneo. The American botanist Asa Gray showed similar interests,
and on 5 September 1857 Darwin sent Gray a detailed outline of his ideas including an abstract of Natural
Selection. In December, Darwin received a letter from Wallace asking if the book would examine human
origins. He responded that he would avoid that subject, "so surrounded with prejudices", while encouraging
Wallace's theorising and adding that "I go much further than you."[105]
Darwin's book was half way when, on 18 June 1858, he received a paper from Wallace describing
natural selection. Shocked that he had been "forestalled", Darwin sent it on to Lyell, as requested, and,
though Wallace had not asked for publication, he suggested he would send it to any journal that Wallace
chose. His family was in crisis with children in the village dying of scarlet fever, and he put matters in the
hands of Lyell and Hooker. They decided on a joint presentation at the Linnean Society on 1 July of On the
Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means
of Selection; however, Darwin's baby son died of the scarlet fever and he was too distraught to attend.[106]
There was little immediate attention to this announcement of the theory; the president of the Linnean
Society remarked in May 1859 that the year had not been marked by any revolutionary discoveries.[107]
Only one review rankled enough for Darwin to recall it later; Professor Samuel Haughton of Dublin claimed
that "all that was new in them was false, and what was true was old."[108] Darwin struggled for thirteen
months to produce an abstract of his "big book", suffering from ill health but getting constant encouragement
from his scientific friends. Lyell arranged to have it published by John Murray.[109]
On the Origin of Species proved unexpectedly popular, with the entire stock of 1,250 copies
oversubscribed when it went on sale to booksellers on 22 November 1859.[110] In the book, Darwin set out
"one long argument" of detailed observations, inferences and consideration of anticipated objections.[111]
His only allusion to human evolution was the understatement that "light will be thrown on the origin of man
and his history".[112] His theory is simply stated in the introduction:
As many more individuals of each species are born than can possibly survive; and as,
consequently, there is a frequently recurring struggle for existence, it follows that any being, if it
vary however slightly in any manner profitable to itself, under the complex and sometimes
varying conditions of life, will have a better chance of surviving, and thus be naturally selected.
From the strong principle of inheritance, any selected variety will tend to propagate its new and
modified form.[113]
He put a strong case for common descent, but avoided the then controversial term "evolution", and at
the end of the book concluded that:
There is grandeur in this view of life, with its several powers, having been originally breathed
into a few forms or into one; and that, whilst this planet has gone cycling on according to the
fixed law of gravity, from so simple a beginning endless forms most beautiful and most
wonderful have been, and are being, evolved.[114]
Responses to the publication
During the Darwin family's 1868 holiday in her Isle of Wight cottage, Julia Margaret Cameron took
portraits showing the bushy beard Darwin had grown by 1866.
An 1871 caricature following publication of The Descent of Man was typical of many showing Darwin
with an ape body, identifying him in popular culture as the leading author of evolutionary theory.[115]
For more details on this topic, see Reaction to Darwin's theory.
The book aroused international interest, with less controversy than had greeted the popular Vestiges
of Creation.[116] Though Darwin's illness kept him away from the public debates, he eagerly scrutinised the
scientific response, commenting on press cuttings, reviews, articles, satires and caricatures, and
corresponded on it with colleagues worldwide.[117] Darwin had only said "Light will be thrown on the origin of
man",[118] but the first review claimed it made a creed of the "men from monkeys" idea from Vestiges.[119]
Amongst early favourable responses, Huxley's reviews swiped at Richard Owen, leader of the scientific
establishment Huxley was trying to overthrow.[120] In April, Owen's review attacked Darwin's friends and
condescendingly dismissed his ideas, angering Darwin,[121] but Owen and others began to promote ideas of
supernaturally guided evolution.[122]
The Church of England's response was mixed. Darwin's old Cambridge tutors Sedgwick and
Henslow dismissed the ideas, but liberal clergymen interpreted natural selection as an instrument of God's
design, with the cleric Charles Kingsley seeing it as "just as noble a conception of Deity".[123] In 1860, the
publication of Essays and Reviews by seven liberal Anglican theologians diverted clerical attention from
Darwin, with its ideas including higher criticism attacked by church authorities as heresy. In it, Baden Powell
argued that miracles broke God's laws, so belief in them was atheistic, and praised "Mr Darwin's masterly
volume [supporting] the grand principle of the self-evolving powers of nature".[124] Asa Gray discussed
teleology with Darwin, who imported and distributed Gray's pamphlet on theistic evolution, Natural Selection
is not inconsistent with Natural Theology.[123][125] The most famous confrontation was at the public 1860
Oxford evolution debate during a meeting of the British Association for the Advancement of Science, where
the Bishop of Oxford Samuel Wilberforce, though not opposed to transmutation of species, argued against
Darwin's explanation and human descent from apes. Joseph Hooker argued strongly for Darwin, and
Thomas Huxley's legendary retort, that he would rather be descended from an ape than a man who misused
his gifts, came to symbolise a triumph of science over religion.[123][126]
Even Darwin's close friends Gray, Hooker, Huxley and Lyell still expressed various reservations but
gave strong support, as did many others, particularly younger naturalists. Gray and Lyell sought
reconciliation with faith, while Huxley portrayed a polarisation between religion and science. He campaigned
pugnaciously against the authority of the clergy in education,[123] aiming to overturn the dominance of
clergymen and aristocratic amateurs under Owen in favour of a new generation of professional scientists.
Owen's claim that brain anatomy proved humans to be a separate biological order from apes was shown to
be false by Huxley in a long running dispute parodied by Kingsley as the "Great Hippocampus Question", and
discredited Owen.[127]
Darwinism became a movement covering a wide range of evolutionary ideas. In 1863 Lyell's
Geological Evidences of the Antiquity of Man popularised prehistory, though his caution on evolution
disappointed Darwin. Weeks later Huxley's Evidence as to Man's Place in Nature showed that anatomically,
humans are apes, then The Naturalist on the River Amazons by Henry Walter Bates provided empirical
evidence of natural selection.[128] Lobbying brought Darwin Britain's highest scientific honour, the Royal
Society's Copley Medal, awarded on 3 November 1864.[129] That day, Huxley held the first meeting of what
became the influential X Club devoted to "science, pure and free, untrammelled by religious dogmas".[130]
By the end of the decade most scientists agreed that evolution occurred, but only a minority supported
Darwin's view that the chief mechanism was natural selection.[131]
The Origin of Species was translated into many languages, becoming a staple scientific text
attracting thoughtful attention from all walks of life, including the "working men" who flocked to Huxley's
lectures.[132] Darwin's theory also resonated with various movements at the time[III] and became a key
fixture of popular culture.[IV] Cartoonists parodied animal ancestry in an old tradition of showing humans with
animal traits, and in Britain these droll images served to popularise Darwin's theory in an unthreatening way.
While ill in 1862 Darwin began growing a beard, and when he reappeared in public in 1866 caricatures of him
as an ape helped to identify all forms of evolutionism with Darwinism.[115]
Descent of Man, sexual selection, and botany
By 1879, an increasingly famous Darwin had suffered years of illness.

More detailed articles cover Darwin's life from Orchids to Variation, from Descent of Man to
Emotions and from Insectivorous Plants to Worms
Despite repeated bouts of illness during the last twenty-two years of his life, Darwin's work continued.
Having published On the Origin of Species as an abstract of his theory, he pressed on with experiments,
research, and writing of his "big book". He covered human descent from earlier animals including evolution of
society and of mental abilities, as well as explaining decorative beauty in wildlife and diversifying into
innovative plant studies.
Enquiries about insect pollination led in 1861 to novel studies of wild orchids, showing adaptation of
their flowers to attract specific moths to each species and ensure cross fertilisation. In 1862 Fertilisation of
Orchids gave his first detailed demonstration of the power of natural selection to explain complex ecological
relationships, making testable predictions. As his health declined, he lay on his sickbed in a room filled with
inventive experiments to trace the movements of climbing plants.[133] Admiring visitors included Ernst
Haeckel, a zealous proponent of Darwinismus incorporating Lamarckism and Goethe's idealism.[134]
Wallace remained supportive, though he increasingly turned to Spiritualism.[135]
The Variation of Animals and Plants under Domestication of 1868 was the first part of Darwin's
planned "big book", and included his unsuccessful hypothesis of pangenesis attempting to explain heredity. It
sold briskly at first, despite its size, and was translated into many languages. He wrote most of a second part,
on natural selection, but it remained unpublished in his lifetime.[136]
Punch's almanac for 1882, published shortly before Darwin's death, depicts him amidst evolution
from chaos to Victorian gentleman with the title Man Is But A Worm.
Lyell had already popularised human prehistory, and Huxley had shown that anatomically humans
are apes.[128] With The Descent of Man, and Selection in Relation to Sex published in 1871, Darwin set out
evidence from numerous sources that humans are animals, showing continuity of physical and mental
attributes, and presented sexual selection to explain impractical animal features such as the peacock's
plumage as well as human evolution of culture, differences between sexes, and physical and cultural racial
characteristics, while emphasising that humans are all one species.[137] His research using images was
expanded in his 1872 book The Expression of the Emotions in Man and Animals, one of the first books to
feature printed photographs, which discussed the evolution of human psychology and its continuity with the
behaviour of animals. Both books proved very popular, and Darwin was impressed by the general assent
with which his views had been received, remarking that "everybody is talking about it without being
shocked."[138] His conclusion was "that man with all his noble qualities, with sympathy which feels for the
most debased, with benevolence which extends not only to other men but to the humblest living creature,
with his god-like intellect which has penetrated into the movements and constitution of the solar system–with
all these exalted powers–Man still bears in his bodily frame the indelible stamp of his lowly origin."[139]
His evolution-related experiments and investigations led to books on Insectivorous Plants, The
Effects of Cross and Self Fertilisation in the Vegetable Kingdom , different forms of flowers on plants of the
same species, and The Power of Movement in Plants. In his last book he returned to The Formation of
Vegetable Mould through the Action of Worms .
He died at Down House on 19 April 1882. He had expected to be buried in St Mary's churchyard at
Downe, but at the request of Darwin's colleagues, William Spottiswoode (President of the Royal Society)
arranged for Darwin to be given a state funeral and buried in Westminster Abbey, close to John Herschel and
Isaac Newton.[140] Only five non-royal personages were granted that honour of a UK state funeral during the
19th century.[13]
Darwin was perceived as a national hero who had changed thinking, and scientists now accepted
evolution as descent with modification, but few agreed with him that "natural selection has been the main but
not the exclusive means of modification".[141] In "the eclipse of Darwinism" most favoured alternative
evolutionary mechanisms, but these proved untenable, and the development of the modern evolutionary
synthesis with population genetics and Mendelian genetics from the 1930s to the 1950s brought a broad
scientific consensus that natural selection was the basic mechanism of evolution. Research and debate has
continued within this frame of reference.[4]
Darwin's children
Darwin and his eldest son William Erasmus Darwin in 1842.

Darwin's Children
William Erasmus Darwin (27 December 1839–1914)
Anne Elizabeth Darwin (2 March 1841–23 April 1851)

Mary Eleanor Darwin (23 September 1842–16 October 1842)
Henrietta Emma "Etty" Darwin (25 September 1843–1929)
George Howard Darwin (9 July 1845–7 December 1912)
Elizabeth "Bessy" Darwin (8 July 1847–1926)
Francis Darwin (16 August 1848–19 September 1925)
Leonard Darwin (15 January 1850–26 March 1943)
Horace Darwin (13 May 1851–29 September 1928)
Charles Waring Darwin (6 December 1856–28 June 1858)

In 1851 Darwin was devastated when his daughter Annie died. By then his faith in Christianity had
dwindled, and he had stopped going to church.[142]
The Darwins had ten children: two died in infancy, and Annie's death at the age of ten had a
devastating effect on her parents. Charles was a devoted father and uncommonly attentive to his children.[7]
Whenever they fell ill, he feared that they might have inherited weaknesses from inbreeding due to the close
family ties he shared with his wife and cousin, Emma Wedgwood. He examined this topic in his writings,
contrasting it with the advantages of crossing amongst many organisms.[143] Despite his fears, most of the
surviving children and many of their descendants went on to have distinguished careers (see Darwin-
Wedgwood family).[144]
Of his surviving children, George, Francis and Horace became Fellows of the Royal Society,[145]
distinguished as astronomer,[146] botanist and civil engineer, respectively. His son Leonard went on to be a
soldier, politician, economist, eugenicist and mentor of the statistician and evolutionary biologist Ronald
Fisher.[147]
Religious views
For more details on this topic, see Charles Darwin's religious views.
Darwin's family tradition was nonconformist Unitarianism, while his father and grandfather were
freethinkers, and his baptism and boarding school were Church of England.[16] When going to Cambridge to
become an Anglican clergyman, he did not doubt the literal truth of the Bible.[21] He learnt John Herschel's
science which, like William Paley's natural theology, sought explanations in laws of nature rather than
miracles and saw adaptation of species as evidence of design.[23][24] On board the Beagle, Darwin was
quite orthodox and would quote the Bible as an authority on morality.[148] He looked for "centres of creation"
to explain distribution,[45] and related the antlion found near kangaroos to distinct "periods of Creation".[47]
By his return he was critical of the Bible as history, and wondered why all religions should not be
equally valid.[148] In the next few years, while intensively speculating on geology and transmutation of
species, he gave much thought to religion and openly discussed this with Emma, whose beliefs also came
from intensive study and questioning.[81] The theodicy of Paley and Thomas Malthus vindicated evils such
as starvation as a result of a benevolent creator's laws which had an overall good effect. To Darwin, natural
selection produced the good of adaptation but removed the need for design,[149] and he could not see the
work of an omnipotent deity in all the pain and suffering such as the ichneumon wasp paralysing caterpillars
as live food for its eggs.[125] He still viewed organisms as perfectly adapted, and On the Origin of Species
reflects theological views. Though he thought of religion as a tribal survival strategy, Darwin still believed that
God was the ultimate lawgiver.[150][151]
Darwin remained close friends with the vicar of Downe, John Innes, and continued to play a leading
part in the parish work of the church,[152] but from around 1849 would go for a walk on Sundays while his
family attended church.[142] He considered it "absurd to doubt that a man might be an ardent theist and an
evolutionist"[153][154] and, though reticent about his religious views, in 1879 he wrote that "I have never
been an atheist in the sense of denying the existence of a God. – I think that generally ... an agnostic would
be the most correct description of my state of mind."[81][153]
The "Lady Hope Story", published in 1915, claimed that Darwin had reverted back to Christianity on
his sickbed. The claims were repudiated by Darwin's children and have been dismissed as false by
historians.[155] His last words were to his family, telling Emma "I am not the least afraid of death –
Remember what a good wife you have been to me – Tell all my children to remember how good they have
been to me", then while she rested, he repeatedly told Henrietta and Francis "It's almost worth while to be
sick to be nursed by you".[156]
Political interpretations
Darwin's fame and popularity led to his name being associated with ideas and movements which at
times had only an indirect relation to his writings, and sometimes went directly against his express
comments.
Caricature from 1871 Vanity Fair
Eugenics
For more details on this topic, see Eugenics.
Darwin was interested by his half-cousin Francis Galton's argument, introduced in 1865, that
statistical analysis of heredity showed that moral and mental human traits could be inherited, and principles
of animal breeding could apply to humans. In The Descent of Man Darwin noted that aiding the weak to
survive and have families could lose the benefits of natural selection, but cautioned that withholding such aid
would endanger the instinct of sympathy, "the noblest part of our nature", and factors such as education
could be more important. When Galton suggested that publishing research could encourage intermarriage
within a "caste" of "those who are naturally gifted", Darwin foresaw practical difficulties, and thought it "the
sole feasible, yet I fear utopian, plan of procedure in improving the human race", preferring to simply
publicise the importance of inheritance and leave decisions to individuals.[157]
Galton named the field of study "eugenics" in 1883, after Darwin's death, and developed biometrics.
Eugenics movements were widespread at a time when Darwin's natural selection was eclipsed by Mendelian
genetics, and in some countries compulsory sterilisation laws were imposed, the most famous of which were
in Nazi Germany. It has been largely abandoned throughout the world.[V]
Social Darwinism
For more details on this topic, see Social Darwinism.
Taking descriptive ideas as moral and social justification creates the ethical is-ought problem. When
Thomas Malthus argued that population growth beyond resources was ordained by God to get humans to
work productively and show restraint in getting families, this was used in the 1830s to justify workhouses and
laissez-faire economics.[158] Evolution was seen as having social implications, and Herbert Spencer's 1851
book Social Statics based ideas of human freedom and individual liberties on his Lamarckian evolutionary
theory.[159]
Darwin's theory of evolution was a matter of explanation. He thought it "absurd to talk of one animal
being higher than another" and saw evolution as having no goal, but soon after the Origin was published in
1859, critics derided his description of a struggle for existence as a Malthusian justification for the English
industrial capitalism of the time. The term Darwinism was used for the evolutionary ideas of others, including
Spencer's "survival of the fittest" as free-market progress, and Ernst Haeckel's racist ideas of human
development. Darwin did not share the racism common at that time: a point examined by the philosopher
Antony Flew, who is at pains to distance Darwin's attitudes from those later attributed to him.[160] Darwin
was strongly against slavery, against "ranking the so-called races of man as distinct species", and against ill-
treatment of native people.[161][VI]
Darwin's views on social and political issues reflected his time and social position. He thought men's
eminence over women was the outcome of sexual selection, a view disputed by Antoinette Brown Blackwell
in The Sexes Throughout Nature.[162] He valued European civilisation and saw colonisation as spreading its
benefits, with the sad but inevitable effect of extermination of savage peoples who did not become civilised.
Darwin's theories presented this as natural, and were cited to promote policies which went against his
humanitarian principles.[163] Writers used natural selection to argue for various, often contradictory,
ideologies such as laissez-faire dog-eat dog capitalism, racism, warfare, colonialism and imperialism.
However, Darwin's holistic view of nature included "dependence of one being on another"; thus pacifists,
socialists, liberal social reformers and anarchists such as Peter Kropotkin stressed the value of co-operation
over struggle within a species.[164] Darwin himself insisted that social policy should not simply be guided by
concepts of struggle and selection in nature.[165]
The term "Social Darwinism" was used infrequently from around the 1890s, but became popular as a
derogatory term in the 1940s when used by Richard Hofstadter to attack the laissez-faire conservatism of
those like William Graham Sumner who opposed reform and socialism. Since then it has been used as a
term of abuse by those opposed to what they think are the moral consequences of evolution.[166][158]
Commemoration
Main article: Commemoration of Charles Darwin
In 1881 Darwin was an eminent figure, still working on his contributions to evolutionary thought that
had had an enormous effect on many fields of science.
During Darwin's lifetime, many geographical features were given his name. An expanse of water
adjoining the Beagle Channel was named Darwin Sound by Robert FitzRoy after Darwin's prompt action,
along with two or three of the men, saved them from being marooned on a nearby shore when a collapsing
glacier caused a large wave that would have swept away their boats,[167] and the nearby Mount Darwin in
the Andes was named in celebration of Darwin's 25th birthday.[168] When the Beagle was surveying
Australia in 1839, Darwin's friend John Lort Stokes sighted a natural harbour which the ship's captain
Wickham named Port Darwin: a nearby settlement was renamed Darwin in 1911, and it became the capital
city of Australia's Northern Territory.[169]
More than 120 species and nine genera have been named after Darwin.[170] In one example, the
group of tanagers related to those Darwin found in the Galápagos Islands became popularly known as
"Darwin's finches" in 1947, fostering inaccurate legends about their significance to his work.[171]
Darwin's work has continued to be celebrated by numerous publications and events. The Linnean
Society of London has commemorated Darwin's achievements by the award of the Darwin–Wallace Medal
since 1908. Darwin Day has become an annual celebration, and in 2009 worldwide events were arranged for
the bicentenary of Darwin's birth and the 150th anniversary of the publication of On the Origin of Species.
[172]
Darwin has been commemorated in the UK, with his portrait printed on the reverse of £10 banknotes
printed along with a hummingbird and the HMS Beagle, issued by the Bank of England.[173]
Works
For more details on this topic, see List of works by Charles Darwin.
Darwin was a prolific writer. Even without publication of his works on evolution, he would have had a
considerable reputation as the author of The Voyage of the Beagle, as a geologist who had published
extensively on South America and had solved the puzzle of the formation of coral atolls, and as a biologist
who had published the definitive work on barnacles. While The Origin of Species dominates perceptions of
his work, The Descent of Man, and Selection in Relation to Sex and The Expression of Emotions in Man and
Animals had considerable impact, and his books on plants including The Power of Movement in Plants were
innovative studies of great importance, as was his final work on The Formation of Vegetable Mould Through
the Action of Worms.[174][175]
See also
• Creation-evolution controversy
• "Darwin among the Machines"
• Darwin's Frog
• Harriet (tortoise)
• List of coupled cousins
• List of independent discoveries
• Patrick Matthew
• Randal Keynes
• History of evolutionary thought
• History of biology
• Portraits of Charles Darwin
• Parson-naturalist
• Tinamou egg of Darwin's collection
Notes
^
I. Darwin was eminent as a naturalist, geologist, biologist, and author; after working as a physician's
assistant and two years as a medical student was educated as a clergyman; and was trained in taxidermy.
[176]
II. ^ Robert FitzRoy was to become known after the voyage for biblical literalism, but at this time he
had considerable interest in Lyell's ideas, and they met before the voyage when Lyell asked for observations
to be made in South America. FitzRoy's diary during the ascent of the River Santa Cruz in Patagonia
recorded his opinion that the plains were raised beaches, but on return, newly married to a very religious
lady, he recanted these ideas. (Browne 1995, pp. 186, 414)
III. ^ See, for example, WILLA volume 4, Charlotte Perkins Gilman and the Feminization of Education
by Deborah M. De Simone: "Gilman shared many basic educational ideas with the generation of thinkers who
matured during the period of "intellectual chaos" caused by Darwin's Origin of the Species. Marked by the
belief that individuals can direct human and social evolution, many progressives came to view education as
the panacea for advancing social progress and for solving such problems as urbanisation, poverty, or
immigration."
IV. ^ See, for example, the song "A lady fair of lineage high" from Gilbert and Sullivan's Princess Ida,
which describes the descent of man (but not woman!) from apes.
V. ^ Geneticists studied human heredity as Mendelian inheritance, while eugenics movements
sought to manage society, with a focus on social class in the United Kingdom, and on disability and ethnicity
in the United States, leading to geneticists seeing this as impractical pseudoscience. A shift from voluntary
arrangements to "negative" eugenics included compulsory sterilisation laws in the United States, copied by
Nazi Germany as the basis for Nazi eugenics based on virulent racism and "racial hygiene".
(Thurtle, Phillip (Updated 17 December 1996). "the creation of genetic identity". SEHR 5 (Supplement:
Cultural and Technological Incubations of Fascism). http://www.stanford.edu/group/SHR/5-
supp/text/thurtle.html. Retrieved 2008-11-11
Edwards, A. W. F. (April 1, 2000). "The Genetical Theory of Natural Selection". Genetics 154 (April 2000):
pp. 1419–1426. PMID 10747041. PMC 1461012.
http://www.genetics.org/cgi/content/full/154/4/1419#The_Eclipse_of_Darwinism. Retrieved 2008-11-11
Wilkins, John. "Evolving Thoughts: Darwin and the Holocaust 3: eugenics".
http://scienceblogs.com/evolvingthoughts/2006/09/darwin_and_the_holocaust_3_eug_1.php. Retrieved
2008-11-11. )
VI. ^ Darwin did not share the then common view that other races are inferior, and said of his
taxidermy tutor John Edmonstone, a freed black slave, "I used often to sit with him, for he was a very
pleasant and intelligent man".[17]
Early in the Beagle voyage he nearly lost his position on the ship when he criticised FitzRoy's
defence and praise of slavery. (Darwin 1958, p. 74) He wrote home about "how steadily the general feeling,
as shown at elections, has been rising against Slavery. What a proud thing for England if she is the first
European nation which utterly abolishes it! I was told before leaving England that after living in slave
countries all my opinions would be altered; the only alteration I am aware of is forming a much higher
estimate of the negro character." (Darwin 1887, p. 246) Regarding Fuegians, he "could not have believed
how wide was the difference between savage and civilized man: it is greater than between a wild and
domesticated animal, inasmuch as in man there is a greater power of improvement", but he knew and liked
civilised Fuegians like Jemmy Button: "It seems yet wonderful to me, when I think over all his many good
qualities, that he should have been of the same race, and doubtless partaken of the same character, with the
miserable, degraded savages whom we first met here."(Darwin 1845, pp. 205, 207–208)
In the Descent of Man he mentioned the Fuegians and Edmonstone when arguing against "ranking
the so-called races of man as distinct species".[177]
He rejected the ill-treatment of native people, and for example wrote of massacres of Patagonian
men, women, and children, "Every one here is fully convinced that this is the most just war, because it is
against barbarians. Who would believe in this age that such atrocities could be committed in a Christian
civilized country?" (Darwin 1845, p. 102)
Citations
The standard author abbreviation Darwin is used to indicate this individual as the author when citing
a botanical name.[178]
1. ^ Coyne, Jerry A. (2009). Why Evolution is True. Oxford: Oxford University Press. p. 17.
ISBN 0-199-23084-6. "In The Origin, Darwin provided an alternative hypothesis for the development ,
diversification, and design of life. Much of that book presents evidence that not only supports
evolution but at the same time refutes creationism. In Darwin's day, the evidence for his theories was
compelling but not completely decisive."
2. ^ Glass, Bentley (1959). Forerunners of Darwin. Baltimore, MD: Johns Hopkins University
Press. p. iv. ISBN 0801802229. "Darwin's solution is a magnificent synthesis of evidence...a
synthesis...compelling in honesty and comprehensiveness"
3. ^ a b c d e f g h van Wyhe 2008
4. ^ a b Bowler 2003, pp. 338, 347
5. ^ The Complete Works of Darwin Online - Biography. darwin-online.org.uk. Retrieved on
2006-12-15
Dobzhansky 1973
6. ^ As Darwinian scholar Joseph Carroll of the University of Missouri–St. Louis puts it in his
introduction to a modern reprint of Darwin's work: "The Origin of Species has special claims on our
attention. It is one of the two or three most significant works of all time—one of those works that
fundamentally and permanently alter our vision of the world...It is argued with a singularly rigorous
consistency but it is also eloquent, imaginatively evocative, and rhetorically compelling." Carroll,
Joseph, ed (2003). On the origin of species by means of natural selection . Peterborough, Ontario:
Broadview. p. 15. ISBN 1551113376.
7. ^ a b Leff 2000, About Charles Darwin
8. ^ Desmond & Moore 1991, pp. 210, 284–285
9. ^ Desmond & Moore 1991, pp. 263–274
10.^ van Wyhe 2007, pp. 184, 187
11.^ Beddall, B. G. (1968). "Wallace, Darwin, and the Theory of Natural Selection" (PDF).
Journal of the History of Biology 1 (2): 261–323. doi:10.1007/BF00351923.
http://www.springerlink.com/content/n1gh3n4474th3385/fulltext.pdf. edit
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13.^ a b "BBC NEWS : Politics : Thatcher state funeral undecided". BBC News. 2008-08-02.
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14.^ Leff 2000, Darwin's Burial
15.^ John H. Wahlert (11 June 2001). "The Mount House, Shrewsbury, England (Charles
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16.^ a b Desmond & Moore 1991, pp. 12–15
Darwin 1958, pp. 21–25
17.^ a b Darwin 1958, pp. 47–51
18.^ Browne 1995, pp. 72–88
19.^ Desmond & Moore 1991, pp. 42–43
20.^ Browne 1995, pp. 47–48, 89–91
21.^ a b Darwin 1958, pp. 57–67
22.^ Browne 1995, p. 97
23.^ a b von Sydow 2005, pp. 5–7
24.^ a b Darwin 1958, pp. 67–68
Browne 1995, pp. 128–129, 133–141
25.^ "Darwin Correspondence Project - Letter 105 — Henslow, J. S. to Darwin, C. R., 24 Aug
1831". http://www.darwinproject.ac.uk/darwinletters/calendar/entry-105.html. Retrieved 2008-12-29.
26.^ Desmond & Moore 1991, pp. 94–97
27.^ a b Keynes 2000, pp. ix–xi
28.^ van Wyhe 2008b, pp. 18–21
29.^ Gordon Chancellor; Randal Keynes (October 2006). "Darwin's field notes on the
Galapagos: 'A little world within itself'". Darwin Online. http://darwin-
online.org.uk/EditorialIntroductions/Chancellor_Keynes_Galapagos.html. Retrieved 2009-09-16.
30.^ Keynes 2001, pp. 21–22
31.^ Browne 1995, pp. 183–190
32.^ Keynes 2001, pp. 41–42
33.^ Darwin 1958, pp. 73–74
34.^ Browne 1995, pp. 223–235
Darwin 1835, p. 7
Desmond & Moore 1991, p. 210
35.^ a b Keynes 2001, pp. 206–209
36.^ Desmond & Moore 1991, pp. 189–192, 198
37.^ Eldredge 2006
38.^ Desmond & Moore 1991, pp. 131, 159
Herbert 1991, pp. 174–179
39.^ "Darwin Online: 'Hurrah Chiloe': an introduction to the Port Desire Notebook". http://darwin-
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40.^ Darwin 1845, pp. 205–208
41.^ Browne 1995, pp. 244–250
42.^ Keynes 2001, pp. 226–227
43.^ Desmond & Moore 1991, pp. 160–168, 182
Darwin 1887, p. 260
44.^ a b Darwin 1958, p 98–99
45.^ a b Keynes 2001, pp. 356–357
46.^ Sulloway 1982, p. 19
47.^ a b "Darwin Online: Coccatoos & Crows: An introduction to the Sydney Notebook".
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48.^ Keynes 2001, pp. 398–399.
49.^ "Darwin Correspondence Project - Letter 301 — Darwin, C.R. to Darwin, C.S., 29 Apr 1836".
http://www.darwinproject.ac.uk/darwinletters/calendar/entry-301.html.
50.^ Browne 1995, p. 336
51.^ a b van Wyhe 2007, p. 197
52.^ Keynes 2000, pp. xix–xx
Eldredge 2006
53.^ Darwin 1859, p. 1
54.^ Darwin 1835, editorial introduction
55.^ Desmond & Moore 1991, pp. 195–198
56.^ Owen 1840, pp. 16, 73, 106
Eldredge 2006
57.^ Desmond & Moore 1991, pp. 201–205
Browne 1995, pp. 349–350
58.^ Browne 1995, pp. 345–347
59.^ Desmond & Moore 1991, pp. 207–210
Sulloway 1982, pp. 20–23
60.^ "Darwin Correspondence Project - Letter 346 — Darwin, C. R. to Darwin, C. S., 27 Feb
proposes a move on Friday 3 March 1837,
Darwin's Journal (Darwin 2006, pp. 12 verso) backdated from August 1838 gives a date of 6 March
1837
61.^ Desmond & Moore 1991, pp. 201, 212–221
62.^ Sulloway 1982, pp. 9, 20–23
63.^ Browne 1995, p. 360
"Darwin, C. R. (Read 14 March 1837) Notes on Rhea americana and Rhea darwinii, Proceedings of
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64.^ Herbert 1980, pp. 7–10
van Wyhe 2008b, p. 44
Darwin 1837, pp. 1–13, 26, 36, 74
Desmond & Moore 1991, pp. 229–232
65.^ UK CPI inflation numbers based on data available from Lawrence H. Officer (2010) "What
Were the UK Earnings and Prices Then?" MeasuringWorth.
66.^ Browne 1995, pp. 367–369
67.^ Keynes 2001, p. xix
68.^ Desmond & Moore 1991, pp. 233–234
"Darwin Correspondence Project - Letter 404 — Buckland, William to Geological Society of London, 9
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69.^ Desmond & Moore 1991, pp. 233–236.
70.^ Desmond & Moore 1991, pp. 241–244, 426
71.^ Browne 1995, p. xii
72.^ Desmond & Moore 1991, pp. 241–244
73.^ Desmond & Moore 1991, pp. 252, 476, 531
Darwin 1958, p. 115
74.^ Desmond & Moore 1991, p. 254
Browne 1995, pp. 377–378
Darwin 1958, p. 84
75.^ Darwin 1958, pp. 232–233
76.^ Desmond & Moore 1991, pp. 256–259
77.^ Darwin 1958, p. 120
78.^ Desmond & Moore 1991, pp. 264–265
Browne 1995, pp. 385–388
Darwin 1842, p. 7
79.^ "Darwin transmutation notebook E p. 75". http://darwin-online.org.uk/content/frameset?
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82.^ Desmond & Moore 1991, pp. 272–279
83.^ Desmond & Moore 1991, p. 279
84.^ Darwin 1958, p. 120
85.^ "Darwin Correspondence Project - Letter 419 — Darwin, C. R. to Fox, W. D., (15 June
1838)". http://www.darwinproject.ac.uk/darwinletters/calendar/entry-419.html. Retrieved 2008-02-08.
86.^ van Wyhe 2007, pp. 186–192
87.^ Darwin 1887, p. 32.
88.^ Desmond & Moore 1991, p. 292
89.^ Desmond & Moore 1991, pp. 292–293
Darwin 1842, pp. xvi–xvii
90.^ Darwin 1954, p. 114
91.^ van Wyhe 2007, pp. 183–184
92.^ "Darwin Correspondence Project - Letter 729 — Darwin, C. R. to Hooker, J. D., (11 January
1844)". http://www.darwinproject.ac.uk/darwinletters/calendar/entry-729.html#back-mark-729.f6.
93.^ "Darwin Correspondence Project - Letter 734 — Hooker, J. D. to Darwin, C. R., 29 January
94.^ Darwin 1887, pp. 114–116
95.^ van Wyhe 2007, p. 188
96.^ Browne 1995, pp. 461–465
97.^ "Darwin Correspondence Project - Letter 814 — Darwin, C. R. to Hooker, J. D., (7 Jan
1845)". http://www.darwinproject.ac.uk/darwinletters/calendar/entry-814.html#back-mark-814.f5.
98.^ van Wyhe 2007, pp. 190–191
99.^ Desmond & Moore 1991, pp. 320–323, 339–348
100.^ "Darwin Correspondence Project - Letter 1236 — Darwin, C. R. to Hooker, J. D., 28 Mar
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101.^ Browne 1995, pp. 498–501
102.^ Darwin 1954, pp. 117–118
103.^ Desmond & Moore 1991, pp. 383–387
104.^ Desmond & Moore 1991, pp. 419–420
105.^ Desmond & Moore 1991, pp. 412–441, 457–458, 462–463
106.^ Desmond & Moore 1991, pp. 466–470
107.^ Browne 2002, pp. 40–42, 48–49
108.^ Darwin 1958, p. 122
109.^ Desmond & Moore 1991, pp. 374–474
110.^ Desmond & Moore 1991, p. 477
111.^ Darwin 1859, p 459
112.^ Darwin 1859, p 490
113.^ Darwin 1859, p 5
114.^ Darwin 1859, p 492
115.^ a b Browne 2002, pp. 373–379
116.^ van Wyhe 2008b, p. 48
117.^ Browne 2002, pp. 103–104, 379
118.^ Darwin 1859, p. 488
119.^ Browne 2002, p. 87
Leifchild 1859
120.^ Desmond & Moore 1991, pp. 477–491
121.^ Browne 2002, pp. 110–112
122.^ Bowler 2003, p. 186
123.^ a b c d "Darwin and design: historical essay". Darwin Correspondence Project. 2007.
124.^ Desmond & Moore 1991, pp. 487–488, 500
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126.^ Bowler 2003, p. 185
127.^ Browne 2002, pp. 156–159
128.^ a b Browne 2002, pp. 217–226
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132.^ Desmond & Moore 1991, pp. 507–508
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139.^ Darwin 1871, p. 405
140.^ Browne 2002, pp. 495–497
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countries visited during the voyage of H.M.S. Beagle round the world, under the Command of Capt.
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Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection". Journal
of the Proceedings of the Linnean Society of London . Zoology 3: 46–50.
• Darwin, Charles (1859). On the Origin of Species by Means of Natural Selection, or the
Preservation of Favoured Races in the Struggle for Life (1st ed.). London: John Murray.
• Darwin, Charles (1868). The variation of animals and plants under domestication. London:
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• Darwin, Charles (1872). The Origin of Species by Means of Natural Selection, or the
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an autobiographical chapter. London: John Murray. ISBN 0404084176. http://darwin-
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11-04.
• Darwin, Charles (1958). Barlow, Nora. ed. The Autobiography of Charles Darwin 1809–1882.
With the original omissions restored. Edited and with appendix and notes by his granddaughter Nora
Barlow. London: Collins.
• Darwin, Charles (2006). "[Darwin's personal 'Journal' (1809-1881)"]. In van Wyhe, John.
Darwin Online. http://darwin-online.org.uk/EditorialIntroductions/vanWyhe_JournalDAR158.html.
• Desmond, Adrian; Moore, James (1991). Darwin. London: Michael Joseph, Penguin Group.
ISBN 0-7181-3430-3.
• Desmond, Adrian; Moore, James; Browne, Janet (2004). Oxford Dictionary of National
Biography. Oxford, England: Oxford University Press. doi:10.1093/ref:odnb/7176.
• Dobzhansky, Theodosius (March 1973). "Nothing in Biology Makes Sense Except in the
Light of Evolution". The American Biology Teacher 35: 125–129.
http://www.2think.org/dobzhansky.shtml. Retrieved 2008-11-04.
• Eldredge, Niles (2006). "Confessions of a Darwinist". The Virginia Quarterly Review (Spring
2006): 32–53. http://www.vqronline.org/articles/2006/spring/eldredge-confessions-darwinist/.
• FitzRoy, Robert (1839). Voyages of the Adventure and Beagle, Volume II . London: Henry
Colburn. http://darwin-online.org.uk/content/frameset?itemID=F10.2&viewtype=text&pageseq=1.
• Freeman, R. B. (1977). The Works of Charles Darwin: An Annotated Bibliographical Handlist .
Folkestone: Wm Dawson & Sons Ltd. ISBN 0208016589. http://darwin-
online.org.uk/content/frameset?itemID=A1&viewtype=text&pageseq=1. Retrieved 2008-11-04.
• Hart, Michael H. (2000). The 100: A Ranking of the Most Influential Persons in History . New
York: Citadel. ISBN 0891041753.
• Herbert, Sandra (1980). "The red notebook of Charles Darwin". Bulletin of the British
Museum (Natural History). Historical Series (7 (24 April)): 1–164. http://darwin-
online.org.uk/content/frameset?viewtype=text&itemID=F1583e&pageseq=1. Retrieved 2009-01-11.
• Herbert, Sandra (1991). "Charles Darwin as a prospective geological author". British Journal
for the History of Science (24): 159–192. http://darwin-online.org.uk/content/frameset?
viewtype=text&itemID=A342&pageseq=1. Retrieved 2008-10-24.
• Keynes, Richard (2000). Charles Darwin's zoology notes & specimen lists from H.M.S.
Beagle.. Cambridge University Press. ISBN 0521465699. http://darwin-
online.org.uk/content/frameset?itemID=F1840&viewtype=text&pageseq=1. Retrieved 2008-11-22.
• Keynes, Richard (2001). Charles Darwin's Beagle Diary. Cambridge University Press.
• Kotzin, Daniel (2004). "Point-Counterpoint: Social Darwinism". Columbia American History
Online. http://caho-test.cc.columbia.edu/pcp/14008.html. Retrieved 2008-11-22.
• Leff, David (2000). "AboutDarwin.com". http://www.aboutdarwin.com/index.html. Retrieved
2008-12-30.
• Leifchild (19 November 1859). "Review of Òrigin'". Athenaeum (1673). http://darwin-
online.org.uk/content/frameset?viewtype=image&itemID=CUL-DAR226.1.8&pageseq=1. Retrieved
2008-11-22.
• Miles, Sara Joan (2001). "Charles Darwin and Asa Gray Discuss Teleology and Design".
Perspectives on Science and Christian Faith 53: 196–201.
http://www.asa3.org/ASA/PSCF/2001/PSCF9-01Miles.html. Retrieved 2008-11-22.
• Moore, James (2005). "Darwin — A 'Devil's Chaplain'?" (PDF). American Public Media.
http://speakingoffaith.publicradio.org/programs/darwin/moore-devilschaplain.pdf. Retrieved 2008-11-
22.
• Moore, James (2006). "Evolution and Wonder - Understanding Charles Darwin". American
Public Media. http://speakingoffaith.publicradio.org/programs/darwin/transcript.shtml. Retrieved
2008-11-22.
• Owen, Richard (1840). Darwin, C. R.. ed. Fossil Mammalia Part 1. The zoology of the voyage
of H.M.S. Beagle. London: Smith Elder and Co.
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Radick, Gregory. The Cambridge Companion to Darwin. Cambridge University Press. pp. 214–239.
ISBN 0-521-77730-5.
• Smith, Charles H. (1999). "Alfred Russel Wallace on Spiritualism, Man, and Evolution: An
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• Sulloway, Frank J. (1982). "Darwin and His Finches: The Evolution of a Legend" (PDF).
Journal of the History of Biology 15 (1): 1–53. doi:10.1007/BF00132004.
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http://www.iep.utm.edu/spencer/. Retrieved 2008-12-16.
• Wilkins, John S. (1997). "Evolution and Philosophy: Does evolution make might right?".
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• Wilkins, John S. (2008). "Darwin". In Tucker, Aviezer. A Companion to the Philosophy of
History and Historiography. Blackwell Companions to Philosophy. Chichester: Wiley-Blackwell.
pp. 405–415. ISBN 1-4051-4908-6.
• van Wyhe, John (27 March 2007). "Mind the gap: Did Darwin avoid publishing his theory for
many years?". Notes and Records of the Royal Society 61: 177–205. doi:10.1098/rsnr.2006.0171.
http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=A544&pageseq=1. Retrieved
2008-02-07.
• van Wyhe, John (2008). "Charles Darwin: gentleman naturalist: A biographical sketch".
Darwin Online. http://darwin-online.org.uk/darwin.html. Retrieved 2008-11-17.
• van Wyhe, John (2008b). Darwin: The Story of the Man and His Theories of Evolution .
London: Andre Deutsch Ltd (published 1 September 2008). ISBN 0-233-00251-0.
• von Sydow, Momme (2005). "Darwin – A Christian Undermining Christianity? On Self-
Undermining Dynamics of Ideas Between Belief and Science". In Knight, David M.; Eddy, Matthew
D.. Science and Beliefs: From Natural Philosophy to Natural Science, 1700–1900 . Burlington:
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• Yates, Simon (2003). "The Lady Hope Story: A Widespread Falsehood". TalkOrigins Archive.
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External links
Find more about Charles Darwin on Wikipedia's sister projects:

• The Complete Works of Charles Darwin Online – Darwin Online; Darwin's publications,
private papers and bibliography, supplementary works including biographies, obituaries and reviews
• Works by Charles Darwin at Project Gutenberg; public domain
• Darwin Correspondence Project Full text and notes for complete correspondence to 1867,
with summaries of all the rest
• Works by Charles Darwin in audio format from LibriVox
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• Archival material relating to Charles Darwin listed at the UK National Register of Archives
• Darwin 200: Celebrating Charles Darwin's bicentenary , Natural History Museum
• A Pictorial Biography of Charles Darwin
• Mis-portrayal of Darwin as a Racist
• Chisholm, Hugh, ed (1911). "Darwin, Charles Robert". Encyclopædia Britannica (Eleventh
ed.). Cambridge University Press.
• The life and times of Charles Darwin , an audio slideshow, The Guardian, Thursday 12
February 2009, (3 min 20 sec).
• CBC Digital Archives: Charles Darwin and the Origins of Evolution
• Darwin's Volcano - a short video discussing Darwin and Agassiz' coral reef formation debate
• Darwin's Brave New World - A 3 part drama-documentary exploring Charles Darwin and the
significant contributions of his colleagues Joseph Hooker, Thomas Huxley and Alfred Russel Wallace
also featuring interviews with Richard Dawkins, David Suzuki, Jared Diamond and Iain McCalman.
• A naturalists voyage around the world Account of the Beagle voyage using animation, in
English from Centre national de la recherche scientifique, Paris.
• Video and radio clips Canadian Broadcasting Corporation
• Anonymous (1873). Cartoon portraits and biographical sketches of men of the day . Illustrated
by Waddy, Frederick. London: Tinsley Brothers. pp. 6–7.
http://en.wikisource.org/wiki/Cartoon_portraits_and_biographical_sketches_of_men_of_the_day/C._
R._Darwin,_F.R.S.. Retrieved 2010-12-28.
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W000
Embryology

This article needs additional citations for verification.
challenged and removed. (July 2007)
1 - morula, 2 - blastula
1 - blastula, 2 - gastrula with blastopore; orange - ectoderm, red - endoderm.

Embryology (from Greek ἔμβρυον, embryon, "unborn, embryo"; and -λογία, -logia) is a science which
is about the development of an embryo from the fertilization of the ovum to the fetus stage. After cleavage,
the dividing cells, or morula, becomes a hollow ball, or blastula, which develops a hole or pore at one end.
In bilateral animals, the blastula develops in one of two ways that divides the whole animal kingdom
into two halves (see: Embryological origins of the mouth and anus). If in the blastula the first pore
(blastopore) becomes the mouth of the animal, it is a protostome; if the first pore becomes the anus then it is
a deuterostome. The protostomes include most invertebrate animals, such as insects, worms and molluscs,
while the deuterostomes include the vertebrates. In due course, the blastula changes into a more
differentiated structure called the gastrula.
The gastrula with its blastopore soon develops three distinct layers of cells (the germ layers) from
which all the bodily organs and tissues then develop:
• The innermost layer, or endoderm, gives rise to the digestive organs, lungs and bladder.
• The middle layer, or mesoderm, gives rise to the muscles, skeleton and blood system.
• The outer layer of cells, or ectoderm, gives rise to the nervous system and skin.
In humans, the term embryo refers to the ball of dividing cells from the moment the zygote implants
itself in the uterus wall until the end of the eighth week after conception. Beyond the eighth week, the
developing human is then called a fetus. Embryos in many species often appear similar to one another in
early developmental stages. The reason for this similarity is because species have a shared evolutionary
history. These similarities among species are called homologous structures, which are structures that have
the same or similar function and mechanism having evolved from a common ancestor.
Contents
[hide]
• 1 History
• 2 Vertebrate and invertebrate embryology
• 3 Modern embryology research
• 4 See also
• 5 References
[edit] History
Human embryo at six weeks gestational age

Histological film 10 day mouse embryo
Beetle larvae
As recently as the 18th century, the prevailing notion in human embryology was preformation: the
idea that semen contains an embryo — a preformed, miniature infant, or " homunculus" — that simply becomes
larger during development. The competing explanation of embryonic development was epigenesis, originally
proposed 2,000 years earlier by Aristotle. According to epigenesis, the form of an animal emerges gradually
from a relatively formless egg. As microscopy improved during the 19th century, biologists could see that
embryos took shape in a series of progressive steps, and epigenesis displaced preformation as the favored
explanation among embryologists.[1]
Modern embryological pioneers include Gavin de Beer, Charles Darwin, Ernst Haeckel, J.B.S.
Haldane, and Joseph Needham, while much early embryology came from the work of Aristotle and the great
Italian anatomists: Aldrovandi, Aranzio, Leonardo da Vinci, Marcello Malpighi, Gabriele Falloppia, Girolamo
Cardano, Emilio Parisano, Fortunio Liceti, Stefano Lorenzini, Spallanzani, Enrico Sertoli, Mauro Rusconi, etc.
[2] Other important contributors include William Harvey, Kaspar Friedrich Wolff, Heinz Christian Pander, Karl
Ernst von Baer, August Weismann, Ernest Everett Just, and Edward B. Lewis.
After the 1950s, with the DNA helical structure being unravelled and the increasing knowledge in the
field of molecular biology, developmental biology emerged as a field of study which attempts to correlate the
genes with morphological change, and so tries to determine which genes are responsible for each
morphological change that takes place in an embryo, and how these genes are regulated.
[edit] Vertebrate and invertebrate embryology

Many principles of embryology apply to both invertebrate animals as well as to vertebrates.[3]
Therefore, the study of invertebrate embryology has advanced the study of vertebrate embryology. However,
there are many differences as well. For example, numerous invertebrate species release a larva before
development is complete; at the end of the larval period, an animal for the first time comes to resemble an
adult similar to its parent or parents. Although invertebrate embryology is similar in some ways for different
invertebrate animals, there are also countless variations. For instance, while spiders proceed directly from
egg to adult form many insects develop through at least one larval stage
[edit] Modern embryology research
Currently, embryology has become an important research area for studying the genetic control of the
development process (e.g. morphogens), its link to cell signalling, its importance for the study of certain
diseases and mutations and in links to stem cell research.
[edit] See also

• Ontogeny
• Embryogenesis
• Recapitulation theory
• Prenatal development
• Protostomes
• Deuterostomes
• Germ layers
• Epigenesis (biology)
• Developmental biology
• Cell signalling
• Hedgehog signaling pathway
• Morphogens
• French flag model
• Embryo drawing
[edit] References
1. ^ Campbell et al. (p. 987)
2. ^ Massimo De Felici, Gregorio Siracus, The rise of embryology in Italy: from the
Renaissance to the early 20th Century, Int. J. Dev. Biol. 44: 515-521 (2000).
3. ^ Parker, Sybil. "Invertebrate Embryology," McGraw-Hill Encyclopedia of Science &
Technology (McGraw-Hill 1997).
Embryology - History of embryology as a science." Science Encyclopedia. Web. 06 Nov. 2009.
<http://science.jrank.org/pages/2452/Embryology.html>.
"Germ layer." Encyclopædia Britannica. 2009. Encyclopædia Britannica Online. 06 Nov. 2009
<http://www.britannica.com/EBchecked/topic/230597/germ-layer>.

• Scott F. Gilbert. Developmental Biology. Sinauer, 2003. ISBN 0-87893-258-5.
• Lewis Wolpert. Principles of Development. Oxford University Press, 2006. ISBN 0-19-
927536-X.

Wikimedia Commons has media related to: Embryology
• Indiana University's Human Embryology Animations
• What is a human admixed embryo?
• UNSW Embryology Large resource of information and media
• Definition of embryo according to Webster
[hide]v · d · eDevelopmental biology > Human embryogenesis (development of embryo) and

development of fetus
First three Fertilization · Oocyte activation · Zygote · Cleavage ·

weeks Week 1
Morula · Blastula (Blastomere) · Blastocyst · Inner cell mass
Week 2
Hypoblast · Epiblast
(Bilaminar)
Archenteron/Primitive streak
Germ (Primitive pit, Primitive knot/Blastopore,
layers Primitive groove) · Gastrula/Gastrulation ·
Regional specification
Week 3
(Trilaminar)
Surface ectoderm ·
Ectoderm Neuroectoderm · Somatopleure ·
Neurulation · Neural crest
Endoderm Splanchnopleure
Chorda- · Paraxial
(Somite/Somitomere/Sclerotome/Myotom
Mesoderm e/Dermatome) · Intermediate · Lateral
plate (Intraembryonic coelom,
Splanchnopleure/Somatopleure)
Trophoblast (Cytotrophoblast, Syncytiotrophoblast)

Blastocoele · Yolk sack/exocoelomic cavity · Heuser's membrane ·
Extraembryonic/ Extraembryonic coelom · Vitelline duct
uterus
Umbilical cord (Umbilical artery, Umbilical vein, Wharton's jelly) · Allantois
Placenta · Decidua (Decidual cells) · Chorionic villi/Intervillous space ·
Gestational sac (Amnion/Amniotic sac/Amniotic cavity, Chorion)
Histogenesis Programmed cell death (Apoptosis) · Stem cells · Germ line development
Limb development: Limb bud · Apical ectodermal ridge/AER

Organogenesis other structures: Eye development · Cutaneous structure development · Heart
development · Development of the urinary and reproductive organs
(Some dates are approximate—see Carnegie stages and a timeline.)
phys/dev mthr/fetu/infc,
M: OBS proc, drug(2A/G2C)
p epon
[hide]v · d · eHuman development of head and neck / branchial apparatus (GA 1.65)
Nasal placode · Olfactory pit · nasal

Nose prominences (Lateral, Medial) ·
Intermaxillary segment
Primitive palate ·
Palate
Secondary palate
Frontonasal
prominence · Maxillary
Mouth/neck prominence · Mandibular
1st prominence (Meckel's
arch cartilage)
Anterior tongue:
Lateral lingual swelling ·
Tuberculum impar
Thyroid (pouches 3-5) Thyroid diverticulum · Thyroglossal
duct · Ultimobranchial body
Pharyngeal groove (Cervical

General sinus) · Pharyngeal arch (1st, 2nd) ·
Pharyngeal pouch (Ultimobranchial body) ·
Copula linguae
anat(n noco(c) proc,
M:
, x, l, /cong/tumr, drug(R1/2/3/5/
RES
c)/phys/devp sysi/epon, injr 6/7)
noco/co proc
M: anat/
fa(c)/cogi/tumr, (peri), drug
MOU devp
sysi (A1)
proc,
anat/p noco(d
M: drug
hys/devp/horm )/cong/tumr,
END (A10/H1/H2/H
/cell sysi/epon
3/H5)
[hide]v · d · eOssification (GA 2.80)
Ossification of humerus ·
Upper limb Ossification of ulna · Ossification of
radius
Lower limb Ossification of tibia
cranium: Ossification of
occipital bone · Ossification of frontal
bone · Ossification of temporal bone ·
Head Ossification of the sphenoid ·
Ossification of ethmoid
facial bones: Ossification of
maxilla · Ossification of the mandible
Other Ossification of scapula

anat(c/f/k noco/co
M: proc,
/f, u, t/p, ng/tumr,
BON/CAR drug(M5)
l)/phys/devp/cell sysi/epon, injr
[hide]v · d · ePrenatal development/Mammalian development of circulatory system (GA 5)
Vasculogenesis, Blood island

angiogenesis,
and lymphangiogenesis Development Dorsal aorta ·
of arteries Aortic arches
Development Cardinal veins ·

of veins Ducts of Cuvier
Fetal umbilical cord:

circulation Umbilical vein →
Ductus venosus →
Inferior vena cava →
Heart → Pulmonary
artery → Ductus
arteriosus → Umbilical
artery
yolk sac:
Vitelline veins · Vitelline
arteries
Truncus arteriosus ·
Primitive Bulbus cordis · Primitive
heart tube ventricle · Primitive atrium ·
Sinus venosus
Endocardial
cushions/Septum
Heart development intermedium · Ostium
Septa/os primum · Septum primum
tia (Ostium secundum) ·
Septum secundum
(Foramen ovale) ·
Aorticopulmonary septum
Atrial canal ·
Other
Interventricular foramen
M: anat( noco/ proc,
VAS a:h, u, t, a, syva/cong/tu drug(C2s/n,
l,v:h, u, t, a, mr, sysi/epon C3, C4, C5,
l)/phys/devp/c
ell/prot C7, C8, C9)
proc,
noco/
M: anat/ drug
cong/tumr,
HRT phys/devp (C1A/1B/1C/1
sysi/epon
D), blte
[hide]v · d · ePrenatal development/Mammalian development of nervous system and integument

(GA 9.733)
Neurogenesis General neural

Notochord · Neuroectoderm · Neural plate ·
development/
Neural folds · Neural groove
neurulation/neurula
Cranial neural crest · Trunk neural crest ·

Neural crest
Cardiac neural crest
Neural tube Neuromere/Rhombomere, Cephalic flexure,

Pontine flexure
Alar plate (sensory) · Basal plate (motor)
Glioblast · Neuroblast
Germinal matrix
Integument Cutaneous structure development · Hair growth
note: NS is mostly ectoderm, but mesoderm is precursor for epineurium, perineurium, and
endoneurium
proc,
M: anat(s, m, p, 4, e, b, d, noco(m, d, e, h, v,
drug(N1A/2AB/C/3/4/7A/B/
CNS c, a, f, l, g)/phys/devp/cell s)/cong/tumr, sysi/epon, injr
C/D)
M: INT, anat/phys/ noco(i, b, d, q, u, r, p, k, c, proc, drug

SF, LCT devp v)/cong/tumr(n, e, d), sysi/epon (D2/3/4/5/8)
anat/phys/dev noco/cong/tumr,
M: SKA proc, drug(D10)
p sysi/epon
[hide]v · d · ePrenatal development/Mammalian development of eye and ear (GA 10.1002)

Neural tube: Optic
vesicles · Optic stalk · Optic
Eye development cup
Surface ectoderm:
Lens placode
Auditory development Auditory vesicle ·

Auditory pit
anat(g, a, proc,
M: noco/con
p)/phys/devp/cell/pro drug(S1A/1E/1F/1L
EYE g/tumr, epon
t )
M: anat(e, noco/cong proc,

EAR p)/phys/devp , epon drug(S2)
[hide]v · d · ePrenatal development/Mammalian development of respiratory system (overview) (GA

11.1071)
Upper Nasal placode

Lower Laryngotracheal
groove · Lung buds
M: anat(n, x, noco(c)/cong proc,
RES l, c)/phys/devp /tumr, sysi/epon, injr drug(R1/2/3/5/6/7)
[hide]v · d · ePrenatal development/Mammalian development of digestive system (GA 11.1101)
Gut Stomodeum
Foregut: upper GI
Upper GI (Buccopharyngeal
tract and membrane, Rathke's pouch,
accessory Tracheoesophageal
septum) · accessory
(Pancreatic bud, Hepatic
diverticulum)
Midgut
Hindgut: Urorectal
septum
Lower GI
tract Proctodeum
Cloacal membrane
Cloaca
Dorsal
Mesentery mesentery · Ventral
Abdominopelvic mesentery
Thoracic Septum
diaphragm transversum
anat( proc,
noco/
M: t, g, drug(A2A/2B/
cong/tumr,
DIG p)/phys/devp/ 3/4/5/6/7/14/1
sysi/epon
cell/enzy 6), blte
[hide]v · d · ePrenatal development/mammalian embryogenesis · Development of the urinary and
reproductive organs (GA 11.1204)
Mesoderm → Intermediate mesoderm

→ Urogenital folds ("UF")
Mesoderm → Lateral plate mesoderm
Common urinary and ("LPM")
reproductive system
Endoderm → Cloaca → Urogenital
sinus ("US")
Endoderm+Ectoderm → Cloacal
membrane
UF → Nephrogenic cord → Kidney

UF → Nephrotome → Pronephros ·
Mesonephros (Mesonephric tubules)
Urinary system
development UF → WD → Ureteric bud +
Metanephric blastema
US → Urinary bladder + Urethra +
Urethral groove + Urachus
Reproductive system UF → Gonadal
development ridge → Indifferent gonad →
Sex cord (Cortical cords,
Testis cords)
UF → Pronephric
Primarily duct/Wolffian
internal duct/mesonephric duct +
Müllerian
duct/paramesonephric
ducts (Vaginal plate)
US → Prostate or
Skene's gland
Primarily LPM → Genital

external tubercle → Labioscrotal
folds → Scrotum or Labia
majora
LPM → Genital
tubercle → Phallus → Penis
or Clitoris
IM →
Gubernaculum
Peritoneum →
Processus vaginalis or
Canal of Nuck
Homologues List of homologues of the human

reproductive system
noco/a proc/it
anat/
M: cba/cong/tumr vp, drug
phys/devp/cel
URI , sysi/epon, (G4B), blte,
l
urte urte
proc/as
noco/
M: ♀ anat/ st, drug
cong/npls,
FRS phys/devp (G1/G2B/G3C
sysi/epon
D)
noco/ proc,
M: ♂ anat/
cong/tumr, drug
MRS phys/devp
sysi/epon (G3B/4B/4C)
Retrieved from "http://en.wikipedia.org/wiki/Embryology"
Categories: Embryology
W000
Termite

Not to be confused with Termit, Thermite, or Turmite.
This article is about insects. For other uses, see Termite (disambiguation).
This article is missing citations or needs footnotes. Please help add inline citations
to guard against copyright violations and factual inaccuracies. (March 2009)
Termite
PreЄ
g Late Triassic - Recent
Formosan subterranean termite soldiers (red colored heads) and workers (pale colored heads).
Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Subclass: Pterygota
Infraclass: Neoptera
Superorder: Dictyoptera
Order: Isoptera
Families
Mastotermitidae
Kalotermitidae
Termopsidae
Hodotermitidae
Rhinotermitidae
Serritermitidae
Termitidae
The termites are a group of eusocial insects usually classified at the taxonomic rank of order Isoptera
(but see also taxonomy below). Along with ants and some bees and wasps which are all placed in the
separate order Hymenoptera, termites divide labour among gender lines, produce overlapping generations
and take care of young collectively. Termites mostly feed on dead plant material, generally in the form of
wood, leaf litter, soil, or animal dung, and about 10% of the estimated 4,000 species (about 2,600
taxonomically known) are economically significant as pests that can cause serious structural damage to
buildings, crops or plantation forests. Termites are major detritivores, particularly in the subtropical and
tropical regions, and their recycling of wood and other plant matter is of considerable ecological importance.
Their role in bioturbation on the Khorat Plateau is under investigation.[1]
As eusocial insects, termites live in colonies that, at maturity, number from several hundred to
several million individuals. Colonies use a decentralised, self-organised systems of activity guided by swarm
intelligence to exploit food sources and environments that could not be available to any single insect acting
alone. A typical colony contains nymphs (semi-mature young), workers, soldiers, and reproductive individuals
of both genders, sometimes containing several egg-laying queens.
Termites are sometimes called "white ants", though they are not closely related to true ants.
Contents
[hide]
• 1 Social organization
• 1.1 Reproductives
• 1.2 Workers
• 1.3 Soldiers
• 1.4 Diet
• 2 Nests
• 2.1 Mounds
• 2.2 Shelter tunnels
• 3 Human interaction
• 3.1 Timber damage
• 3.2 Termites in the human diet
• 3.3 Agriculture
• 3.4 Termites as a source of power
• 3.5 Ground water divining in Ancient India
• 4 Ecology
• 4.1 Plant defences against termites
• 5 Taxonomy, evolution and systematics
• 5.1 Evolutionary history
• 5.2 Systematics
• 6 See also
[edit] Social organization
[edit] Reproductives
Preserved specimen of fertile termite queen, showing distended abdomen. The rest of its body is the
same size as that of a worker.
A female that has flown, mated, and is producing eggs is called a "queen". Similarly, a male that has
flown, mated, and remains in proximity to a queen, is termed a "king". Research using genetic techniques to
determine relatedness of colony members is showing that the idea that colonies are only ever headed by a
monogamous royal pair is wrong. Multiple pairs of reproductives within a colony are not uncommon. In the
families Rhinotermitidae and Termitidae, and possibly others, sperm competition does not seem to occur
(male genitalia are very simple and the sperm are anucleate), suggesting that only one male (king) generally
mates within the colony.
At maturity, a primary queen has a great capacity to lay eggs. In physogastric species, the queen
adds an extra set of ovaries with each molt, resulting in a greatly distended abdomen and increased
fecundity, often reported to reach a production of more than two thousand eggs a day. The distended
abdomen increases the queen's body length to several times more than before mating and reduces her
ability to move freely, though attendant workers provide assistance. The queen is widely believed to be a
primary source of pheromones useful in colony integration, and these are thought to be spread through
shared feeding (trophallaxis).
The king grows only slightly larger after initial mating and continues to mate with the queen for life.
This is very different from ant colonies, in which a queen mates once with the male(s) and stores the
gametes for life, and the male ants die shortly after mating.
Two termites in the process of shedding their wings after mating. Maun, Botswana.
The winged (or 'alate') caste, also referred to as the reproductive caste, are generally the only
termites with well-developed eyes (although workers of some harvesting species do have well-developed
compound eyes, and, in other species, soldiers with eyes occasionally appear). Termites on the path to
becoming alates (going through incomplete metamorphosis) form a sub-caste in certain species of termites,
functioning as workers ('pseudergates') and also as potential supplementary reproductives. Supplementaries
have the ability to replace a dead primary reproductive and, at least in some species, several are recruited
once a primary queen is lost.
In areas with a distinct dry season, the alates leave the nest in large swarms after the first good
soaking rain of the rainy season. In other regions, flights may occur throughout the year or more commonly in
the spring and autumn. Termites are relatively poor fliers and are readily blown downwind in windspeeds of
less than 2 km/h, shedding their wings soon after landing at an acceptable site, where they mate and attempt
to form a nest in damp timber or earth.
[edit] Workers
Worker termite
Worker termites undertake the labors of foraging, food storage, brood and nest maintenance, and
some defense duties in certain species. Workers are the main caste in the colony for the digestion of
cellulose in food and are the most likely to be found in infested wood. This is achieved in one of two ways. In
all termite families except the Termitidae, there are flagellate protists in the gut that assist in cellulose
digestion. However, in the Termitidae, which account for approximately 60% of all termite species, the
flagellates have been lost and this digestive role is taken up, in part, by a consortium of prokaryotic
organisms. This simple story, which has been in entomology textbooks for decades, is complicated by the
finding that all studied termites can produce their own cellulase enzymes, and therefore can digest wood in
the absence of their symbiotic microbes. Our knowledge of the relationships between the microbial and
termite parts of their digestion is still rudimentary. What is true in all termite species, however, is that the
workers feed the other members of the colony with substances derived from the digestion of plant material,
either from the mouth or anus. This process of feeding of one colony member by another is known as
trophallaxis and is one of the keys to the success of the group. It frees the parents from feeding all but the
first generation of offspring, allowing for the group to grow much larger and ensuring that the necessary gut
symbionts are transferred from one generation to another. Some termite species do not have a true worker
caste, instead relying on nymphs that perform the same work without moulting into a separate caste.
[edit] Soldiers
A picture of a soldier termite (Macrotermitinae) with an enlarged jaw in the Okavango Delta.
The soldier caste has anatomical and behavioural specializations, providing strength and armour
which are primarily useful against ant attack. The proportion of soldiers within a colony varies both within and
among species. Many soldiers have jaws so enlarged that they cannot feed themselves, but instead, like
juveniles, are fed by workers. The pan-tropical sub-family Nasutitermitinae have soldiers with the ability to
exude noxious liquids through either a horn-like nozzle (nasus) or simple hole in the head (fontanelle).
Fontanelles which exude defensive secretions are also a feature of the family Rhinotermitidae. Many species
are readily identified using the characteristics of the soldiers' heads, mandibles, or nasus. Among the
drywood termites, a soldier's globular ("phragmotic") head can be used to block their narrow tunnels. Termite
soldiers are usually blind, but in some families, soldiers developing from the reproductive line may have at
least partly functional eyes.
A nasute
The specialization of the soldier caste is principally a defense against predation by ants. The wide
range of jaw types and phragmotic heads provides methods which effectively block narrow termite tunnels
against ant entry. A tunnel-blocking soldier can rebuff attacks from many ants. Usually more soldiers stand
by behind the initial soldier so once the first one falls another soldier will take the place. In cases where the
intrusion is coming from a breach that is larger than the soldier's head, defense requires special formations
where soldiers form a phalanx-like formation around the breach and blindly bite at intruders or shoot toxic
glue from the nasus. This formation involves self-sacrifice because once the workers have repaired the
breach during fighting, no return is provided, thus leading to the death of all defenders. Another form of self-
sacrifice is performed by South-East Asian tar-baby termites (Globitermes sulphureus). The soldiers of this
species commit suicide by autothysis - rupturing a large gland just beneath the surface of their cuticle. The
thick yellow fluid in the gland becomes very sticky on contact with the air, entangling ants or other insects
who are trying to invade the nest.[2][3]
Termites undergo incomplete metamorphosis, with their freshly hatched young taking the form of tiny
termites that grow without significant morphological changes (other than wings and soldier specializations).
Some species of termite have dimorphic soldiers (up to three times the size of smaller soldiers). Though their
value is unknown, speculation is that they may function as an elite class that defends only the inner tunnels
of the mound. Evidence for this is that, even when provoked, these large soldiers do not defend themselves
but retreat deeper into the mound. On the other hand, dimorphic soldiers are common in some Australian
species of Schedorhinotermes that neither build mounds nor appear to maintain complex nest structures.
Some termite taxa are without soldiers; perhaps the best known of these are the Apicotermitinae.
[edit] Diet
Termites are generally grouped according to their feeding behaviour. Thus, the commonly used
general groupings are subterranean, soil-feeding, drywood, dampwood, and grass-eating. Of these,
subterraneans and drywoods are primarily responsible for damage to human-made structures.
All termites eat cellulose in its various forms as plant fibre. Cellulose is a rich energy source (as
demonstrated by the amount of energy released when wood is burned), but remains difficult to digest.
Termites rely primarily upon symbiotic protozoa (metamonads) such as Trichonympha, and other microbes in
their gut to digest the cellulose for them and absorb the end products for their own use. Gut protozoa, such
as Trichonympha, in turn rely on symbiotic bacteria embedded on their surfaces to produce some of the
necessary digestive enzymes. This relationship is one of the finest examples of mutualism among animals.
Most so called "higher termites", especially in the Family Termitidae, can produce their own cellulase
enzymes. However, they still retain a rich gut fauna and primarily rely upon the bacteria. Due to closely
related bacterial species, it is strongly presumed that the termites' gut flora are descended from the gut flora
of the ancestral wood-eating cockroaches, like those of the genus Cryptocercus.
Some species of termite practice fungiculture. They maintain a 'garden' of specialized fungi of genus
Termitomyces, which are nourished by the excrement of the insects. When the fungi are eaten, their spores
pass undamaged through the intestines of the termites to complete the cycle by germinating in the fresh
faecal pellets.[4][5] They are also well known for eating smaller insects in a last resort environment.
[edit] Nests
An arboreal termite nest in Mexico
Termite workers build and maintain nests to house their colony. These are elaborate structures made
using a combination of soil, mud, chewed wood/cellulose, saliva, and faeces. A nest has many functions
such as to provide a protected living space and to collect water through condensation. There are
reproductive chambers and some species even maintain fungal gardens which are fed on collected plant
matter, providing a nutritious mycelium on which the colony then feeds (see "Diet", above). Nests are
punctuated by a maze of tunnel-like galleries that effectively provide air conditioning and control the CO 2/O2
balance, as well as allow the termites to move through the nest.
Nests are commonly built underground, in large pieces of timber, inside fallen trees or atop living
trees. Some species build nests above-ground, and they can develop into mounds. Homeowners need to be
careful of tree stumps that have not been dug up. These are prime candidates for termite nests and being
close to homes, termites usually end up destroying the siding and sometimes even wooden beams.
[edit] Mounds
A termite mound (Macrotermitinae) in the Okavango Delta just outside of Maun, Botswana
Mounds (also known as "termitaria"[6]) occur when an above-ground nest grows beyond its initially
concaling surface. They are commonly called "anthills" in Africa and Australia, despite the technical
incorrectness of that name.
In tropical savannas the mounds may be very large, with an extreme of 9 metres (30 ft) high in the
case of large conical mounds constructed by some Macrotermes species in well-wooded areas in Africa[7].
Two to three metres, however, would be typical for the largest mounds in most savannas. The shape ranges
from somewhat amorphous domes or cones usually covered in grass and/or woody shrubs, to sculptured
hard earth mounds, or a mixture of the two. Despite the irregular mound shapes, the different species in an
area can usually be identified by simply looking at the mounds.
The sculptured mounds sometimes have elaborate and distinctive blue forms, such as those of the
compass termite (Amitermes meridionalis & A. laurensis) which build tall wedge-shaped mounds with the
long axis oriented approximately north-south. This orientation has been experimentally shown to help in
thermoregulation.
The column of hot air rising in the above ground mounds helps drive air circulation currents inside the
subterranean network. The structure of these mounds can be quite complex. The temperature control is
essential for those species that cultivate fungal gardens and even for those that don't, much effort and energy
is spent maintaining the brood within a narrow temperature range, often only plus or minus one degree C
over a day.
In some parts of the African savanna, a high density of above-ground mounds dominates the
landscape. For instance, in some parts of the Busanga Plain area of Zambia, small mounds of about 1 m
diameter with a density of about 100 per hectare can be seen on grassland between larger tree- and bush-
covered mounds about 25 m in diameter with a density around 1 per hectare, and both show up well on high-
resolution satellite images taken in the wet season.[8].
Magnetic Mounds (nearly Termite mound in
Cathedral Mounds in the North-South Axis) Queensland / Australia
Northern Territory of Australia
Wikimedia Commons has media related to: Termite mounds

[edit] Shelter tunnels
Tunnels on a tree trunk provide a passage from the nest to the forest floor
Termites are very weak and fragile insects. They can be easily overpowered by ants and other
predators when exposed. To avoid these perils termites cover their tracks with tubing made of faeces, plant
matter, and soil. Thus the termites can remain hidden and wall out unfavourable environmental conditions.
Sometimes these shelter tubes will extend for many metres, such as up the outside of a tree reaching from
the soil to dead branches.
To a subterranean termite any breach of their tunnels or nest is a cause for alarm. When the
Formosan subterranean termite (Coptotermes formosanus) and the Eastern subterranean termite
(Reticulitermes flavipes) detect a potential breach, the soldiers will usually bang their heads apparently to
attract other soldiers for defense and recruit additional workers to repair any breach.
[edit] Human interaction

[edit] Timber damage
The result of an infestation is severe wood damage

Termite damage on external structure
Termite damage in wooden house stumps
Due to their wood-eating habits, many termite species can do great damage to unprotected buildings
and other wooden structures. Their habit of remaining concealed often results in their presence being
undetected until the timbers are severely damaged and exhibit surface changes. Once termites have entered
a building, they do not limit themselves to wood; they also damage paper, cloth, carpets, and other cellulosic
materials. Particles taken from soft plastics, plaster, rubber, and sealants such as silicone rubber and acrylics
are often employed in construction.
Humans have moved many wood-eating species between continents, but have also caused drastic
population decline in others through habitat loss and pesticide application.
Precautions:
• Avoid contact of susceptible timber with ground by using termite-resistant concrete, steel, or
masonry foundation with appropriate barriers. Even so, termites are able to bridge these with shelter
tubes, and it has been known for termites to chew through piping made of soft plastics and even
some metals, such as lead, to exploit moisture. In general, new buildings should be constructed with
embedded physical termite barriers so that there are no easy means for termites to gain concealed
entry. While barriers of poisoned soil, so called termite pre-treatment, have been in general use since
the 1970s, it is preferable that these be used only for existing buildings without effective physical
barriers.
• The intent of termite barriers (whether physical, poisoned soil, or some of the new poisoned
plastics) is to prevent the termites from gaining unseen access to structures. In most instances,
termites attempting to enter a barriered building will be forced into the less favourable approach of
building shelter tubes up the outside walls, and thus, they can be clearly visible both to the building
occupants and a range of predators.
• Timber treatment.
• Use of timber that is naturally resistant to termites such as Syncarpia glomulifera (Turpentine
Tree), Callitris glaucophylla (White Cypress), or one of the Sequoias. Note that there is no tree
species whose every individual tree yields only timbers that are immune to termite damage, so that
even with well known termite-resistant timber types, there will occasionally be pieces that are
attacked. No species of tree produces timber that is completely immune to damage from every
species of termite, some individual pieces of wood may be attacked.
When termites have already penetrated a building, the first action is usually to destroy the colony
with insecticides before removing the termites' means of access and fixing the problems that encouraged
them in the first place. Baits (feeder stations) with small quantities of disruptive insect hormones or other very
slow acting toxins have become the preferred least-toxic management tool in most western countries. This
has replaced the dusting of toxins direct into termite tunnels that had been widely done since the early 1930s
(originating in Australia). The main dust toxicants have been the inorganic metallic poison arsenic trioxide,
insect growth regulators (hormones) such as triflumuron and, more recently fipronil, a phenyl-pyrazole.
Blowing dusts into termite workings is a highly skilled process. All these slow-acting poisons can be
distributed by the workers for hours or weeks before any symptoms occur and are capable of destroying the
entire colony. More modern variations include chlorfluazuron, diflubenzuron, hexaflumuron, and
novaflumuron as bait toxicants and fipronil and imidacloprid as soil poisons. Soil poisons are the least-
preferred method of control as this requires much larger doses of toxin and results in uncontrollable release
to the environment.
The termite’s effects are damaging, costing the southwestern United States approximately $1.5
billion each year in wood structure damage. In order to better control the population of termites, researchers
at the Agricultural Research Service have found a way to track the movement of the destructive pests. In
1990, researchers found a way to safely and reliably track termites using immunoglobulin G (IgG) marker
proteins from rabbits or chickens. In field tests, termite bait was laced with the rabbit IgG and the termites
were randomly exposed to feeding on this bait. Termites were later collected from the field and tested for the
rabbit-IgG markers using a rabbit-IgG-specific assay. However, this method of testing for the tracking
proteins is expensive. Recently, researchers have developed a new way of tracking the termites using egg
white, cow milk, or soy milk proteins which can be sprayed on the termites in the field. This new method is
less expensive because the proteins can be traced using a protein-specific ELISA test. The ELISA test is
more affordable because it is designed for mass production. Researchers hope to use this method of tracking
termites to find a more cost-effective way to control the damaging pests. [3]
Agricultural Research Service scientists have developed a more affordable method to track the
movement of termites using traceable proteins.[2]
[edit] Termites in the human diet
In many cultures, termites (particularly the winged ones known as alates) are used for food. The
alates are nutritious, having a good store of fat and protein, and are palatable in most species with a nutty
flavour when cooked. They are easily gathered at the beginning of the rainy season in West, Central and
Southern Africa when they swarm, as they are attracted to lights and can be gathered up when they land on
nets put up around a lamp. The wings are shed and can be removed by a technique similar to winnowing.
They are best gently roasted on a hot plate or lightly fried until slightly crisp; oil is not usually needed since
their bodies are naturally high in oil. Traditionally they make a welcome treat at the beginning of the rainy
season when livestock is lean, new crops have not yet produced food, and stored produce from the previous
growing season is running low.[citation needed]
They are also eaten in Indonesia, including Central Java, where they are roasted or fried.[citation
needed]
[edit] Agriculture
Termites can be major agricultural pests, particularly in Africa and Asia, where crop losses can be
severe. Counterbalancing this is the greatly improved water infiltration where termite tunnels in the soil allow
rainwater to soak in deeply and help reduce runoff and consequent soil erosion.
[edit] Termites as a source of power

The US Department of Energy is researching ways to replace fossil fuels with renewable sources of
cleaner energy, and termites are considered a possible way to reach this goal through metagenomics.[9]
Termites may produce up to two litres of hydrogen from digesting a single sheet of paper, making
them one of the planet's most efficient bioreactors.[10] Termites achieve this high degree of efficiency by
exploiting the metabolic capabilities of about 200 different species of microbes that inhabit their hindguts. The
microbial community in the termite gut efficiently manufactures large quantities of hydrogen; the complex
lignocellulose polymers within wood are broken down into simple sugars by fermenting bacteria in the
termite's gut, using enzymes that produce hydrogen as a byproduct. A second wave of bacteria uses the
simple sugars and hydrogen to make the acetate the termite requires for energy. By sequencing the termite's
microbial community, the DOE hopes to get a better understanding of these biochemical pathways. If it can
be determined which enzymes are used to create hydrogen, and which genes produce them, this process
could potentially be scaled up with bioreactors to generate hydrogen from woody biomass, such as poplar, in
commercial quantities.
Skeptics regard this as unlikely to become a carbon-neutral commercial process due to the energy
inputs required to maintain the system. For decades, researchers have sought to house termites on a
commercial scale (like worm farms) to break down woody debris and paper, but funding has been scarce and
the problems of developing a continuous process that does not disrupt the termites' homeostasis have not
been overcome.[11]
[edit] Ground water divining in Ancient India

Varaha Mihira (505 C.E- 587 C.E), the famous astronomer, mathematician and astrologer of India, in
his treatise "Brihat Samhita", also spelled "Vrahat Sanhita", refers to Dakargala (Sanskrit word meaning
'science of underground water exploration'), wherein the role of termite knolls, as an indicator of underground
water has been elaborately explained.[12]
In Verse.S.54.9 of the Samhita, it is stated that sweet ground water would be found near a termite
mound located east of a Jambu tree (botanical names - Eugenia Jambus,Engenia Jambolana), at a specific
distance and a specific depth of 15 ft to the south of the tree.[12]
The above verse has been justified with an explanation:
Without exception the water requirements of the insects are generally very high, and they need
to protect themselves against fatal desiccation by living and working within the climatically
sealed environment of their nest or within earth covered galleries. According to present level of
research, the atmosphere within the nest has to be maintained practically saturation moisture
level ( 99-100 % humidity). It is a matter of common observation that whenever a termite nest or
runway, is damaged, the insects immediately rush to the breach and repairs it with wet soil
brought up from within the nest. From an over-all consideration of the evidence it seems to be
safe to conclude that, while normally the insects use every readily available source of water
close to the ground surface, under condition of severe climatic stress, they can and they
probably do descend to the water table, no matter how deep it may be. Hence, a well-
developed, active, permanent colony of mound-building termites can be taken as an indication
of underground springs in proximity[12].
Two examples mentioned in the referred publication are, a) termiteries seen in the Katanga province
(Congo Kinshasa) right up to the hill slopes where springs emerge, b) in the dry jungle uplands of coastal
zone of Karnataka state (old Mysore state) and c) in the Deccan Plateau area[12].
It is also asserted in the verse Vr.S.54.85 that among a group of termite mounds, a water vein is sure
to be found below the taller of the mounds. Verse 52 mentions that in a desert region, if a group of five
termite mounds are found, and if the middle one is in white colour, then water will be found within a depth of
Fifty five Purushas (in Sanskrit one Purusha is equivalent to 7.5 ft) or 412.5 ft[12].
As a common observation of a combination of different symptoms, termite mounds are said to be
found close to trees, and ancient Hindus exploited this knowledge in the exploration of underground springs.
[12].
[edit] Ecology
A matabele ant (Dorylus) with a captured worker termite (Macrotermitinae) in the Okavango Delta,
Botswana.
Ecologically, termites are important in nutrient recycling, habitat creation, soil formation and quality
and, particularly the winged reproductives, as food for countless predators. The role of termites in hollowing
timbers and thus providing shelter and increased wood surface areas for other creatures is critical for the
survival of a large number of timber-inhabiting species. Larger termite mounds play a role in providing a
habitat for plants and animals, especially on plains in Africa that are seasonally inundated by a rainy season,
providing a retreat above the water for smaller animals and birds, and a growing medium for woody shrubs
with root systems that cannot withstand inundation for several weeks. In addition, scorpions, lizards, snakes,
small mammals, and birds live in abandoned or weathered mounds, and aardvarks dig substantial caves and
burrows in them, which then become homes for larger animals such as hyenas and mongooses.
As detrivores, termites clear away leaf and woody litter and so reduce the severity of the annual bush
fires in African savannas, which are not as destructive as those in Australia and the USA.
Globally, termites are found roughly between 50 degrees North & South, with the greatest biomass in
the tropics and the greatest diversity in tropical forests and Mediterranean shrublands. Termites are also
considered to be a major source of atmospheric methane, one of the prime greenhouse gases. Termites
have been common since at least the Cretaceous period. Termites also eat bone and other parts of
carcasses, and their traces have been found on dinosaur bones from the middle Jurassic in China.[13]
[edit] Plant defences against termites

Many plants have developed effective defences against termites, and in most ecosystems, there is
an observable balance between the growth of plants and the feeding of termites. Defence is typically
achieved by secreting anti-feedant chemicals (such as oils, resins, and lignins) into the woody cell walls. This
reduces the ability of termites to efficiently digest the cellulose. Many of the strongly termite-resistant tree
species have heartwood timber that is extremely dense (such as Eucalyptus camaldulensis) due to accretion
of these resins. Over the years there has been considerable research into these natural defensive chemicals
with scientists seeking to add them to timbers from susceptible trees. A commercial product, "Blockaid", has
been developed in Australia and uses a range of plant extracts to create a paint-on nontoxic termite barrier
for buildings. In 2005, a group of Australian scientists "discovered" (announced) a treatment based on an
extract of a species of Eremophila that repels termites.[14] Tests have shown that termites are strongly
repelled by the toxic material to the extent that they will starve rather than consume cross treated samples.
When kept close to the extract, they become disoriented and eventually die. Scientists hope to use this toxic
compound commercially to prevent termite feeding.
[edit] Taxonomy, evolution and systematics
The famous Giant Northern Termite Mastotermes darwiniensis attests to the close relationship of
termites and cockroaches.
Recent DNA evidence[15][16] has supported the hypothesis, originally based on morphology, that
termites are most closely related to the wood-eating cockroaches (genus Cryptocercus), to which the singular
and very primitive Mastotermes darwiniensis shows some telltale similarities. Most recently, this has led
some authors to propose that termites be reclassified as a single family, Termitidae, within the order
Blattaria, which contains cockroaches [17][18][19]. However, most researchers advocate the less drastic
measure of retaining the termites as Isoptera but as a group subordinate to true roaches, preserving the
internal classification of termites [20].

The oldest unambiguous termite fossils date to the early Cretaceous, although structures from the
late Triassic have been interpreted as fossilized termite nests.[21] Given the diversity of Cretaceous termites,
it is likely that they had their origin at least sometime in the Jurassic. Weesner believes that Mastotermitidae
termites may go back to the Permian[22] and fossil wings have been discovered in the Permian of Kansas
which have a close resemblance to wings of Mastotermes of the Mastotermitidae, which is the most primitive
living termite. It is thought to be the descendant of Cryptocercus genus, the wood roach. This fossil is called
Pycnoblattina. It folded its wings in a convex pattern between segments 1a and 2a. Mastotermes is the only
living insect that does the same,[23]
It has long been accepted that termites are closely related to cockroaches and mantids, and they are
classified in the same superorder (Dictyoptera), but new research has shed light on the details of termite
evolution.[24] There is now strong evidence suggesting that termites are really highly modified, social, wood-
eating cockroaches. A study conducted by scientists has found that endosymbiotic bacteria from termites and
a genus of cockroaches, Cryptocercus, share the strongest phylogenetical similarities out of all other
cockroaches. Both termites and Cryptocercus also share similar morphological and social features—most
cockroaches do not show social characteristics, but Cryptocercus takes care of its young and exhibits other
social behaviour. As mentioned above, the primitive Giant Northern Termite (Mastotermes darwiniensis)
exhibits numerous cockroach-like characteristics that are not shared with other termites.
[edit] Systematics
As of 1996, about 2,800 termite species are recognized, classified in seven families [4]. These are
arranged here in a phylogenetic sequence, from the most basal to the most advanced:
• Mastotermitidae (1 species, Mastotermes darwiniensis)
• Hodotermitidae (3 genera, 19 species)
• Hodotermitinae
• Kalotermitidae (22 genera, 419 species)
• Termopsidae (5 genera, 20 species)
• Termopsinae
• Porotermitinae
• Stolotermitinae
• Rhinotermitidae (14 genera, 343 species)
• Coptotermitinae Holmgren
• Heterotermitinae Froggatt
• Prorhinoterminae Quennedey & Deligne, 1975
• Psammotermitinae Holmgren
• Rhinotermitinae Froggatt
• Stylotermitinae Holmgren, K & N, 1917
• Termitogetoninae Holmgren
• Serritermitidae (1 species, Serritermes serrifer)
• Termitidae (236 genera, 1958 species)
• Apicotermitinae (42 genera, 208 species)
• Foraminitermitinae (2 genera, 9 species)
• Macrotermitinae (13 genera, 362 species)
• Nasutitermitinae (80 genera, 576 species)
• Sphaerotermitinae (1 genera, 1 species)
• Syntermitinae (13 genera, 99 species)
• Termitinae (90 genera, 760 species)
The most current classification of termites is summarized by Engel & Krishna (2004).
[edit] See also

• Coatonachthodes ovambolandicus
• Decompiculture
• International Union for the Study of Social Insects
• Nasutitermes corniger
• Stigmergy
• Xylophagy
[edit] Gallery
Worker termites
Termites with some A winged termite (Macrotermitinae) closing
nasute soldiers. after the first good rains in A Giant a newly exposed shaft
Maun, Botswana. Northern Termite. inside a termite mound to
prevent the entry of
predators.
Termites and other Termite mound in
insects in copal. Tanzania.
[edit] References
• Grimaldi, D. and Engel, M.S. (2005). Evolution of the Insects. Cambridge University Press.
ISBN 0-521-82149-5.
• Engel, M.S. and K. Krishna (2004). "Family-group names for termites (Isoptera)". American
Museum Novitates 3432: 1–9. doi:10.1206/0003-0082(2004)432<0001:FNFTI>2.0.CO;2.
• Earthlife
• Termite terms
• Cretaceous termites
1. ^ Lofjle & Kubiniok, Landform development and bioturbation on the Khorat plateau,
Northeast Thailand, Nat.Hist.Bull.Siam Soc. (56), 1996 [1]
2. ^ Piper, Ross (2007), Extraordinary Animals: An Encyclopedia of Curious and Unusual
Animals, Greenwood Press.
3. ^ C. Bordereau, A. Robert, V. Van Tuyen & A. Peppuy (1997). "Suicidal defensive behavior
by frontal gland dehiscence in Globitermes sulphureus Haviland soldiers (Isoptera)". Insectes
Sociaux 44 (3): 289–297. doi:10.1007/s000400050049.
4. ^ The evolution of fungus-growing termites and their mutualistic fungal symbionts by Duur K.
Aanen, Paul Eggleton, Corinne Rouland-Lefèvre, Tobias Guldberg-Frøslev, Søren Rosendahl &
Jacobus J. Boomsma
5. ^ Fungus-farming insects: Multiple origins and diverse evolutionary histories by Ulrich G.
Mueller & Nicole Gerardo
6. ^ Professor Lobeck, A.K. 1939. Geomorphology: An introduction to the study of landscape.
McGraw-Hill Book Company, New York.
7. ^ "Termite." Encyclopædia Britannica Online Library Edition. Retrieved 19 November 2007.
8. ^ Google Earth, at lat -14.6565° long 25.8337°. The smaller termite mounds are the light
patches; the larger ones are clumps of bushes with lighter patches of bare earth. Retrieved 19
November 2007.
9. ^ JGI - Organization responsible for sequencing the termite.
10.^ "Termite (Order: Isoptera) - Wiki". http://www.animalpicturesarchive.com/view.php?
tid=3&did=28077. Retrieved 2009-05-09.
11.^ Original article on termites as bioreactors
12.^ a b c d e f Pages 58 to 60 of the publication titled "Hydrology in Ancient India",published by
the National Institute of Hydrology, Roorkee, India, as India's contribution to International Hydrology
Programme (IHP), published in September 1990
13.^ 403 Forbidden
14.^ Plant extract stops termites dead
15.^ Lo, N. et al. Evidence for cocladogenesis between diverse dictyopteran lineages and their
intracellular endosymbionts. Molecular Biology and Evolution, 20, 907–913 (2003)
16.^ Ware,J.L. et al. Relationships among the major lineages of Dictyoptera: the effect of
outgroup selection on dictyopteran tree topology. Systematic Entomology, 33, 429–450 (2008)
17.^ Inward, D., G. Beccaloni, and P. Eggleton. 2007. Death of an order: a comprehensive
molecular phylogenetic study confirms that termites are eusocial cockroaches. Biology Letters 3:331-
335.
18.^ "Termites are 'social cockroaches'". BBC News. 13 April 2007.
http://news.bbc.co.uk/1/hi/sci/tech/6553219.stm.
19.^ Eggleton, P. &al. (2007), Biological Letters, June 7, cited in Science News vol. 171, p. 318
20.^ Lo, N. &al. (2007), Biology Letters, 14 August 2007, doi 10.1098/rsbl.2007.0264
21.^ Gay and Calaby 1970 Termites of the Australian region. in; Krishna K Weesner FM eds.
Biology of Termites, Vol. II Academic Press NY p401
22.^ Weesner FM (1960) Evolution biology of termites. Annual Review of Entomology. 5; 153-
170.
23.^ Tilyard RJ (1937) Kansas Permian insects.. Part XX the cockroaches, or order BlattariaI, II
Am. Journal of Science 34; 169-202, 249-276.
24.^ Evidence for Cocladogenesis Between Diverse Dictyopteran Lineages and Their
Intracellular Endosymbionts

Abe T., Bignell D.E., Higashi M. (eds.) (2000). Termites: evolution, sociality, symbioses, ecology,
ecolab. Kluwer academic publishers. ISBN 0792363612.

Wikispecies has information related to: Isoptera
Wikimedia Commons has media related to: Isoptera
• University of Nebraska page on Termites

• Termite Hub from National Pest Management Association - includes FAQs, types of termites,
etc.
• A summary of termite control methods
• University of California advice on Drywood Termites
• Termite Pest Control Information - USA National Pesticide Information Center
• Catalogue of the termites of the World
• Pictures of termites
• Transitional Species in Insect Evolution
• Cretaceous Termites and Soil Phosphorus
• Beneficial Uses of Termites
• Texas A&M University Department of Entomology - Center for Urban & Structural
Entomology
• The Soul of the White Ant - Eugène N. Marais
• Urban Entomology Program University of Toronto
• List of Termite Types
• Isoptera: termites (CSIRO Australia Entomology) .
• 'Termite guts can save the planet', says Nobel laureate
On the UF / IFAS Featured Creatures Web site
• Amitermes floridensis , Florida darkwinged subterranean termite
• Coptotermes formosanus , Formosan subterranean termite
• Coptotermes gestroi, Asian subterranean termite
• Cryptotermes brevis, West Indian drywood termite
• Heterotermes sp., West Indian subterranean termite
• Cryptotermes cavifrons, a drywood termite
• Incisitermes minor, western drywood termite
• Neotermes spp., Florida dampwood termites
• Prorhinotermes simplex, Cuban subterranean termite
• Reticulitermes spp., native U.S.A. subterranean termites
Retrieved from "http://en.wikipedia.org/wiki/Termite"
Categories: Termites | Insects | Household pest insects | Building defects | Invasive animal species
W000
Alfred Russel Wallace


"Alfred Wallace" redirects here. For the painter, see Alfred Wallis.
Alfred Russel Wallace
8 January 1823(1823-01-08)
Born
Usk, Monmouthshire, Wales, United Kingdom
7 November 1913(1913-11-07) (aged 90)

Died
Broadstone, Dorset, England
Citizenship British
Fields exploration, biology, biogeography, social reform, botany
Known for his co-discovery of natural selection and his work on biogeography
Royal Society's Royal Medal (1866) and Copley Medal (1908), Order of
Notable awards
Merit (1908)
Alfred Russel Wallace, OM, FRS (8 January 1823 – 7 November 1913) was a British naturalist,
explorer, geographer, anthropologist and biologist. He is best known for independently proposing a theory of
evolution due to natural selection that prompted Charles Darwin to publish his own theory.
Wallace did extensive fieldwork, first in the Amazon River basin and then in the Malay Archipelago,
where he identified the Wallace Line that divides the Indonesian archipelago into two distinct parts, one in
which animals closely related to those of Australia are common, and one in which the species are largely of
Asian origin. He was considered the 19th century's leading expert on the geographical distribution of animal
species and is sometimes called the "father of biogeography".[1] Wallace was one of the leading evolutionary
thinkers of the 19th century and made a number of other contributions to the development of evolutionary
theory besides being co-discoverer of natural selection. These included the concept of warning colouration in
animals, and the Wallace effect, a hypothesis on how natural selection could contribute to speciation by
encouraging the development of barriers against hybridization.
Wallace was strongly attracted to unconventional ideas. His advocacy of Spiritualism and his belief in
a non-material origin for the higher mental faculties of humans strained his relationship with the scientific
establishment, especially with other early proponents of evolution. In addition to his scientific work, he was a
social activist who was critical of what he considered to be an unjust social and economic system in 19th-
century Britain. His interest in biogeography resulted in his being one of the first prominent scientists to raise
concerns over the environmental impact of human activity. Wallace was a prolific author who wrote on both
scientific and social issues; his account of his adventures and observations during his explorations in
Indonesia and Malaysia, The Malay Archipelago, was one of the most popular and influential journals of
scientific exploration published during the 19th century.
Contents
[hide]
• 1 Biography
• 1.1 Early life
• 1.2 Exploration and study of the natural world
• 1.3 Return to the UK, marriage and children
• 1.4 Financial struggles
• 1.5 Social activism
• 1.6 Death
• 2 Theory of evolution
• 2.1 Early evolutionary thinking
• 2.2 Natural selection and Darwin
• 2.2.1 Differences between Darwin's and
Wallace's ideas on natural selection
• 2.2.2 Warning colouration and sexual
selection
• 2.2.3 Wallace effect
• 2.3 Application of theory to man, and role of
teleology in evolution
• 2.4 Assessment of Wallace's role in history of
evolutionary theory
• 3 Spiritualism
[edit] Biography
[edit] Early life
A photograph from Wallace's autobiography shows the building Wallace and his brother John
designed and built for the Mechanics' Institute of Neath.
Wallace was born in the Welsh village of Llanbadoc, near Usk, Monmouthshire.[2] He was the
seventh of eight children of Thomas Vere Wallace and Mary Anne Greenell. Thomas Wallace was of Scottish
ancestry. His family, like many Scottish Wallaces, claimed a connection to William Wallace, a Scottish leader
during the Wars of Scottish Independence in the 13th century.[3] Thomas Wallace received a law degree, but
never actually practiced law. He inherited some income-generating property, but bad investments and failed
business ventures resulted in a steady deterioration of the family's financial position. His mother was from a
respectable middle-class English family from Hertford, north of London.[3] When Wallace was five years old,
his family moved to Hertford. There he attended Hertford Grammar School until financial difficulties forced his
family to withdraw him in 1836.[4]
Wallace then moved to London to live and work with his older brother John, a 19-year-old apprentice
builder. (In 1979, a plaque was placed at 44 St. Peter's Road in Croydon commemorating the fact that he
lived there at one point during this period.) This was a stopgap measure until William, his oldest brother, was
ready to take him on as an apprentice surveyor. While there, he attended lectures and read books at the
London Mechanics Institute. Here he was exposed to the radical political ideas of the Welsh social reformer
Robert Owen and Thomas Paine. He left London in 1837 to live with William and work as his apprentice for
six years. At the end of 1839, they moved to Kington, Hereford, near the Welsh border before eventually
settling at Neath in Glamorgan in Wales. Between 1840 and 1843, Wallace did surveying work in the
countryside of the west of England and Wales.[5][6] By the end of 1843, William's business had declined due
to difficult economic conditions. Wallace left in January, aged 20. One result of Wallace's early travels has
been a modern controversy about his nationality. Since Wallace was born in Gwent (then called
Monmouthshire), Wales, some sources have considered him to be Welsh.[7] However some historians have
questioned this because neither of his parents was Welsh, his family only briefly lived in Monmouthshire, the
Welsh people Wallace knew in his childhood considered him to be English, and because Wallace himself
consistently referred to himself as English rather than Welsh (even when writing about his time in Wales).
One Wallace scholar has stated that because of these facts the most reasonable interpretation was that he
was an Englishman born in Wales.[8]
After a brief period of unemployment, he was hired as a master at the Collegiate School in Leicester
to teach drawing, mapmaking, and surveying. Wallace spent a lot of time at the Leicester library where he
read An Essay on the Principle of Population by Thomas Malthus and where one evening he met the
entomologist Henry Bates. Bates was only 19 years old, but had already published a paper on beetles in the
journal Zoologist. He befriended Wallace and started him collecting insects.[9][10] William died in March
1845, and Wallace left his teaching position to assume control of his brother's firm in Neath, but he and his
brother John were unable to make the business work. After a couple of months, Wallace found work as a civil
engineer for a nearby firm that was working on a survey for a proposed railway in the Vale of Neath.
Wallace's work on the survey involved spending a lot of time outdoors in the countryside, allowing him to
indulge his new passion for collecting insects. Wallace was able to persuade his brother John to join him in
starting another architecture and civil engineering firm, which carried out a number of projects, including the
design of a building for the Mechanics' Institute of Neath. William Jevons, the founder of that institute, was
impressed by Wallace and persuaded him to give lectures there on science and engineering. In the autumn
of 1846, he, aged 23, and John were able to purchase a cottage near Neath, where they lived with their
mother and sister Fanny (his father had died in 1843).[11][12] During this period, he read avidly, exchanging
letters with Bates about Robert Chambers' anonymously published evolutionary treatise Vestiges of the
Natural History of Creation, Charles Darwin's Journal, and Charles Lyell's Principles of Geology.[13][14]
[edit] Exploration and study of the natural world
A map from The Malay Archipelago shows the physical geography of the archipelago and Wallace's
travels around the area. The thin black lines indicate where Wallace travelled, and the red lines indicate
chains of volcanoes.
Inspired by the chronicles of earlier traveling naturalists, including Alexander von Humboldt, Charles
Darwin and William Henry Edwards, Wallace decided that he too wanted to travel abroad as a naturalist.[15]
In 1848, Wallace and Henry Bates left for Brazil aboard the Mischief. Their intention was to collect insects
and other animal specimens in the Amazon rainforest and sell them to collectors back in the United Kingdom.
They also hoped to gather evidence of the transmutation of species. Wallace and Bates spent most of their
first year collecting near Belém do Pará, then explored inland separately, occasionally meeting to discuss
their findings. In 1849, they were briefly joined by another young explorer, botanist Richard Spruce, along
with Wallace's younger brother Herbert. Herbert left soon thereafter (dying two years later from yellow fever),
but Spruce, like Bates, would spend over ten years collecting in South America.[16]
Wallace continued charting the Rio Negro for four years, collecting specimens and making notes on
the peoples and languages he encountered as well as the geography, flora, and fauna.[17] On 12 July 1852,
Wallace embarked for the UK on the brig Helen. After twenty-eight days at sea, the ship's cargo caught fire
and the crew was forced to abandon ship. All of the specimens Wallace had on the ship, the vast majority of
what he had collected during his entire trip, were lost. He could only save part of his diary and a few
sketches. Wallace and the crew spent ten days in an open boat before being picked up by the brig Jordeson,
which was sailing from Cuba to London. The Jordenson's provisions were strained by the unexpected
passengers, but after a difficult passage on very short rations the ship finally reached its destination on 1
October 1852.[18][19]
After his return to the UK, Wallace spent eighteen months in London living on the insurance payment
for his lost collection and selling a few specimens that had been shipped back to Britain prior to his starting
his exploration of the Rio Negro. During this period, despite having lost almost all of the notes from his South
American expedition, he wrote six academic papers (which included "On the Monkeys of the Amazon") and
two books; Palm Trees of the Amazon and Their Uses and Travels on the Amazon.[20] He also made
connections with a number of other British naturalists—most significantly, Darwin.[19][21][22]
An illustration from The Malay Archipelago depicts the flying frog Wallace discovered.
From 1854 to 1862, age 31 to 39, Wallace travelled through the Malay Archipelago or East Indies
(now Malaysia and Indonesia), to collect specimens for sale and to study nature. His observations of the
marked zoological differences across a narrow strait in the archipelago led to his proposing the
zoogeographical boundary now known as the Wallace line. Wallace collected more than 125,000 specimens
in the Malay Archipelago (more than 80,000 beetles alone). More than a thousand of them represented
species new to science.[23] One of his better-known species descriptions during this trip is that of the gliding
tree frog Rhacophorus nigropalmatus, known as Wallace's flying frog. While he was exploring the
archipelago, he refined his thoughts about evolution and had his famous insight on natural selection. In 1858
he sent an article outlining his theory to Darwin; it was published, along with a description of Darwin's own
theory, in the same year.
Accounts of his studies and adventures there were eventually published in 1869 as The Malay
Archipelago. The Malay Archipelago became one of the most popular journals of scientific exploration of the
19th century, kept continuously in print by its original publisher (Macmillan) into the second decade of the
20th century. It was praised by scientists such as Darwin (to whom the book was dedicated), and Charles
Lyell, and by non-scientists such as the novelist Joseph Conrad, who called it his "favorite bedside
companion" and used it as source of information for several of his novels, especially Lord Jim.[24]
[edit] Return to the UK, marriage and children
A photograph of A.R. Wallace taken in Singapore in 1862
In 1862, Wallace returned to the UK, where he moved in with his sister Fanny Sims and her husband
Thomas. While recovering from his travels, Wallace organised his collections and gave numerous lectures
about his adventures and discoveries to scientific societies such as the Zoological Society of London. Later
that year, he visited Darwin at Down House, and became friendly with both Charles Lyell and Herbert
Spencer.[25] During the 1860s, Wallace wrote papers and gave lectures defending natural selection. He also
corresponded with Darwin about a variety of topics, including sexual selection, warning colouration, and the
possible effect of natural selection on hybridisation and the divergence of species.[26] In 1865, he began
investigating spiritualism.[27]
After a year of courtship, Wallace became engaged in 1864 to a young woman whom, in his
autobiography, he would only identify as Miss L. However, to Wallace's great dismay, she broke off the
engagement.[28] In 1866, Wallace married Annie Mitten. Wallace had been introduced to Mitten through the
botanist Richard Spruce, who had befriended Wallace in Brazil and who was also a good friend of Annie
Mitten's father, William Mitten, an expert on mosses. In 1872, Wallace built the Dell, a house of concrete, on
land he leased in Grays in Essex, where he lived until 1876. The Wallaces had three children: Herbert (1867–
1874) who died in childhood, Violet (1869–1945), and William (1871–1951).[29]
[edit] Financial struggles

In the late 1860s and 1870s, Wallace was very concerned about the financial security of his family.
While he was in the Malay Archipelago, the sale of specimens had brought in a considerable amount of
money, which had been carefully invested by the agent who sold the specimens for Wallace. However, on his
return to the UK, Wallace made a series of bad investments in railways and mines that squandered most of
the money, and he found himself badly in need of the proceeds from the publication of The Malay
Archipelago.[30] Despite assistance from his friends, he was never able to secure a permanent salaried
position such as curatorship of a museum. In order to remain financially solvent, Wallace worked grading
government examinations, wrote 25 papers for publication between 1872 and 1876 for various modest sums,
and was paid by Lyell and Darwin to help edit some of their own works.[31] In 1876, Wallace needed a £500
advance from the publisher of The Geographical Distribution of Animals to avoid having to sell some of his
personal property.[32] Darwin was very aware of Wallace's financial difficulties and lobbied long and hard to
get Wallace awarded a government pension for his lifetime contributions to science. When the £200 annual
pension was awarded in 1881, it helped to stabilise Wallace's financial position by supplementing the income
from his writings.[33]
[edit] Social activism

John Stuart Mill was impressed by remarks criticizing English society that Wallace had included in
The Malay Archipelago. Mill asked him to join the general committee of his Land Tenure Reform Association,
but the association dissolved after Mill's death in 1873. Wallace wrote only a handful of articles on political
and social issues between 1873 and 1879, when, aged 56, he entered the debates over trade policy and land
reform in earnest. He believed that rural land should be owned by the state and leased to people who would
make whatever use of it that would benefit the largest number of people, thus breaking the often-abused
power of wealthy landowners in English society. In 1881, Wallace was elected as the first president of the
newly formed Land Nationalisation Society. In the next year, he published a book, Land Nationalisation; Its
Necessity and Its Aims, on the subject. He criticised the UK's free trade policies for the negative impact they
had on working class people.[22][34] In 1889, Wallace read Looking Backward by Edward Bellamy and
declared himself a socialist.[35] These ideas led him to oppose both social Darwinism and eugenics, ideas
supported by other prominent 19th-century evolutionary thinkers, on the grounds that contemporary society
was too corrupt and unjust to allow any reasonable determination of who was fit or unfit.[36] In 1898, Wallace
wrote a paper advocating a pure paper money system, not backed by silver or gold, which impressed the
economist Irving Fisher so much that he dedicated his 1920 book Stabilizing the Dollar to Wallace.[37]
Wallace wrote extensively on other social topics including his support for women's suffrage, and the dangers
and wastefulness of militarism.[38][39] Wallace continued his social activism for the rest of his life, publishing
the book The Revolt of Democracy just weeks before his death.[40]
Wallace continued his scientific work in parallel with his social commentary. In 1880, he published
Island Life as a sequel to The Geographic Distribution of Animals. In November 1886, Wallace began a ten-
month trip to the United States to give a series of popular lectures. Most of the lectures were on Darwinism
(evolution and natural selection), but he also gave speeches on biogeography, spiritualism, and socio-
economic reform. During the trip, he was reunited with his brother John who had emigrated to California
years before. He also spent a week in Colorado, with the American botanist Alice Eastwood as his guide,
exploring the flora of the Rocky Mountains and gathering evidence that would lead him to a theory on how
glaciation might explain certain commonalities between the mountain flora of Europe, Asia and North
America, which he published in 1891 in the paper "English and American Flowers". He met many other
prominent American naturalists and viewed their collections. His 1889 book Darwinism used information he
collected on his American trip, and information he had compiled for the lectures.[41][42]
[edit] Death
Wallace's grave in Broadstone Cemetery, Broadstone, Dorset, which was restored by the A. R.
Wallace Memorial Fund in 2000. It features a 7-foot (2.1 m) tall fossil tree trunk from Portland mounted on a
block of Purbeck limestone.
On 7 November 1913, Wallace died at home in the country house he called Old Orchard, which he
had built a decade earlier.[43] He was 90 years old. His death was widely reported in the press. The New
York Times called him "the last of the giants belonging to that wonderful group of intellectuals that included,
among others, Darwin, Huxley, Spencer, Lyell, and Owen, whose daring investigations revolutionised and
evolutionised the thought of the century." Another commentator in the same edition said “No apology need be
made for the few literary or scientific follies of the author of that great book on the 'Malay Archipelago'.”[44]
Some of Wallace's friends suggested that he be buried in Westminster Abbey, but his wife followed his
wishes and had him buried in the small cemetery at Broadstone, Dorset.[43] Several prominent British
scientists formed a committee to have a medallion of Wallace placed in Westminster near where Darwin had
been buried. The medallion was unveiled on 1 November 1915.
[edit] Theory of evolution

[edit] Early evolutionary thinking
Unlike Darwin, Wallace began his career as a travelling naturalist already believing in the
transmutation of species. The concept had been advocated by Jean-Baptiste Lamarck, Geoffroy Saint-
Hilaire, Erasmus Darwin, and Robert Grant, among others. It was widely discussed, but not generally
accepted by leading naturalists, and was considered to have radical, even revolutionary connotations.[45][46]
Prominent anatomists and geologists such as Georges Cuvier, Richard Owen, Adam Sedgwick, and Charles
Lyell attacked it vigorously.[47][48] It has been suggested that Wallace accepted the idea of the
transmutation of species in part because he was always inclined to favour radical ideas in politics, religion
and science,[45] and because he was unusually open to marginal, even fringe, ideas in science.[49]
He was also profoundly influenced by Robert Chambers' work Vestiges of the Natural History of
Creation, a highly controversial work of popular science published anonymously in 1844 that advocated an
evolutionary origin for the solar system, the earth, and living things.[50] Wallace wrote to Henry Bates in
1845:
I have a rather more favourable opinion of the ‘Vestiges’ than you appear to have. I do not
consider it a hasty generalization, but rather as an ingenious hypothesis strongly supported by
some striking facts and analogies, but which remains to be proven by more facts and the
additional light which more research may throw upon the problem. It furnishes a subject for
every student of nature to attend to; every fact he observes will make either for or against it, and
it thus serves both as an incitement to the collection of facts, and an object to which they can be
applied when collected.[49]
Wallace deliberately planned some of his field work to test the hypothesis that under an evolutionary
scenario closely related species should inhabit neighbouring territories.[45] During his work in the Amazon
basin, he came to realise that geographical barriers—such as the Amazon and its major tributaries—often
separated the ranges of closely allied species, and he included these observations in his 1853 paper "On the
Monkeys of the Amazon".[51] Near the end of the paper he asks the question "Are very closely allied species
ever separated by a wide interval of country?"
In February 1855, while working in the state of Sarawak on the island of Borneo, Wallace wrote "On
the Law Which has Regulated the Introduction of Species", a paper which was published in the Annals and
Magazine of Natural History in September 1855. In this paper, he gathered and enumerated general
observations regarding the geographic and geologic distribution of species (biogeography). His conclusion
that "Every species has come into existence coincident both in space and time with a closely allied species"
has come to be known as the "Sarawak Law". Wallace thus answered the question he had posed in his
earlier paper on the monkeys of the Amazon river basin. Although it contained no mention of any possible
mechanisms for evolution, this paper foreshadowed the momentous paper he would write three years later.
[52]
The paper shook Charles Lyell's belief that species were immutable. Although his friend Charles
Darwin had written to him in 1842 expressing support for transmutation, Lyell had continued to be strongly
opposed to the idea. Around the start of 1856, he told Darwin about Wallace's paper, as did Edward Blyth
who thought it "Good! Upon the whole!... Wallace has, I think put the matter well; and according to his theory
the various domestic races of animals have been fairly developed into species." Despite this hint, Darwin
mistook Wallace's conclusion for the progressive creationism of the time and wrote that it was "nothing very
new ... Uses my simile of tree [but] it seems all creation with him." Lyell was more impressed, and opened a
notebook on species, in which he grappled with the consequences, particularly for human ancestry. Darwin
had already shown his theory to their mutual friend Joseph Hooker and now, for the first time, he spelt out the
full details of natural selection to Lyell. Although Lyell could not agree, he urged Darwin to publish to
establish priority. Darwin demurred at first, then began writing up a species sketch of his continuing work in
May 1856.[53]
[edit] Natural selection and Darwin

See also: Publication of Darwin's theory
By February 1858, Wallace had been convinced by his biogeographical research in the Malay
Archipelago of the reality of evolution. As he later wrote in his autobiography:
The problem then was not only how and why do species change, but how and why do they
change into new and well defined species, distinguished from each other in so many ways; why
and how they become so exactly adapted to distinct modes of life; and why do all the
intermediate grades die out (as geology shows they have died out) and leave only clearly
defined and well marked species, genera, and higher groups of animals?[54]
According to his autobiography, it was while he was in bed with a fever that Wallace thought about
Thomas Malthus's idea of positive checks on human population growth and came up with the idea of natural
selection.[55] Wallace said in his autobiography that he was on the island of Ternate at the time; but
historians have questioned this, saying that on the basis of the collection registries he wrote at the time, he
was more likely to have been on the island of Gilolo.[56] Wallace describes it as follows:
It then occurred to me that these causes or their equivalents are continually acting in the case of
animals also; and as animals usually breed much more quickly than does mankind, the
destruction every year from these causes must be enormous in order to keep down the numbers
of each species, since evidently they do not increase regularly from year to year, as otherwise
the world would long ago have been crowded with those that breed most quickly. Vaguely
thinking over the enormous and constant destruction which this implied, it occurred to me to ask
the question, why do some die and some live? And the answer was clearly, on the whole the
best fitted live ... and considering the amount of individual variation that my experience as a
collector had shown me to exist, then it followed that all the changes necessary for the
adaptation of the species to the changing conditions would be brought about ... In this way every
part of an animals organization could be modified exactly as required, and in the very process of
this modification the unmodified would die out, and thus the definite characters and the clear
isolation of each new species would be explained.[57]
The Darwin–Wallace Medal was issued by the Linnean society on the 50th anniversary of the reading
of Darwin and Wallace's papers on natural selection.
Wallace had once briefly met Darwin, and was one of the correspondents whose observations
Darwin used to support his own theories. Although Wallace's first letters to Darwin have been lost, Wallace
carefully kept the letters he received.[58] In the first letter, dated 1 May 1857, Darwin commented that
Wallace's letter of 10 October which he had recently received, as well as Wallace's paper "On the Law which
has regulated the Introduction of New Species" of 1855, showed that they were both thinking alike and to
some extent reaching similar conclusions, and said that he was preparing his own work for publication in
about two years time.[59] The second letter, dated 22 December 1857, said how glad he was that Wallace
was theorising about distribution, adding that "without speculation there is no good and original observation"
while commenting that "I believe I go much further than you".[60] Wallace trusted Darwin's opinion on the
matter and sent him his February 1858 essay, "On the Tendency of Varieties to Depart Indefinitely From the
Original Type", with the request that Darwin would review it and pass it on to Charles Lyell if he thought it
worthwhile.[61] On 18 June 1858, Darwin received the manuscript from Wallace. While Wallace's essay did
not employ Darwin's term "natural selection", it did outline the mechanics of an evolutionary divergence of
species from similar ones due to environmental pressures. In this sense, it was very similar to the theory that
Darwin had worked on for twenty years, but had yet to publish. Darwin sent the manuscript to Charles Lyell
with a letter saying "he could not have made a better short abstract! Even his terms now stand as heads of
my chapters ... he does not say he wishes me to publish, but I shall, of course, at once write and offer to send
to any journal."[62] Distraught about the illness of his baby son, Darwin put the problem to Charles Lyell and
Joseph Hooker, who decided to publish the essay in a joint presentation together with unpublished writings
which highlighted Darwin's priority. Wallace had not asked for publication of his essay, but publishing the
contents of letters from far-off naturalists was a common event in those times. Wallace's essay was
presented to the Linnean Society of London on 1 July 1858, along with excerpts from an essay which Darwin
had disclosed privately to Hooker in 1847 and a letter Darwin had written to Asa Gray in 1857.[63]
Communication with Wallace in far-off Malay was impossible without months of delay, so he was not
part of this rapid publication. Wallace accepted the arrangement after the fact, happy that he had been
included at all, and never expressed public or private bitterness. Darwin's social and scientific status was far
greater than Wallace's, and it was unlikely that, without Darwin, Wallace's views on evolution would have
been taken seriously. Lyell and Hooker's arrangement relegated Wallace to the position of co-discoverer, and
he was not the social equal of Darwin or the other prominent British natural scientists. However, the joint
reading of their papers on natural selection associated Wallace with the more famous Darwin. This,
combined with Darwin's (as well as Hooker's and Lyell's) advocacy on his behalf, would give Wallace greater
access to the highest levels of the scientific community.[64] The reaction to the reading was muted, with the
president of the Linnean remarking in May 1859 that the year had not been marked by any striking
discoveries;[65] but, with Darwin's publication of On the Origin of Species later in 1859, its significance
became apparent. When Wallace returned to the UK, he met Darwin. Although some of Wallace's
iconoclastic opinions in the ensuing years would test Darwin's patience, they remained on friendly terms for
the rest of Darwin's life. Over the years, a few people have questioned this version of events. In the early
1980s, two books, one written by Arnold Brackman and another by John Langdon Brooks, even suggested
that not only had there been a conspiracy to rob Wallace of his proper credit, but that Darwin had actually
stolen a key idea from Wallace to finish his own theory. These claims have been examined in detail by a
number of scholars who have not found them to be convincing.[66][67][68]
After the publication of Darwin’s On the Origin of Species, Wallace became one of its staunchest
defenders. In one incident in 1863 that particularly pleased Darwin, Wallace published the short paper
"Remarks on the Rev. S. Haughton's Paper on the Bee's Cell, And on the Origin of Species" in order to
utterly demolish a paper by a professor of geology at the University of Dublin that had sharply criticised
Darwin’s comments in the Origin on how hexagonal honey bee cells could have evolved through natural
selection.[69] Another notable defence of the Origin was "Creation by Law", a review Wallace wrote in 1867
for The Quarterly Journal of Science of the book The Reign of Law, which had been written by the Duke of
Argyll as a refutation of natural selection.[70] After an 1870 meeting of the British Association, Wallace wrote
to Darwin complaining that there were "no opponents left who know anything of natural history, so that there
are none of the good discussions we used to have."[71]
[edit] Differences between Darwin's and Wallace's ideas on natural selection

Historians of science have noted that, while Darwin considered the ideas in Wallace's paper to be
essentially the same as his own, there were differences.[72] Darwin emphasised competition between
individuals of the same species to survive and reproduce, whereas Wallace emphasised environmental
pressures on varieties and species forcing them to become adapted to their local environment.[73][74]
Others have noted that another difference was that Wallace appeared to have envisioned natural
selection as a kind of feedback mechanism keeping species and varieties adapted to their environment.[75]
They point to a largely overlooked passage of Wallace's famous 1858 paper:
The action of this principle is exactly like that of the centrifugal governor of the steam engine,
which checks and corrects any irregularities almost before they become evident; and in like
manner no unbalanced deficiency in the animal kingdom can ever reach any conspicuous
magnitude, because it would make itself felt at the very first step, by rendering existence difficult
and extinction almost sure soon to follow.[61]
The cybernetician and anthropologist Gregory Bateson would observe in the 1970s that, though
writing it only as an example, Wallace had "probably said the most powerful thing that’d been said in the 19 th
Century".[76] Bateson revisited the topic in his 1979 book Mind and Nature: A Necessary Unity, and other
scholars have continued to explore the connection between natural selection and systems theory.[75]
[edit] Warning colouration and sexual selection
In 1867, Darwin wrote to Wallace about a problem he was having understanding how some
caterpillars could have evolved conspicuous colour schemes. Darwin had come to believe that sexual
selection, an agency to which Wallace did not attribute the same importance as Darwin did, explained many
conspicuous animal colour schemes. However, Darwin realised that this could not apply to caterpillars.
Wallace responded that he and Henry Bates had observed that many of the most spectacular butterflies had
a peculiar odour and taste, and that he had been told by John Jenner Weir that birds would not eat a certain
kind of common white moth because they found it unpalatable. "Now, as the white moth is as conspicuous at
dusk as a coloured caterpillar in the daylight", Wallace wrote back to Darwin that it seemed likely that the
conspicuous colour scheme served as a warning to predators and thus could have evolved through natural
selection. Darwin was impressed by the idea. At a subsequent meeting of the Entomological Society,
Wallace asked for any evidence anyone might have on the topic. In 1869, Weir published data from
experiments and observations involving brightly coloured caterpillars that supported Wallace’s idea. Warning
colouration was one of a number of contributions Wallace made in the area of the evolution of animal
colouration in general and the concept of protective colouration in particular.[77] It was also part of a life-long
disagreement Wallace had with Darwin over the importance of sexual selection. In his 1878 book Tropical
Nature and Other Essays, he wrote extensively on the colouration of animals and plants and proposed
alternative explanations for a number of cases Darwin had attributed to sexual selection.[78] He revisited the
topic at length in his 1889 book Darwinism.
[edit] Wallace effect

In 1889, Wallace wrote the book Darwinism, which explained and defended natural selection. In it, he
proposed the hypothesis that natural selection could drive the reproductive isolation of two varieties by
encouraging the development of barriers against hybridisation. Thus it might contribute to the development of
new species. He suggested the following scenario. When two populations of a species had diverged beyond
a certain point, each adapted to particular conditions, hybrid offspring would be less well-adapted than either
parent form and, at that point, natural selection will tend to eliminate the hybrids. Furthermore, under such
conditions, natural selection would favour the development of barriers to hybridisation, as individuals that
avoided hybrid matings would tend to have more fit offspring, and thus contribute to the reproductive isolation
of the two incipient species. This idea came to be known as the Wallace effect.[79] Wallace had suggested to
Darwin that natural selection could play a role in preventing hybridization in private correspondence as early
as 1868, but had not worked it out to this level of detail.[80] It continues to be a topic of research in
evolutionary biology today, with both computer simulation and empirical results supporting its validity.[81]
[edit] Application of theory to man, and role of teleology in evolution
An illustration from the chapter on the application of natural selection to man in Wallace's 1889 book
Darwinism shows a chimpanzee.
In 1864, Wallace published a paper, "The Origin of Human Races and the Antiquity of Man Deduced
from the Theory of 'Natural Selection'", applying the theory to humankind. Darwin had not yet publicly
addressed the subject, although Thomas Huxley had in Evidence as to Man's Place in Nature. He explained
the apparent stability of the human stock by pointing to the vast gap in cranial capacities between humans
and the great apes. Unlike some other Darwinists, including Darwin himself, he did not "regard modern
primitives as almost filling the gap between man and ape".[82] He saw the evolution of man in two stages:
achieving a bipedal posture freeing the hands to carry out the dictates of the brain, and the "recognition of the
human brain as a totally new factor in the history of life. Wallace was apparently the first evolutionist to
recognize clearly that...with the emergence of that bodily specialization which constitutes the human brain,
bodily specialization itself might be said to be outmoded."[82] For this paper he won Darwin's praise.
Shortly afterwards, Wallace became a spiritualist. At about the same time, he began to maintain that
natural selection cannot account for mathematical, artistic, or musical genius, as well as metaphysical
musings, and wit and humour. He eventually said that something in "the unseen universe of Spirit" had
interceded at least three times in history. The first was the creation of life from inorganic matter. The second
was the introduction of consciousness in the higher animals. And the third was the generation of the higher
mental faculties in mankind. He also believed that the raison d'être of the universe was the development of
the human spirit.[83] These views greatly disturbed Darwin, who argued that spiritual appeals were not
necessary and that sexual selection could easily explain apparently non-adaptive mental phenomena. While
some historians have concluded that Wallace's belief that natural selection was insufficient to explain the
development of consciousness and the human mind was directly caused by his adoption of spiritualism, other
Wallace scholars have disagreed, and some maintain that Wallace never believed natural selection applied
to those areas.[84][85] Reaction to Wallace's ideas on this topic among leading naturalists at the time varied.
Charles Lyell endorsed Wallace's views on human evolution rather than Darwin's.[86][87] However, many,
including Huxley, Hooker, and Darwin himself, were critical of Wallace.[88] As one historian of science has
pointed out, Wallace's views in this area were at odds with two major tenets of the emerging Darwinian
philosophy, which were that evolution was not teleological and that it was not anthropocentric.[89]
[edit] Assessment of Wallace's role in history of evolutionary theory
In many accounts of the of the development of evolutionary theory, Wallace is mentioned only in
passing as simply being the stimulus to the publication of Darwin's own theory.[90] In reality, Wallace
developed his own distinct evolutionary views which diverged from Darwin's, and was considered by many
(especially Darwin) to be a leading thinker on evolution in his day, whose ideas could not be ignored. One
historian of science has pointed out that, through both private correspondence and published works, Darwin
and Wallace exchanged knowledge and stimulated each other's ideas and theories over an extended period.
[91] Wallace is the most-cited naturalist in Darwin's Descent of Man, often in strong disagreement.[92]
Wallace remained an ardent defender of natural selection for the rest of his life. By the 1880s, evolution was
widely accepted in scientific circles, but Wallace and August Weismann were nearly alone among prominent
biologists in believing that natural selection was the major driving force behind it.[93][94] In 1889, Wallace
published the book Darwinism as a response to the scientific critics of natural selection.[95] Of all Wallace's
books, it is cited by scholarly publications the most.[96]
[edit] Spiritualism
In a letter to his brother-in-law in 1861, Wallace wrote:
... I remain an utter disbeliever in almost all that you consider the most sacred truths. I will pass
over as utterly contemptible the oft-repeated accusation that sceptics shut out evidence because
they will not be governed by the morality of Christianity ... I am thankful I can see much to
admire in all religions. To the mass of mankind religion of some kind is a necessity. But whether
there be a God and whatever be His nature; whether we have an immortal soul or not, or
whatever may be our state after death, I can have no fear of having to suffer for the study of
nature and the search for truth, or believe that those will be better off in a future state who have
lived in the belief of doctrines inculcated from childhood, and which are to them rather a matter
of blind faith than intelligent conviction.[97]
Wallace was an enthusiast of phrenology.[98] Early in his career, he experimented with hypnosis,
then known as mesmerism. He used some of his students in Leicester as subjects, with considerable
success.[99] When he began his experiments with mesmerism, the topic was very controversial and early
experimenters, such as John Elliotson, had been harshly criticised by the medical and scientific
establishment.[100] Wallace drew a connection between his experiences with mesmerism and his later
investigations into spiritualism. In 1893, he wrote:
I thus learnt my first great lesson in the inquiry into these obscure fields of knowledge, never to
accept the disbelief of great men or their accusations of imposture or of imbecility, as of any
weight when opposed to the repeated observation of facts by other men, admittedly sane and
honest. The whole history of science shows us that whenever the educated and scientific men of
any age have denied the facts of other investigators on a priori grounds of absurdity or
impossibility, the deniers have always been wrong.[101]
Wallace began investigating spiritualism in the summer of 1865, possibly at the urging of his older
sister Fanny Sims, who had been involved with it for some time.[102] After reviewing the literature on the
topic and attempting to test the phenomena he witnessed at séances, he came to accept that the belief was
connected to a natural reality. For the rest of his life, he remained convinced that at least some séance
phenomena were genuine, no matter how many accusations of fraud sceptics made or how much evidence
of trickery was produced. Historians and biographers have disagreed about which factors most influenced his
adoption of spiritualism. It has been suggested by one biographer that the emotional shock he had received a
few months earlier, when his first fiancée broke their engagement, contributed to his receptiveness to
spiritualism.[103] Other scholars have preferred to emphasise instead Wallace's desire to find rational and
scientific explanations for all phenomena, both material and non-material, of the natural world and of human
society.[100][104]
Spiritualism appealed to many educated Victorians who no longer found traditional religious doctrine,
such as that of the Church of England, acceptable yet were unsatisfied with the completely materialistic and
mechanical view of the world that was increasingly emerging from 19th-century science.[105] However,
several scholars who have researched Wallace's views in depth have emphasised that, for him, spiritualism
was a matter of science and philosophy rather than religious belief.[100][104] Among other prominent 19th-
century intellectuals involved with spiritualism were the social reformer Robert Owen, who was one of
Wallace’s early idols,[106] the physicists William Crookes and Lord Rayleigh, the mathematician Augustus
De Morgan, and the Scottish publisher Robert Chambers.[105][107]
Wallace's very public advocacy of spiritualism and his repeated defence of spiritualist mediums
against allegations of fraud in the 1870s damaged his scientific reputation. It strained his relationships with
previously friendly scientists such as Henry Bates, Thomas Huxley, and even Darwin, who felt he was overly
credulous. Others, such as the physiologist William Benjamin Carpenter and zoologist E. Ray Lankester
became openly and publicly hostile to Wallace over the issue. Wallace and other scientists who defended
spiritualism, notably William Crookes, were subject to much criticism from the press, with The Lancet as the
leading English medical journal of the time being particularly harsh. The controversy affected the public
perception of Wallace’s work for the rest of his career.[108] When, in 1879, Darwin first tried to rally support
among naturalists to get a civil pension awarded to Wallace, Joseph Hooker responded:
Wallace has lost caste considerably, not only by his adhesion to Spiritualism, but by the fact of
his having deliberately and against the whole voice of the committee of his section of the British
Association, brought about a discussion of on Spiritualism at one of its sectional meetings. That
he is said to have done so in an underhanded manner, and I well remember the indignation it
gave rise to in the B.A. Council.[109]
Hooker eventually relented and agreed to support the pension request.[110]
[edit] Biogeography and ecology
A map of the world from The Geographical Distribution of Animals shows Wallace's six
biogeographical regions.
In 1872, at the urging of many of his friends, including Darwin, Philip Sclater, and Alfred Newton,
Wallace began research for a general review of the geographic distribution of animals. He was unable to
make much progress initially, in part because classification systems for many types of animals were in flux at
the time.[111] He resumed the work in earnest in 1874 after the publication of a number of new works on
classification.[112] Extending the bird system developed by Sclater—which divided the earth into six separate
geographic regions for describing species distribution—to cover mammals, reptiles and insects as well,
Wallace created the basis for the zoogeographic regions still in use today. He discussed all of the factors
then known to influence the current and past geographic distribution of animals within each geographical
region. These included the effects of the appearance and disappearance of land bridges (such as the one
currently connecting North America and South America) and the effects of periods of increased glaciation. He
provided maps that displayed factors, such as elevation of mountains, depths of oceans, and the character of
regional vegetation, that affected the distribution of animals. He also summarised all the known families and
genera of the higher animals and listed their known geographic distributions. The text was organised so that
it would be easy for a traveler to learn what animals could be found in a particular location. The resulting two-
volume work, The Geographical Distribution of Animals , was published in 1876 and would serve as the
definitive text on zoogeography for the next 80 years.[113]
In 1880, Wallace published the book Island Life as a sequel to The Geographical Distribution of
Animals. It surveyed the distribution of both animal and plant species on islands. Wallace classified islands
into three different types. Oceanic islands, such as the Galapagos and Hawaiian Islands (then known as the
Sandwich Islands) formed in mid-ocean and had never been part of any large continent. Such islands were
characterised by a complete lack of terrestrial mammals and amphibians, and their inhabitants (with the
exceptions of migratory birds and species introduced by human activity) were typically the result of accidental
colonization and subsequent evolution. He divided continental islands into two separate classes depending
on whether they had recently been part of a continent (like Britain) or much less recently (like Madagascar)
and discussed how that difference affected the flora and fauna. He talked about how isolation affected
evolution and how that could result in the preservation of classes of animals, such as the lemurs of
Madagascar that were remnants of once widespread continental faunas. He extensively discussed how
changes of climate, particularly periods of increased glaciation, may have affected the distribution of flora
and fauna on some islands, and the first portion of the book discusses possible causes of these great ice
ages. Island Life was considered a very important work at the time of its publication. It was discussed
extensively in scientific circles both in published reviews and in private correspondence.[114]
[edit] Environmental issues

Wallace’s extensive work in biogeography made him aware of the impact of human activities on the
natural world. In Tropical Nature and Other Essays (1878), he warned about the dangers of deforestation and
soil erosion, especially in tropical climates prone to heavy rainfall. Noting the complex interactions between
vegetation and climate, he warned that the extensive clearing of rainforest for coffee cultivation in Ceylon (Sri
Lanka) and India would adversely impact the climate in those countries and lead to their eventual
impoverishment due to soil erosion.[115] In Island Life, Wallace again talked about deforestation and also the
impact of invasive species. He wrote the following about the impact of European colonization on the island of
Saint Helena:
... yet the general aspect of the island is now so barren and forbidding that some persons find it
difficult to believe that it was once all green and fertile. The cause of this change is, however,
very easily explained. The rich soil formed by decomposed volcanic rock and vegetable deposits
could only be retained on the steep slopes so long as it was protected by the vegetation to which
it in great part owed its origin. When this was destroyed, the heavy tropical rains soon washed
away the soil, and has left a vast expanse of bare rock or sterile clay. This irreparable
destruction was caused, in the first place, by goats, which were introduced by the Portuguese in
1513, and increased so rapidly that in 1588 they existed in the thousands. These animals are
the greatest of all foes to trees, because they eat off the young seedlings, and thus prevent the
natural restoration of the forest. They were, however, aided by the reckless waste of man. The
East India Company took possession of the island in 1651, and about the year 1700 it began to
be seen that the forests were fast diminishing, and required some protection. Two of the native
trees, redwood and ebony, were good for tanning, and, to save trouble, the bark was wastefully
stripped from the trunks only, the remainder being left to rot; while in 1709 a large quantity of the
rapidly disappearing ebony was used to burn lime for building fortifications![116]
[edit] Other controversies

[edit] Flat Earth wager
See also: Bedford Level experiment
In 1870, a Flat-Earth proponent named John Hampden offered a £500 wager (equivalent to about
£35000 in present day terms[117]) in a magazine advertisement to anyone who could demonstrate a convex
curvature in a body of water such as a river, canal, or lake. Wallace, intrigued by the challenge and short of
money at the time, designed an experiment in which he set up two objects along a six-mile (10 km) stretch of
canal. Both objects were at the same height above the water and in a straight line with a telescope he
mounted on a bridge. When seen through the telescope, one object appeared higher than the other, showing
the curvature of the earth. The judge for the wager, the editor of Field magazine, declared Wallace the
winner, but Hampden refused to accept the result. He sued Wallace and launched a campaign, which
persisted for several years, of writing letters to various publications and to organisations of which Wallace
was a member denouncing him as a swindler and a thief. Wallace won multiple libel suits against Hampden,
but the resulting litigation cost Wallace more than the amount of the wager and the controversy frustrated him
for years.[118]
[edit] Anti-vaccination campaign
In the early 1880s, Wallace was drawn into the debate over mandatory smallpox vaccination.
Wallace originally saw the issue as a matter of personal liberty; but, after studying some of the statistics
provided by anti-vaccination activists, he began to question the efficacy of vaccination. At the time, the germ
theory of disease was very new and far from universally accepted. Moreover, no one knew enough about the
human immune system to understand why vaccination worked. When Wallace did some research, he
discovered some cases where supporters of vaccination had used questionable statistics. Always suspicious
of authority, Wallace became convinced that reductions in the incidence of smallpox that had been attributed
to vaccination were, in fact, due to better hygiene and improvements in public sanitation. He also suspected
that physicians had a vested interest in promoting vaccination.[119] Wallace and other anti-vaccinationists
pointed out that vaccination, which was often done in a sloppy unsanitary manner, could be dangerous.[120]
In 1890, Wallace gave evidence before a Royal Commission investigating the controversy. When the
commission examined the material he had submitted to support his testimony, they found errors, including
some questionable statistics. The Lancet stated that Wallace and the other anti-vaccination activists were
being selective in their choice of statistics, ignoring large quantities of data inconsistent with their position.
The commission found that smallpox vaccination was effective and should remain compulsory, though they
did recommend some changes in procedures to improve safety, and that the penalties for people who
refused to comply be made less severe. Years later, in 1898, Wallace wrote a pamphlet attacking the
commission’s findings. It, in turn, was attacked by The Lancet, which stated that it contained many of the
same errors as his evidence given to the commission.[119]
[edit] Martian canals

In 1907, Wallace wrote the short book Is Mars Habitable? to criticise the claims made by Percival
Lowell that there were Martian canals built by intelligent beings. Wallace did months of research, consulted
various experts, and produced his own scientific analysis of the Martian climate and atmospheric conditions.
[121] Among other things, Wallace pointed out that spectroscopic analysis had shown no signs of water
vapour in the Martian atmosphere, that Lowell's analysis of Mars's climate was seriously flawed and badly
overestimated the surface temperature, and that low atmospheric pressure would make liquid water, let alone
a planet-girding irrigation system, impossible.[122] Wallace originally became interested in the topic because
his anthropocentric philosophy inclined him to believe that man would likely be unique in the universe.[123]
[edit] Legacy and historical perception
A portrait of Alfred Russel Wallace is shown above his signature on the frontispiece of Darwinism
(1889).
As a result of his writing, at the time of his death Wallace had been for many years a well-known
figure both as a scientist and as a social activist. He was often sought out by journalists and others for his
views on a variety of topics.[124] He received honorary doctorates and a number of professional honours,
such as election to the Royal Society, the Copley Medal, and one honour from the British monarch: the Order
of Merit.[125] Above all, his role as the co-discoverer of natural selection and his work on zoogeography
marked him out as an exceptional figure. He was undoubtedly one of the greatest natural history explorers of
the 19th century. Despite this, his fame faded quickly after his death. For a long time, he was treated as a
relatively obscure figure in the history of science.[90] A number of reasons have been suggested for this lack
of attention, including his modesty, his willingness to champion unpopular causes without regard for his own
reputation, and the discomfort of much of the scientific community with some of his unconventional ideas.
Recently, he has become a less obscure figure with the publication of several book length biographies on
him, as well as anthologies of his writings. In 2007 a literary critic for New Yorker magazine observed that
five such biographies and two such anthologies had been published since 2000.[126] There has also been a
web page created that is dedicated to Wallace scholarship.[127]
[edit] Awards, honours, and memorials

• Among the many awards presented to Wallace were the Order of Merit (1908), the Royal
Society's Royal Medal (1868) and Copley Medal (1908), the Royal Geographical Society's Founder's
Medal (1892) as well as the Linnean Society's Gold Medal (1892) and their Darwin–Wallace Medal
(1908).
• Elected head of the anthropology section of the British Association in 1866.
• Elected president of the Entomological Society of London in 1870.
• Elected head of the biology section of the British Association in 1876.
• Awarded a civil pension of £200 a year, in large part due to lobbying by Darwin and Huxley,
by British government in 1881.
• Elected to the Royal Society in 1893.
• Asked to chair the International Congress of Spiritualists (which was meeting in London) in
1898.
• In 1928, a house at Richard Hale School (at the time called Hertford Grammar School) was
named after Wallace. Wallace attended Richard Hale as a student from 1828–36.
• On 1 November 1915, a medallion with his name on it was placed in Westminster Abbey.
• He is also honoured by having craters on Mars and the Moon named after him.
• A centre for biodiversity research in Sarawak named in his memory was proposed in 2005.
[128]
• The Geography and Biology building at Swansea University is named after Wallace.
• A large lecture theatre at Cardiff University (Main Building 0.13) is named after Wallace.
[edit] Writings by Wallace

Wallace was a prolific author. In 2002, a historian of science published a quantitative analysis of
Wallace's publications. He found that Wallace had published 22 full-length books and at least 747 shorter
pieces, 508 of which were scientific papers (191 of them published in Nature). He further broke down the 747
short pieces by their primary subjects as follows. 29% were on biogeography and natural history, 27% were
on evolutionary theory, 25% were social commentary, 12% were on Anthropology, and 7% were on
spiritualism and phrenology.[129] An online bibliography of Wallace's writings has more than 750 entries.[22]
[edit] Selected books
• Wallace, Alfred Russel (1853) (Biodiversity Heritage Library). Palm trees of the Amazon and
their uses.. London. http://www.biodiversitylibrary.org/item/42833. Retrieved 2009-08-20.
• Wallace, Alfred Russel (1869). The Malay Archipelago. Harper.
• Wallace, Alfred Russel (1870) (Google Books). Contributions to the Theory of Natural
Selection (2nd ed.). Macmillan and Company. http://books.google.com/?id=uGSFcFcSBmkC.
• Wallace, Alfred Russel (1876) (Google Books). The Geographical Distribution of Animals.
Harper and brothers. http://books.google.com/?id=HmqtZfTfQUMC. Retrieved 2008-12-09.
• Wallace, Alfred Russel (1878) (Google Books). Tropical Nature, and Other Essays.
Macmillan. http://books.google.com/?id=09TeahwIfN0C. Retrieved 2008-12-09.
• Wallace, Alfred Russel (1881) (Google Books). Island Life. Harper and brothers.
http://books.google.com/?id=ghcPAAAAYAAJ. Retrieved 2009-02-28.
• Wallace, Alfred Russel (1889) (Google Books). Darwinism: An Exposition of the Theory of
Natural Selection, with Some of Its Applications (1912 ed.). Macmillan. http://books.google.com/?
id=jURSAAAAMAAJ. Retrieved 2008-12-09.
• Wallace, Alfred Russel (1889) (Google Books). Travels on the Amazon and Rio Negro (1889
ed.). Ward, Lock. http://books.google.com/?id=iEQTAAAAYAAJ. Retrieved 2008-12-09.
• Wallace, Alfred Russel (1905) (Google Books). My Life. Chapman & Hall.
http://books.google.com/?id=_dYEAAAAYAAJ. Retrieved 2009-02-28.
[edit] Selected papers
• 1853: On the Monkeys of the Amazon. Speculates on the effect of rivers and other
geographical barriers on the distribution of closely allied species.
• 1855: On the Law Which Has Regulated the Introduction of New Species. Wallace's thoughts
on the laws governing the geographic distribution of closely allied species and the implications of
those laws for the transmutation of species.
• 1857: On the Natural History of the Aru Islands. First methodical biogeographic study.
• 1858: On the Tendency of Varieties to Depart Indefinitely From the Original Type. Paper on
natural selection sent by Wallace to Darwin.
• 1859: On the Zoological Geography of the Malay Archipelago. Contains first description of
Wallace Line.
• 1863: Remarks on the Rev. S. Haughton's Paper on the Bee's Cell, And on the Origin of
Species. Wallace's defence of the Origin on the topic of evolution of the hexagonal bee cell.
• 1863: On the Physical Geography of the Malay Archipelago. Paper on the geography and
possible geographic history of Indonesia with concluding remarks on importance of biogeography
and biodiversity that are frequently cited in modern conservation circles.
• 1864: On the phenomena of variation and geographical distribution as illustrated by the
Papilionidae of the Malayan region. Monograph on Indonesian butterfly family with discussion of
different kinds of variability including individual variation, polymorphic forms, geographical races,
variation influenced by local conditions, and closely allied species.
• 1891: English and American Flowers. Contains speculation on how glaciation may have
affected distribution of mountain flora in North America and Eurasia.
A more comprehensive list of Wallace's publications that are available online, as well as a full
bibliography of all of Wallace's writings,[22] has been compiled by the historian Charles H. Smith at the The
Alfred Russel Wallace Page.
[edit] See also

Indonesia portal
• Wallacea
• Operation Wallacea
• Fauna of Indonesia
• Flora of Indonesia
• List of independent discoveries
• History of biology
[edit] Notes
1. ^ Smith, Charles H.. "Alfred Russel Wallace: Evolution of an Evolutionist Introduction". The
Alfred Russel Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/chsarwin.htm. Retrieved 2007-04-27.
2. ^ Wilson The Forgotten Naturalist p. 1.
3. ^ a b Smith, Charles H.. "Alfred Russel Wallace: A Capsule Biography". The Alfred Russel
Wallace Page hosted by Western Kentucky University. http://www.wku.edu/~smithch/index1.htm.
4. ^ Wilson pp. 6–10.
5. ^ Raby Bright Paradise pp. 77–78.
6. ^ Slotten The Heretic in Darwin's Court pp. 11–14.
7. ^ "28. Alfred Russel Wallace". 100 Welsh heroes.
http://www.100welshheroes.com/en/biography/alfredrussellwallace. Retrieved 2008-09-23.
8. ^ Smith, Charles H.. "Responses to Questions Frequently Asked About Wallace: Was
Wallace actually a Welshman, as seems to be increasingly claimed?". The Alfred Russel Wallace
Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/FAQ.htm#Welsh. Retrieved 2008-01-20.
9. ^ Shermer In Darwin's Shadow p. 53.
10.^ Slotten pp. 22–26.
11.^ Slotten pp. 26–29.
12.^ Wilson pp. 19–20.
13.^ Raby p. 78.
14.^ Wallace My Life pp. 254, 256
15.^ Slotten pp. 34–37.
16.^ Wilson p. 36; Raby pp. 89, 98–99, 120–21.
17.^ Raby pp. 89–95.
18.^ Shermer pp. 72–73.
19.^ a b Slotten pp. 84–88
20.^ Wilson p. 45.
21.^ Raby p. 148.
22.^ a b c d Wallace, Alfred. "Bibliography of the Published Writings of Alfred Russel Wallace
(1823–1913)". The Alfred Russel Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/bib4.htm. Retrieved 2007-05-06.
23.^ Shermer p. 14.
24.^ Slotten p. 267.
25.^ Shermer pp. 151–52.
26.^ Slotten pp. 249–58.
29.^ Slotten pp. 239–40.
30.^ Slotten pp. 265–67.
31.^ Slotten pp. 299–300.
33.^ Slotten pp. 361–64.
34.^ Slotten pp. 365–72.
37.^ Wallace, Alfred. "Paper Money as a Standard of Value (S557: 1898)". The Alfred Russel
Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/S557.htm. Retrieved 2007-05-06.
38.^ Slotten pp. 366, 453, 487–88.
39.^ Shermer pp. 23, 279.
40.^ Wallace, Alfred. "The Revolt of Democracy (S734: 1913)". The Alfred Russel Wallace Page
hosted by Western Kentucky University. http://www.wku.edu/~smithch/wallace/S734.htm. Retrieved
2007-05-06.
41.^ Shermer pp. 274–78.
42.^ Slotten pp. 379–400.
43.^ a b Slotten p. 490.
45.^ a b c Larson Evolution p. 73.
46.^ Bowler & Morus "Making Modern Science" p. 141.
47.^ McGowan The Dragon Seekers pp. 101, 154–55.
48.^ Larson pp. 23–24, 37–38.
49.^ a b Shermer p. 54.
50.^ Slotten p. 31.
51.^ Slotten p. 94.
52.^ Wallace, Alfred Russel (1855). "On the Law Which has Regulated the Introduction of
Species". The Alfred Russel Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/%7Esmithch/wallace/S020.htm. Retrieved 2007-05-08.
53.^ Desmond & Moore Darwin 1991, p. 438;
Browne Charles Darwin: Voyaging pp. 537–46.
54.^ Wallace My Life p. 361.
55.^ Slotten pp. 144–45.
57.^ Wallace My Life pp. 361–62.
58.^ Marchant, 1916. p. 105
59.^ Darwin, Francis, 1887, The life and letters of Charles Darwin p. 95
60.^ Darwin, Francis, 1887, The life and letters of Charles Darwin p. 108
61.^ a b Wallace, Alfred. "On the Tendency of Varieties to Depart Indefinitely From the Original
Type". The Alfred Russel Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/S043.htm. Retrieved 2007-04-22.
62.^ Slotten pp. 153–54
Darwin, Francis, 1887, The life and letters of Charles Darwin p. 116
63.^ Browne Charles Darwin: The Power of Place pp. 33–42.
64.^ Shermer pp. 148–50.
65.^ Browne Charles Darwin: The Power of Place pp. 40–42.
66.^ Slotten pp. 157–62.
67.^ Shermer, Michael. "In Darwin’s Shadow: Excerpt". michaelshermer.com.
http://www.michaelshermer.com/darwins-shadow/excerpt/. Retrieved 2008-04-29.
68.^ Smith, Charles. "Responses to Questions Frequently Asked About Wallace: Did Darwin
really steal material from Wallace to complete his theory of natural selection?". The Alfred Russel
Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/FAQ.htm. Retrieved 2008-04-29.
69.^ Slotten pp. 197–99.
70.^ Wallace, Alfred. "Creation by Law (S140: 1867)". The Alfred Russel Wallace Page hosted
by Western Kentucky University. http://www.wku.edu/~smithch/wallace/S140.htm. Retrieved 2007-
05-23.
72.^ Kutschera, U. (2003-12-19). "A comparative analysis of the Darwin–Wallace papers and the
development of the concept of natural selection". Theory in Biosciences 122 (4): 343–359.
doi:10.1007/s12064-003-0063-6.
73.^ Larson p. 75.
74.^ Bowler & Morus p. 149.
75.^ a b Smith, Charles H.. "Wallace's Unfinished Business". Complexity (publisher Wiley
Periodicals, Inc.) Volume 10, No 2, 2004. http://www.wku.edu/~smithch/essays/UNFIN.htm.
76.^ Brand, Stewart. "For God’s Sake, Margaret". CoEvolutionary Quarterly, June 1976.
http://www.oikos.org/forgod.htm. Retrieved 2007-04-04.
77.^ Slotten pp. 251–54.
78.^ Slotten pp. 353–56.
79.^ Slotten pp. 413–15.
81.^ Ollerton, J. "Flowering time and the Wallace Effect" (PDF). Heredity, August 2005.
http://oldweb.northampton.ac.uk/aps/env/lbrg/journals/papers/OllertonHeredityCommentary2005.pdf.
82.^ a b Eiseley, Loren (1958). Darwin's Century. Anchor Book.
83.^ Wallace Darwinism p. 477.
84.^ Shermer pp. 157–60.
85.^ Smith, Charles H.. "Alfred Russel Wallace: Evolution of an Evolutionist Chapter Six. A
Change of Mind?". The Alfred Russel Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/chsarw6.htm. Retrieved 2007-04-29.
86.^ Larson p. 100.
88.^ Slotten pp. 280–96.
89.^ Shermer pp. 208–09.
92.^ Slotten pp. 289–90.
93.^ Larson p. 123.
94.^ Bowler & Morus p. 154.
96.^ Shermer p. 18.
97.^ Wallace, Alfred. "1861 Letter from Wallace to Thomas Sims". The Alfred Russel Wallace
Page hosted by Western Kentucky University. http://www.wku.edu/~smithch/wallace/quotes.htm.
98.^ Slotten pp. 203–05.
99.^ Slotten pp. 234–35.
100.^ a b c Smith, Charles H.. "Alfred Russel Wallace: Evolution of an Evolutionist Chapter One.
Belief and Spiritualism". The Alfred Russel Wallace Page hosted by Western Kentucky University.
http://www.wku.edu/~smithch/wallace/chsarw1.htm. Retrieved 2007-04-20.
101.^ Wallace, Alfred. "Notes on the Growth of Opinion as to Obscure Psychical Phenomena
During the Last Fifty Years". The Alfred Russel Wallace Page hosted by Western Kentucky
University. http://www.wku.edu/~smithch/wallace/S478.htm. Retrieved 2007-04-20.
102.^ Slotten p. 231.
103.^ Slotten p. 236.
104.^ a b Shermer pp. 199–201.
106.^ Slotten p. 232.
107.^ Shermer p. 183.
108.^ Slotten pp. 298–351.
109.^ Slotten pp. 357–58.
110.^ Slotten p. 362.
111.^ Slotten p. 301.
112.^ Slotten p. 315.
113.^ Slotten pp. 320–25.
114.^ Slotten p. 361.
115.^ Slotten pp. 352–53.
116.^ Wallace Island Life pp. 283–84.
117.^ UK CPI inflation numbers based on data available from Lawrence H. Officer (2010) "What
Were the UK Earnings and Prices Then?" MeasuringWorth.
118.^ Shermer pp. 258–61.
119.^ a b Slotten pp. 422–36.
120.^ Shermer p. 216.
121.^ Slotten p. 474.
122.^ Wallace, Alfred. "Is Mars Habitable (S730: 1907)". The Alfred Russel Wallace Page
hosted by Western Kentucky University. http://www.wku.edu/~smithch/wallace/S730.htm. Retrieved
2007-05-13.
123.^ Shermer p. 294.
124.^ Shermer pp. 292–94.
125.^ London Gazette: (Supplement) no. 28194, p. 8162, 9 November 1908. Retrieved 2009-01-
08.
126.^ Rosen, Jonathan. "Missing Link: Alfred Russel Wallace, Charles Darwin’s neglected
double". The New Yorker Feb 2007.
http://www.newyorker.com/arts/critics/atlarge/2007/02/12/070212crat_atlarge_rosen. Retrieved
2007-04-25.
127.^ "The Alfred Russel Wallace Page". hosted by Western Kentucky University.
http://www.wku.edu/~smithch/index1.htm. Retrieved 2007-05-13.
128.^ Sibon, Peter (2005-07-14). "Relishing Wallace's enlightenment" (PDF). Sarawak Tribune.
http://www.cm.sarawak.gov.my/cm/cmweb.nsf/0/47186e7957e667b64825706600087643/$FILE/St14
0705.pdf. Retrieved 2007-04-09.
129.^ Shermer pp. 15–17.
[edit] References
• Bowler, Peter J.; Iwan Rhys Morus (2005). Making Modern Science. The University of
Chicago Press. ISBN 0-226-06861-7.
• Browne, Janet (1995). Charles Darwin: Voyaging: Volume I of a Biography. Princeton
• Browne, Janet (2002). Charles Darwin: The Power of Place: Volume II of a Biography .
Princeton University Press. ISBN 0-691-11439-0.
• Darwin, Charles. Darwin, F. ed. The life and letters of Charles Darwin, including an
autobiographical chapter. Vol. 2. London: John Murray.
http://www.gutenberg.org/catalog/world/readfile?fk_files=39003&pageno=1. Retrieved 2007-05-12.
• Desmond, Adrian; Moore, James (1991). Darwin. London: Michael Joseph, Penguin Group.
ISBN 0-7181-3430-3.
• Larson, Edward J. (2004). Evolution: The Remarkable History of Scientific Theory. Modern
Library. ISBN 0-679-64288-9.
• Marchant, James (1916). Alfred Russel Wallace: letters and reminiscences. New York:
Harper & Brothers. http://darwin-online.org.uk/content/frameset?
itemID=F1593&viewtype=image&pageseq=1.
• McGowan, Christopher (2001). The Dragon Seekers. Cambridge: Perseus Pub.
ISBN 0738202827.
• Raby, Peter (1996). Bright Paradise: Victorian Scientific Travellers. Princeton University
Press. ISBN 0-691-04843-6.
• Raby, Peter (2002). Alfred Russel Wallace: A Life. Princeton University Press. ISBN 978-0-
691-10240-5.
• Shermer, Michael (2002). In Darwin's Shadow: The Life and Science of Alfred Russel
Wallace. Oxford University press. ISBN 0-19-514830-4.
• Slotten, Ross A. (2004). The Heretic in Darwin's Court: the life of Alfred Russel Wallace . New
York: Columbia University Press. ISBN 0231130104.
• Wallace, Alfred Russel (1889). "Darwinism, Chapter 15". The Alfred Russel Wallace Page.
http://www.wku.edu/~smithch/wallace/S724CH15.htm. Retrieved 2007-04-04.
• Wallace, Alfred Russel (1881). Island Life. Google Books. http://books.google.com/?
id=oJ8KAAAAMAAJ&pg=RA1-PR19&lpg=RA1-PR19&dq=Wallace++Island+Life#PRA1-PR10,M1.
• Wallace, Alfred Russel (1905). My Life. Chapman and Hall, London.
http://books.google.com/?id=tqqYSNoOgfoC&pg=PR3&lpg=PA2&dq=alfred%2Brussel%2Bwallace.
Vol. 1, Vol. 2.
• Wilson, John (2000). The Forgotten Naturalist: In search of Alfred Russel Wallace. City:
Arcadia/Australian Scholarly Publishing Pty Ltd. ISBN 1875606726.

• Fichman, Martin (2004). An elusive Victorian: the evolution of Alfred Russel Wallace.
Chicago: University of Chicago Press. ISBN 0226246132.
• Quammen, David (December 2008). "The Man Who Wasn't Darwin". National Geographic
(National Geographic Society): 106–33.
http://ngm.nationalgeographic.com/2008/12/wallace/quammen-text. Retrieved 2008-12-03.
• Quammen, David (1996). The song of the dodo: island biogeography in an age of
extinctions. New York: Scribner. ISBN 0684800837.
• Severin, Tim (1997). The Spice Islands Voyage: The Quest for Alfred Wallace, the Man Who
Shared Darwin's Discovery of Evolution. New York: Carroll & Graf Publishers. ISBN 0786705183.
• Berry, Andrew (2003). Infinite Tropics: An Alfred Russel Wallace Anthology . London: Verso.
ISBN 1859844782.
• Crawforth, Anthony (2009). The Butterfly Hunter: The life of Henry Walter Bates. The
University of Buckingham Press. ISBN 9780956071613.

• The Alfred Russel Wallace Page
• The Alfred Russel Wallace Website
• The A. R. Wallace Correspondence Project website
• "Missing Link-Alfred Russel Wallace, Charles Darwin's neglected double" by Jonathan
Rosen, The New Yorker, February 12, 2007
• The Malay Archipelago illustrated edition at Papua WebProject
• Wallace at 100 Welsh Heroes
• Works by Alfred Russel Wallace at Project Gutenberg
• Works by or about Alfred Russel Wallace in libraries (WorldCat catalog)
• BBC article on Wallace and Indonesia's efforts to honor him
• National Geographic Magazine, December 2008 - The Man Who Wasn't Darwin Biography
• "The Work In Darwin's Shadow" by Joel Achenbach, The Washington Post, February 9, 2009
[edit] Sister project links

• Media related to Alfred Russel Wallace at Wikimedia Commons
• Quotations related to Alfred Russel Wallace at Wikiquote

• Chisholm, Hugh, ed (1911). "Wallace, Alfred Russel". Encyclopædia Britannica (Eleventh
ed.). Cambridge University Press.
W000
Adaptive evolution in the human genome


This article includes a list of references, related reading or external links, but its
sources remain unclear because it lacks inline citations. Please improve this article by
introducing more precise citations where appropriate. (December 2010)
Adaptive evolution results from the propagation of advantageous mutations through positive
selection. This is the modern synthesis of the process which Darwin and Wallace originally identified as the
mechanism of evolution. However, in the last half century there has been considerable debate as to whether
evolutionary changes at the molecular level are largely driven by natural selection or random genetic drift.
Unsurprisingly, the forces which drive evolutionary changes in our own species’ lineage have been of
particular interest. Quantifying adaptive evolution in the human genome gives insights into our own
evolutionary history and helps to resolve this neutralist-selectionist debate. Identifying specific regions of the
human genome that show evidence of adaptive evolution helps us find functionally significant genes,
including genes important for human health, such as those associated with diseases.
Contents
[hide]
• 1 Methods
• 2 Amount of adaptive evolution
• 2.1 Coding DNA
• 2.2 Non-coding DNA
• 3 Variation between human populations
• 4 Rate of adaptive evolution
• 5 Strength of positive selection
• 6 Regions of the genome which show evidence of adaptive
evolution
• 7 Difficulties in identifying positive selection
• 7.1 Table 1: Estimates of the amount of adaptive
evolution in the human genome
• 7.2 Table 2: Examples of human genes which show
evidence of adaptive evolution
• 8 References
• 9 See also
[edit] Methods
The methods used to identify adaptive evolution are generally devised to test the null hypothesis of
neutral evolution, which, if rejected, provides evidence of adaptive evolution. These tests can be broadly
divided into two categories. Firstly, there are methods that use a comparative approach to search for
evidence of function altering mutations. The dn/ds test detects adaptive evolution if dn (the number of
nonsynonymous substitutions; fitness effect is either neutral, advantageous or deleterious) is greater than ds
(the number of synonymous substitutions; fitness effect is assumed neutral) (Yang and Bielawski 2000). The
McDonald-Kreitman (MK) test quantifies the amount of adaptive evolution occurring by estimating the
proportion of nonsynonymous substitutions which are adaptive, referred to as α (McDonald and Kreitman
1991, Eyre-Walker 2006). α is calculated as: α = 1-(dsps/dnps), where dn and ds are as above, and pn and
ps are the number of nonsynonymous (fitness effect assumed neutral or deleterious) and synonymous
(fitness effect assumed neutral) polymorphisms respectively (Eyre-Walker 2006). Note, both these tests are
presented here in basic forms, and these tests are normally modified considerably to account for other
factors, such as the effect of slightly deleterious mutations. The other methods for detecting adaptive
evolution use genome wide approaches, often to look for evidence of selective sweeps. Evidence of
complete selective sweeps is shown by a decrease in genetic diversity, and can be inferred from comparing
the patterns of the Site Frequency Spectrum (SFS, i.e. the allele frequency distribution) obtained with the
SFS expected under a neutral model (Willamson et al. 2007). Partial selective sweeps provide evidence of
the most recent adaptive evolution, and the methods identify adaptive evolution by searching for regions with
a high proportion of derived alleles (Sabeti et al. 2006). Examining patterns of Linkage Disequilibrium (LD)
can locate signatures of adaptive evolution (Hawks et al. 2007, Voight et al. 2006). LD tests work on the
basic principle that, assuming equal recombination rates, LD will rise with increasing natural selection. These
genomic methods can also be applied to search for adaptive evolution in non-coding DNA, where putatively
neutral sites are hard to identify (Ponting and Lunter 2006). Another recent method used to detect selection
in non-coding sequences examines insertions and deletions (indels), rather than point mutations (Lunter et
al. 2006).
[edit] Amount of adaptive evolution

[edit] Coding DNA
Many different studies have attempted to quantify the amount of adaptive evolution in the human
genome, the vast majority using the comparative approaches outlined above. Although there are
discrepancies between studies, generally there is relatively little evidence of adaptive evolution in protein
coding DNA, with estimates of adaptive evolution often near 0% (see Table 1). The most obvious exception
to this is the 35% estimate of α (Fay et al. 2001). This comparatively early study used relatively few loci
(fewer than 200) for their estimate, and the polymorphism and divergence data used was obtained from
different genes, both of which may have lead to an overestimate of α. The next highest estimate is the 20%
value of α (Zhang and Li 2005). However, the MK test used in this study was sufficiently weak that the
authors state that this value of α is not statistically significantly different from 0%. Nielsen et al. (2005a)’s
estimate that 9.8% of genes have undergone adaptive evolution also has a large margin of error associated
with it, and their estimate shrinks dramatically to 0.4% when they stipulate that the degree of certainty that
there has been adaptive evolution must be 95% or more. This raises an important issue, which is that many
of these tests for adaptive evolution are very weak. Therefore the fact that many estimates are at (or very
near to) 0% does not rule out the occurrence of any adaptive evolution in the human genome, but simply
shows that positive selection is not frequent enough to be detected by the tests. In fact, the most recent study
I mention states that confounding variables, such as demographic changes, means that the true value of α
may be as high as 40% (Eyre-Walker and Keightley 2009). Another recent study, which uses a relatively
robust methodology, estimates α at 10-20% Boyko et al. (2008). I will comment on weaknesses in the
methods in a subsequent section, but it is clear that the debate over the amount of adaptive evolution
occurring in human coding DNA is not yet resolved. Even if low estimates of α are accurate, a small
proportion of substitutions evolving adaptively can still equate to a considerable amount of coding DNA.
Many authors, whose studies have small estimates of the amount of adaptive evolution in coding DNA,
nevertheless accept that there has been some adaptive evolution in this DNA, because these studies identify
specific regions within the human genome which have been evolving adaptively (e.g. Bakewell et al. (2007)).
More genes underwent positive selection in chimpanzee evolution than in human), something I will examine
later. The generally low estimates of adaptive evolution in human coding DNA can be contrasted with other
species. Bakewell et al. (2007) found more evidence of adaptive evolution in chimpanzees than humans, with
1.7% of chimpanzee genes showing evidence of adaptive evolution (compared with the 1.1% estimate for
humans; see Table 1). Comparing humans with more distantly related animals, an early estimate for α in
Drosophila species was 45% (Smith and Eyre-Walker 2002), and later estimates largely agree with this
(Eyre-Walker 2006). Bacteria and viruses generally show even more evidence of adaptive evolution;
research shows values of α in a range of 50-85%, depending on the species examined (Eyre-Walker 2006).
Generally, there does appear to be a positive correlation between (effective) population size of the species,
and amount of adaptive evolution occurring in the coding DNA regions. This may be because random genetic
drift becomes less powerful at altering allele frequencies, compared to natural selection, as population size
increases.
[edit] Non-coding DNA

Estimates of the amount of adaptive evolution in non-coding DNA are generally very low, although
fewer studies have been done on non-coding DNA. As with the coding DNA however, the methods currently
used are relatively weak. Ponting and Lunter (2006) speculate that underestimates may be even more
severe in non-coding DNA, because non-coding DNA may undergo periods of functionality (and adaptive
evolution), followed by periods of neutrality. If this is true, current methods for detecting adaptive evolution
are inadequate to account for such patterns. Additionally, even if low estimates of the amount of adaptive
evolution are correct, this can still equate to a large amount of adaptively evolving non-coding DNA, since
non-coding DNA makes up approximately 98% of the DNA in the human genome. For example, Ponting and
Lunter (2006) detect a modest 0.03% of non-coding DNA showing evidence of adaptive evolution, but this
still equates to approximately 1 Mb of adaptively evolving DNA. Where there is evidence of adaptive
evolution (which implies functionality) in non-coding DNA, these regions are generally thought to be involved
in the regulation of protein coding sequences. As with humans, fewer studies have searched for adaptive
evolution in non-coding regions of other organisms. However, where research has been done on Drosophila,
there appears to be large amounts of adaptively evolving non-coding DNA. Andolfatto (2005) estimated that
adaptive evolution has occurred in 60% of untranslated mature portions of mRNAs, and in 20% of intronic
and intergenic regions. If this is true, this would imply that much non-coding DNA could be of more functional
importance than coding DNA, dramatically altering the consensus view. However, this would still leave
unanswered what function all this non-coding DNA performs, as the regulatory activity observed thus far is in
just a tiny proportion of the total amount of non-coding DNA. Ultimately, significantly more evidence needs to
be gathered to substantiate this viewpoint.
[edit] Variation between human populations

Several recent studies have compared the amounts of adaptive evolution occurring between different
populations within the human species. Williamson et al. (2007) found more evidence of adaptive evolution in
European and Asian populations than African American populations. Assuming African Americans are
representative of Africans, these results makes sense intuitively, because humans spread out of Africa
approximately 50,000 years ago (according to the consensus Out-of-Africa hypothesis of human origins
(Klein 2009)), and these humans would have adapted to the new environments they encountered. By
contrast, African populations remained in a similar environment for the following tens of thousands of years,
and were therefore probably nearer their adaptive peak for the environment. However, Voight et al. (2006)
found evidence of more adaptive evolution in Africans, than in Non-Africans (East Asian and European
populations examined), and Boyko et al. (2008) found no significant difference in the amount of adaptive
evolution occurring between different human populations. Therefore, the evidence obtained so far is
inconclusive as to what extent different human populations have undergone different amounts of adaptive
evolution.
[edit] Rate of adaptive evolution

The rate of adaptive evolution in the human genome has often assumed to be constant over time.
For example, the 35% estimate for α calculated by Fay et al. (2001) led them to conclude that there was one
adaptive substitution in the human lineage every 200 years since human divergence from old-world
monkeys. However, even if the original value of α is accurate for a particular time period, this extrapolation is
still invalid. This is because there has been a large acceleration in the amount of positive selection in the
human lineage over the last 40,000 years, in terms of the number of genes that have undergone adaptive
evolution (Hawks et al. 2007). This agrees with simple theoretical predictions, because the human population
size has expanded massively in the last 40,000 years, and with more people, there should be more adaptive
substitutions. Hawks et al. (2007) argue that demographic changes (particularly population expansion) may
greatly facilitate adaptive evolution, an argument that corroborates somewhat with the positive correlation
inferred between population size and amount of adaptive evolution occurring mentioned previously. It has
been suggested that cultural evolution may have replaced genetic evolution, and hence slowed the rate of
adaptive evolution over the past 10,000 years. However, it is possible that cultural evolution could actually
increase genetic adaption. Cultural evolution has vastly increased communication and contact between
different populations, and this provides much greater opportunities for genetic admixture between the
different populations (Hawks et al. 2007). However, recent cultural phenomena, such as modern medicine
and the smaller variation in modern family sizes, may reduce genetic adaption as natural selection is relaxed,
overriding the increased potential for adaptation due to greater genetic admixture.
[edit] Strength of positive selection

Studies don’t generally attempt to quantify the average strength of selection propagating
advantageous mutations in the human genome. Many models make assumptions about how strong selection
is, and some of the discrepancies between the estimates of the amounts of adaptive evolution occurring have
been attributed to the use of differing such assumptions (Eyre-Walker 2006). The way to accurately estimate
the average strength of positive selection acting on the human genome is by inferring the distribution of
fitness effects (DFE) of new advantageous mutations in the human genome, but this DFE is difficult to infer
because new advantageous mutations are very rare (Boyko et al. 2008). The DFE may be exponential
shaped in an adapted population (Eyre-Walker and Keightley 2007). However, more research is required to
produce more accurate estimates of the average strength of positive selection in humans, which will in turn
improve the estimates of the amount of adaptive evolution occurring in the human genome (Boyko et al.
2008).
[edit] Regions of the genome which show evidence of adaptive

evolution
A considerable number of studies have used genomic methods to identify specific human genes that
show evidence of adaptive evolution. Table 2 gives selected examples of such genes for each gene type
discussed, but provides nowhere near an exhaustive list of the human genes showing evidence of adaptive
evolution. Below are listed some of the types of gene which show strong evidence of adaptive evolution in
the human genome.
• Disease genes
Bakewell et al. (2007) found that a relatively large proportion (9.7%) of positively selected genes
were associated with diseases. This may be because diseases can be adaptive in some contexts. For
example, schizophrenia has been linked with increased creativity (Crespi et al. 2007), perhaps a useful trait
for obtaining food or attracting mates in Palaeolithic times. Alternatively, the adaptive mutations may be the
ones which reduce the chance of disease arising due to other mutations. However, this second explanation
seems unlikely, because the mutation rate in the human genome is fairly low, so selection would be relatively
weak.
• Immune genes
417 genes involved in the immune system showed strong evidence of adaptive evolution in the study
of Nielsen et al. (2005a). This is probably because the immune genes may become involved in a
coevolutionary arms race with bacteria and viruses. These pathogens evolve very rapidly, so selection
pressures change quickly, giving more opportunity for adaptive evolution.
• Testes genes
247 genes in the testes showed evidence of adaptive evolution in the study of Nielsen et al. (2005a).
This could be partially due to sexual antagonism. Male-female competition could facilitate an arms race of
adaptive evolution. However, in this situation you would expect to find evidence of adaptive evolution in the
female sexual organs also, but there is less evidence of this. Sperm competition is another possible
explanation. Sperm competition is strong, and sperm can improve their chances of fertilising the female egg
in a variety of ways, including increasing their speed, stamina or response to chemoattractants (Swanson
and Vacquier 2002).
• Olfactory genes
Genes involved in detecting smell show strong evidence of adaptive evolution (Voight et al. 2006),
probably due to the fact that the smells encountered by humans have changed recently in their evolutionary
history (Williamson et al. 2007). Humans’ sense of smell has played an important role in determining the
safety of food sources.
• Nutrition genes
Genes involved in lactose metabolism show particularly strong evidence of adaptive evolution
amongst the genes involved in nutrition. A mutation linked to lactase persistence shows very strong evidence
of adaptive evolution in European and American populations (Williamson et al. 2007), populations where
pastoral farming for milk has been historically important.
• Pigmentation genes
Pigmentation genes show particularly strong evidence of adaptive evolution in non-African
populations (Williamson et al. 2007). This is likely to be because those humans that left Africa approximately
50,000 years ago, entered less sunny climates, and so were under new selection pressures to obtain enough
Vitamin D from the weakened sunlight.
• Brain genes?
There is relatively little evidence of adaptive evolution in genes linked to brain development (Voight
et al. 2006), and where there is evidence, these genes are often associated with diseases, e.g. microcephaly
(see Table 2). However, there is a particular interest in the search for adaptive evolution in brain genes,
despite the ethical issues surrounding such research. If more adaptive evolution was discovered in brain
genes in one human population than another, then this information could be misinterpreted as showing
greater intelligence in the more adaptively evolved population. Researchers should be very careful in how
they present and discuss such results.
• Other
Other gene types showing considerable evidence of adaptive evolution (but generally less evidence
than the types discussed) include: genes on the X chromosome, nervous system genes, genes involved in
apoptosis, genes coding for skeletal traits, and possibly genes associated with speech (Nielsen et al. 2005a,
Williamson et al. 2007, Voight et al. 2006, Krause et al. 2007).
[edit] Difficulties in identifying positive selection

As noted previously, many of the tests used to detect adaptive evolution have very large degrees of
uncertainty surrounding their estimates. It is beyond the purview of this article to look at all the modifications
applied to individual tests to overcome the associated problems. However, it will briefly discuss in general
terms two of what may be the most important confounding variables that may hinder accurate detection of
adaptive evolution. Demographic changes are particularly problematic and may severely bias estimates of
adaptive evolution. The human lineage has undergone both rapid population size contractions and
expansions over its evolutionary history, and these events will change many of the signatures thought to be
characteristic of adaptive evolution (Nielsen et al. 2007). Some genomic methods have been shown through
simulations to be relatively robust to demographic changes (e.g. Willamson et al. 2007). However, no tests
are completely robust to demographic changes, and new genetic phenomena linked to demographic changes
have recently been discovered. This includes the concept of “surfing mutations”, where new mutations can
be propagated with a population expansion (Klopfstein et al. 2006). A phenomenon which could severely
alter the way we look for signatures of adaptive evolution is bias gene conversion (BGC) (Galtier and Duret
2007). Meiotic recombination between homologous chromosomes that are heterozygous at a particular locus
can produce a DNA mismatch. DNA repair mechanisms are biased towards repairing a mismatch to the CG
base pair. This will lead allele frequencies to change, leaving a signature of non-neutral evolution (Galtier et
al. 2001). The excess of AT to GC mutations in human genomic regions with high substitution rates (human
accelerated regions, HARs) implies that BGC has occurred frequently in the human genome (Pollard et al.
2006, Galtier and Duret 2007). Initially, it was postulated that BGC could have been adaptive (Galtier et al.
2001), but more recent observations have made this seem unlikely. Firstly, some HARs show no substantial
signs of selective sweeps around them. Secondly, HARs tend to be present in regions with high
recombination rates (Pollard et al. 2006). In fact, BGC could lead to HARs containing a high frequency of
deleterious mutations (Galtier and Duret 2007). However, it is unlikely that HARs are generally maladaptive,
because DNA repair mechanisms themselves would be subject to strong selection if they propagated
deleterious mutations. Either way, BGC should be further investigated, because it may force radical alteration
of the methods which test for the presence of adaptive evolution.
[edit] Table 1: Estimates of the amount of adaptive evolution in the human genome
(format of table and some data displayed as in Table 1 of Eyre-Walker (2006))
α or
proportion of loci that Outgroup
Locus type Method Study
have undergone species
adaptive evolution (%)
20 Protein Chimpanzee MK Zhang and Li

2005
Bustamante et
6 Protein Chimpanzee MK
al. 2005
Chimpanzee
Sequencing and
0-9 Protein Chimpanzee MK
Analysis Consortium
2005
Boyko et al.
10-20 Protein Chimpanzee MK
2008
Nielsen et al.
9.8 Protein Chimpanzee dn/ds
2005a
Bakewell et al.
1.1 Protein Chimpanzee dn/ds
2007
Old-world
35 Protein MK Fay et al. 2001
monkey
Old-world Zhang and Li

0 Protein MK
monkey 2005
0 Protein Old-world MK Eyre-Walker

monkey and Keightley 2009
Old-world Nielsen et al.

0.4 Protein dn/ds
monkey 2005b
Zhang and Li
0 Protein Mouse MK
2005
Keightley et al.
0.11-0.14 Non-coding Chimpanzee MK
2005
Chimpanzee
Haygood et al.
4 Non-coding and Old-world dn/ds
2007
monkey
Old-world Eyre-Walker
0 Non-coding MK
monkey and Keightley 2009
Ponting and
0.03 Non-coding N/A Indel
Lunter 2006
[edit] Table 2: Examples of human genes which show evidence of adaptive evolution
Gene Phenotype produced by
Type of gene Study
name gene/Region where gene expressed
Microcephaly (characterised by Mekel-Bobrov et
Disease ASPM
small head and mental retardation) al. 2005
Nielsen et al.
Disease HYAL3 Cancers, tumour suppression
2005a
Crespi et al.
Disease DISC1 Schizophrenia
2007
Nielsen et al.
Immune CD72 Immune system signalling
2005a
Links immunoglobulin Williamson et al.

Immune IGJ
monomers 2007
Bakewell et al.
Immune PTCRA Pre T-cell antigen receptor
2007
Nielsen et al.
Testes USP26 Testes specific expression
2005a
Testes RSBN1 Protein structure of sperm Voight et al. 2006
Bakewell et al.
Testes SPAG5 Sperm associated antigen 5
2007
Olfactory OR2B2 Olfactory receptor Nielsen et al.

2005a
Williamson et al.
Olfactory OR4P4 Olfactory receptor
2007
Bakewell et al.
Olfactory OR10H3 Olfactory receptor 10H3
2007
Williamson et al.
Nutrition LCT Lactose metabolism
2007
Nuclear hormone receptor

Williamson et al.
Nutrition NR1H4 related to phenotypes including bile
2007
acid and lipoprotein
Nutrition SLC27A4 Uptake of fatty acids Voight et al. 2006
Pigmentation OCA2 Lightened skin Voight et al. 2006
Willamson et al.
Pigmentation ATRN Skin pigmentation
2007
Pigmentation TYRP1 Lightened skin Voight et al. 2006

[edit] References
• Andolfatto, P. (2005), Adaptive evolution in non-coding DNA in Drosophila, Nature, Vol. 437
pp. 1149–1152
• Bakewell, M., Shi, P., and Zhang, J. (2007), More genes underwent positive selection in
chimpanzee evolution than in human evolution, Proc. Natl. Acad. Sci. USA, Vol. 104 pp. 7489–7494
• Boyko, A.R., Williamson, S.H., Indap, A.R., Degenhardt, J.D., Hernandez, R.D., Lohmueller,
K.E., Adams, M.D., Schmidt, S., Sninsky, J.J., Sunyaev, S.R., White, T.J., Nielsen, R., Clark, A.G.,
and Bustamante, C.D. (2008), Assessing the evolutionary impact of amino acid mutations in the
human genome, PLoS Genetics, Vol. 4 pp. 1–13
• Bustamante, C., Fledel-Alon, A., Williamson, S., Nielsen, R., Hubisz, M.T., Glanowski, S.,
Tenenbaum, D.M., White, T.J., Sninsky, J.J., Hernandez, R.D., Civello, D., Adams, M.D., Cargill, M.,
and Clark, A.G. (2005), Natural selection on protein-coding genes in the human genome, Nature,
Vol. 437 pp. 1153–1156
• Chimpanzee Sequencing and Analysis Consortium (2005), Initial sequence of the
chimpanzee genome and comparison with the human genome, Nature, Vol. 437 pp. 69–87
• Crespi, B., Summers, K., Dorus, S. (2007), Adaptive evolution in the genes underlying
schizophrenia, Proceedings of the Royal Society B, Vol. 274 pp. 2801–2810
• Eyre-Walker, A. (2006), The genomic rate of adaptive evolution, Trends in Ecology and
Evolution, Vol. 21 pp. 569–575
• Eyre-Walker, A., and Keightley, P.D. (2009), Estimating the rate of adaptive molecular
evolution in the presence of slightly deleterious mutations and population size change, Molecular
Biology and Evolution, Vol. 26 pp. 2097–2108
• Eyre-Walker, A., and Keightley, P.D. (2007), The distribution of fitness effects of new
mutations, Nature Review Genetics, Vol. 8 pp. 610–618
• Fay, J.C., Wyckoff, G.J., and Wu, C. (2001), Positive and negative selection on the human
genome, Genetics, Vol. 158 pp. 1227–1234
• Galtier, N., and Duret, L. (2007), Adaption or bias gene conversion? Extending the null
hypothesis of molecular evolution, Trends in Genetics, Vol. 23 pp. 273–277
• Galtier, N., Piganeau, G., Mouchiroud, D., and Duret, L. (2001), GC-content evolution in
mammalian genomes: the biased gene conversion hypothesis, Genetics, Vol. 159 pp. 907–911
• Hawks, J., Wang, E.T., Cochran, G.M., Harpending, H.C., and Moyzsis, R.K. (2007), Recent
acceleration of human adaptive evolution, Proc. Natl. Acad. Sci. USA, Vol. 104 pp. 20753–20758
• Keightley, P.D., Lercher, M.J., Eyre-Walker, A. (2005), Evidence for widespread degradation
of gene control regions in hominid genomes, PloS Biology, Vol. 282-288
• Klein, R.G. (2009), Darwin and the recent African origin of modern humans, Proc. Natl. Acad.
Sci. USA, Vol. 106 pp. 16007–16009
• Klopfstein, S., Currat, M., and Excoffier, L. (2006), The fate of mutations surfing on the wave
of a range expansion, Molecular Biology and Evolution, Vol. 23 pp. 482–490
• Krause, J., Lalueza-Fox, C., Orlando, L., Enard, W., Green, R.E., Burbano, H.A., Hublin, J.,
Hanni, C., Fortea, J., de la Rasilla, M., Bertranpetit, J., Rosas, A., and Paabo S. (2007), The derived
FOXp2 variant of modern humans was shared with Neanderthals, Current Biology, Vol. 17 pp. 1908–
1912
• Lunter, G., Ponting, C., Hein, J. (2006), Genome-wide identification of human functional DNA
using a neutral indel model, PLoS Computational Biology, Vol. 2 pp. 2–12
• McDonald, J.H., and Kreitman, M. (1991), Adaptive protein evolution at the Adh locus in
Drosophila, Nature, Vol. 351 pp. 652–654
• Mekel-Bobrov, N., Gilbert, S.L., Evans, P.D., Vallender, E.J., Anderson, J.R., Hudson, R.R.,
Tishkoff, S.A., Lahn, B.T. (2009), Ongoing adaptive evolution of ASPM, a brain size determinant in
Homo sapiens, Science, Vol. 209 pp. 1720–1722
• Nielsen, R., Bustamante, C., Clark, A.G., Glanoski, S., Sackton, T.B., Hubisz, M.J., Fledel-
Alon, A., Tanenbaum, D.M., Civello, D., White, T.J., Sninsky, J.J., Adams, M.D., Cargill, M. (2005a),
A scan for positively selected genes in the genomes of humans and chimpanzees, PloS Biology, Vol.
3 pp. 976–985
• Nielsen, R., Williamson, S., and Kim, Y., Hubisz, M.J., Clark, A.G., and Bustamante, C.
(2005b), Genomic scans for selective sweeps using SNP data, Genome Research, Vol. 15 pp. 1566–
1575
• Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., and Clark, A.G. (2007), Recent and
ongoing selection in the human genome, Nature Review Genetics, Vol. 8 pp. 857–868
• Pollard, K.S., Salama, S.R, Kings, B., Kern, A.D., Dreszer, T., Katzman, S., Siepel, A.,
Pedersen, J.S., Bejerano, G., Baertsch, R., Rosenbloom, K.R., Kent, J., and Haussler, D. (2006),
Forces shaping the fastest evolving regions of the human genome, PLoS Genetics, Vol. 2 pp. 1599–
1611
• Ponting, C.P., and Lunter G. (2006), Signatures of adaptive evolution within human non-
coding sequence, Human Molecular Genetics, Vol. 15 pp. 170–175
• Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A.,
Mikkelsen, T.S., Altshuler, D., and Lander, E.S. (2006), Positive natural selection in the human
lineage, Science, Vol. 312 pp. 1614–1620
• Suzuki, Y., and Gojobori, T. (1999), A method for detecting positive selection at single amino
acid sites, Molecular Biology and Evolution, Vol. 16 pp. 1315–1328
• Swanson, W.J., and Vacquier, V.D. (2002), The rapid evolution of reproductive proteins,
Nature Review Genetics, Vol. 3 pp. 137–144
• Voight, B.F., Kudaravalli, S., Wen, X., and Pritchard J.K. (2006), A map of recent positive
selection in the human genome, PLoS Biology, Vol. 4 pp. 446–458
• Williamson, S.H., Hubisz, M.J., Clark, A.G., Payseur, B.A., Bustamante, C.D., and Nielsen,
R. (2007), Localizing recent adaptive evolution in the human genome, PLoS Genetics, Vol. 3 pp. 901–
915
• Yang, Z., and Bielawski, J.P. (2000), Statistical methods for detecting molecular evolution,
Trends in Ecology and Evolution, Vol. 15 pp. 496–503
• Zhang, L., and Li, W. (2005), Human SNPs reveal no evidence of frequent positive selection,
Molecular Biology and Evolution, Vol. 22 pp. 2504–2507
[edit] See also

Evolutionary biology portal
• Adaptation
• Adaptive radiation
• Co-adaptation
• Neutral theory of molecular evolution
Retrieved from "http://en.wikipedia.org/wiki/Adaptive_evolution_in_the_human_genome"
Categories: Evolutionary biology | Genetics | Mutation

W000
History of molecular evolution


The history of molecular evolution starts in the early 20th century with "comparative biochemistry",
but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular
biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based
sequence comparison, and to use the differences between homologous sequences as a molecular clock to
estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution
provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were
controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as
the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular
evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a
reconceptualization of the early history of life.
Contents
[hide]
• 1 Early history
• 1.1 Genetic load, the classical/balance controversy,
and the measurement of heterozygosity
• 1.2 Protein sequences and the molecular clock
• 2 The "molecular wars"
• 2.1 Gene-centered view of evolution
• 3 The neutral theory of molecular evolution
• 3.1 The neutralist-selectionist debate and near-
neutrality
• 4 Microbial phylogeny
• 5 Notes
• 6 References
[edit] Early history

Before the rise of molecular biology in the 1950s and 1960s, a small number of biologists had
explored the possibilities of using biochemical differences between species to study evolution. Ernest
Baldwin worked extensively on comparative biochemistry beginning in the 1930s, and Marcel Florkin
pioneered techniques for constructing phylogenies based on molecular and biochemical characters in the
1940s. However, it was not until the 1950s that biologists developed techniques for producing biochemical
data for the quantitative study of molecular evolution.[1]
The first molecular systematics research was based on immunological assays and protein
"fingerprinting" methods. Alan Boyden—building on immunological methods of G. H. F. Nuttall—developed
new techniques beginning in 1954, and in the early 1960s Curtis Williams and Morris Goodman used
immunological comparisons to study primate phylogeny. Others, such as Linus Pauling and his students,
applied newly developed combinations of electrophoresis and paper chromatography to proteins subject to
partial digestion by digestive enzymes to create unique two-dimensional patterns, allowing fine-grained
comparisons of homologous proteins.[2]
Beginning in the 1950s, a few naturalists also experimented with molecular approaches—notably
Ernst Mayr and Charles Sibley. While Mayr quickly soured on paper chromatography, Sibley successfully
applied electrophoresis to egg-white proteins to sort out problems in bird taxonomy, soon supplemented that
with DNA hybridization techniques—the beginning of a long career built on molecular systematics.[3]
While such early biochemical techniques found grudging acceptance in the evolutionary biology
community, for the most part they did not impact the main theoretical problems of evolution and population
genetics. This would change as molecular biology shed more light on the physical and chemical nature of
genes.
[edit] Genetic load, the classical/balance controversy, and the
measurement of heterozygosity
At the time that molecular biology was coming into its own in the 1950s, there was a long-running
debate—the classical/balance controversy—over the causes of heterosis, the increase in fitness observed
when inbred lines are crossed. In 1950, James F. Crow offered two different explanations (later dubbed the
classical and balance positions) based the paradox first articulated by J. B. S. Haldane in 1937: the effect of
deleterious mutations on the average fitness of a population depends only on the rate of mutations (not the
degree of harm caused by each mutation) because more-harmful mutations are eliminated more quickly by
natural selection, while less-harmful mutations remain in the population longer. H. J. Muller dubbed this
"genetic load".[4]
Muller, motivated by his concern about the effects of radiation on human populations, argued that
heterosis is primarily the result of deleterious homozygous recessive alleles, the effects of which are masked
when separate lines are crossed—this was the dominance hypothesis, part of what Dobzhansky labeled the
classical position. Thus, ionizing radiation and the resulting mutations produce considerable genetic load
even if death or disease does not occur in the exposed generation, and in the absence of mutation natural
selection will gradually increase the level of homozygosity. Bruce Wallace, working with J. C. King, used the
overdominance hypothesis to develop the balance position, which left a larger place for overdominance
(where the heterozygous state of a gene is more fit than the homozygous states). In that case, heterosis is
simply the result of the increased expression of heterozygote advantage. If overdominant loci are common,
then a high level of heterozygosity would result from natural selection, and mutation-induced radiation may in
fact facilitate an increase in fitness due to overdominance. (This was also the view of Dobzhansky.)[5]
Debate continued through 1950s, gradually becoming a central focus of population genetics. A 1958
study of Drosophila by Wallace suggested that radiation-induced mutations increased the viability of
previously homozygous flies, providing evidence for heterozygote advantage and the balance position;
Wallace estimated that 50% of loci in natural Drosophila populations were heterozygous. Motoo Kimura's
subsequent mathematical analyses reinforced what Crow had suggested in 1950: that even if overdominant
loci are rare, they could be responsible for a disproportionate amount of genetic variability. Accordingly,
Kimura and his mentor Crow came down on the side of the classical position. Further collaboration between
Crow and Kimura led to the infinite alleles model, which could be used to calculate the number of different
alleles expected in a population, based on population size, mutation rate, and whether the mutant alleles
were neutral, overdominant, or deleterious. Thus, the infinite alleles model offered a potential way to decide
between the classical and balance positions, if accurate values for the level of heterozygosity could be found.
[6]
By the mid-1960s, the techniques of biochemistry and molecular biology—in particular,
electrophoresis—provided a way to measure the level of heterozygosity in natural populations: a possible
means to resolve the classical/balance controversy. In 1963, Jack L. Hubby published an electrophoresis
study of protein variation in Drosophila[7]; soon after, Hubby began collaborating with Richard Lewontin to
apply Hubby's method to the classical/balance controversy by measuring the proportion of heterozygous loci
in natural populations. Their two landmark papers, published in 1966, established a significant level of
heterozygosity for Drosophila (12%, on average).[8] However, these findings proved difficult to interpret. Most
population geneticists (including Hubby and Lewontin) rejected the possibility of widespread neutral
mutations; explanations that did not involve selection were anathema to mainstream evolutionary biology.
Hubby and Lewontin also ruled out heterozygote advantage as the main cause because of the segregation
load it would entail, though critics argued that the findings actually fit well with overdominance hypothesis.[9]
[edit] Protein sequences and the molecular clock
While evolutionary biologists were tentatively branching out into molecular biology, molecular
biologists were rapidly turning their attention toward evolution.
After developing the fundamentals of protein sequencing with insulin between 1951 and 1955,
Frederick Sanger and his colleagues had published a limited interspecies comparison of the insulin
sequence in 1956. Francis Crick, Charles Sibley and others recognized the potential for using biological
sequences to construct phylogenies, though few such sequences were yet available. By the early 1960s,
techniques for protein sequencing had advanced to the point that direct comparison of homologous amino
acid sequences was feasible.[10] In 1961, Emanuel Margoliash and his collaborators completed the
sequence for horse cytochrome c (a longer and more widely distributed protein than insulin), followed in short
order by a number of other species.
In 1962, Linus Pauling and Emile Zuckerkandl proposed using the number of differences between
homologous protein sequences to estimate the time since divergence, an idea Zuckerkandl had conceived
around 1960 or 1961. This began with Pauling's long-time research focus, hemoglobin, which was being
sequenced by Walter Schroeder; the sequences not only supported the accepted vertebrate phylogeny, but
also the hypothesis (first proposed in 1957) that the different globin chains within a single organism could
also be traced to a common ancestral protein.[11] Between 1962 and 1965, Pauling and Zuckerkandl refined
and elaborated this idea, which they dubbed the molecular clock, and Emil L. Smith and Emanuel Margoliash
expanded the analysis to cytochrome c. Early molecular clock calculations agreed fairly well with established
divergence times based on paleontological evidence. However, the essential idea of the molecular clock—that
individual proteins evolve at a regular rate independent of a species' morphological evolution—was extremely
provocative (as Pauling and Zuckerkandl intended it to be).[12]
[edit] The "molecular wars"
From the early 1960s, molecular biology was increasingly seen as a threat to the traditional core of
evolutionary biology. Established evolutionary biologists—particularly Ernst Mayr, Theodosius Dobzhansky
and G. G. Simpson, three of the founders of the modern evolutionary synthesis of the 1930s and 1940s—were
extremely skeptical of molecular approaches, especially when it came to the connection (or lack thereof) to
natural selection. Molecular evolution in general—and the molecular clock in particular—offered little basis for
exploring evolutionary causation. According to the molecular clock hypothesis, proteins evolved essentially
independently of the environmentally determined forces of selection; this was sharply at odds with the
panselectionism prevalent at the time. Moreover, Pauling, Zuckerkandl, and other molecular biologists were
increasingly bold in asserting the significance of "informational macromolecules" (DNA, RNA and proteins)
for all biological processes, including evolution.[13] The struggle between evolutionary biologists and
molecular biologists—with each group holding up their discipline as the center of biology as a whole—was later
dubbed the "molecular wars" by Edward O. Wilson, who experienced firsthand the domination of his biology
department by young molecular biologists in the late 1950s and the 1960s.[14]
In 1961, Mayr began arguing for a clear distinction between functional biology (which considered
proximate causes and asked "how" questions) and evolutionary biology (which considered ultimate causes
and asked "why" questions)[15] He argued that both disciplines and individual scientists could be classified
on either the functional or evolutionary side, and that the two approaches to biology were complementary.
Mayr, Dobzhansky, Simpson and others used this distinction to argue for the continued relevance of
organismal biology, which was rapidly losing ground to molecular biology and related disciplines in the
competition for funding and university support.[16] It was in that context that Dobzhansky first published his
famous statement, "nothing in biology makes sense except in the light of evolution", in a 1964 paper affirming
the importance of organismal biology in the face of the molecular threat; Dobzhansky characterized the
molecular disciplines as "Cartesian" (reductionist) and organismal disciplines as "Darwinian".[17]
Mayr and Simpson attended many of the early conferences where molecular evolution was
discussed, critiquing what they saw as the overly simplistic approaches of the molecular clock. The molecular
clock, based on uniform rates of genetic change driven by random mutations and drift, seemed incompatible
with the varying rates of evolution and environmentally-driven adaptive processes (such as adaptive
radiation) that were among the key developments of the evolutionary synthesis. At the 1962 Wenner-Gren
conference, the 1964 Colloquium on the Evolution of Blood Proteins in Bruges, Belgium, and the 1964
Conference on Evolving Genes and Proteins at Rutgers University, they engaged directly with the molecular
biologists and biochemists, hoping to maintain the central place of Darwinian explanations in evolution as its
study spread to new fields.[18]
[edit] Gene-centered view of evolution

Though not directly related to molecular evolution, the mid-1960s also saw the rise of the gene-
centered view of evolution, spurred by George C. Williams's Adaptation and Natural Selection (1966). Debate
over units of selection, particularly the controversy over group selection, led to increased focus on individual
genes (rather than whole organisms or populations) as the theoretical basis for evolution. However, the
increased focus on genes did not mean a focus on molecular evolution; in fact, the adaptationism promoted
by Williams and other evolutionary theories further marginalized the apparently non-adaptive changes
studied by molecular evolutionists.
[edit] The neutral theory of molecular evolution

Further information: Neutral theory of molecular evolution
The intellectual threat of molecular evolution became more explicit in 1968, when Motoo Kimura
introduced the neutral theory of molecular evolution.[19] Based on the available molecular clock studies (of
hemoglobin from a wide variety of mammals, cytochrome c from mammals and birds, and triosephosphate
dehydrogenase from rabbits and cows), Kimura (assisted by Tomoko Ohta) calculated an average rate of
DNA substitution of one base pair change per 300 base pairs (encoding 100 amino acids) per 28 million
years. For mammal genomes, this indicated a substitution rate of one every 1.8 years, which would produce
an unsustainably high genetic load unless the preponderance of substitutions was selectively neutral. Kimura
argued that neutral mutations occur very frequently, a conclusion compatible with the results of the
electrophoretic studies of protein heterozygosity. Kimura also applied his earlier mathematical work on
genetic drift to explain how neutral mutations could come to fixation, even in the absence of natural selection;
he soon convinced James F. Crow of the potential power of neutral alleles and genetic drift as well.[20]
Kimura's theory—described only briefly in a letter to Nature—was followed shortly after with a more
substantial analysis by Jack L. King and Thomas H. Jukes—who titled their first paper on the subject "non-
Darwinian evolution".[21] Though King and Jukes produced much lower estimates of substitution rates and
the resulting genetic load in the case of non-neutral changes, they agreed that neutral mutations driven by
genetic drift were both real and significant. The fairly constant rates of evolution observed for individual
proteins was not easily explained without invoking neutral substitutions (though G. G. Simpson and Emil
Smith had tried). Jukes and King also found a strong correlation between the frequency of amino acids and
the number different of codons for each; this pointed to amino acid sequences as largely the product of
random genetic drift.[22]
King and Jukes' paper, especially with the provocative title, was seen as a direct challenge to
mainstream neo-Darwinism, and it brought molecular evolution and the neutral theory to the center of
evolutionary biology. It provided a mechanism for the molecular clock and a theoretical basis for exploring
deeper issues of molecular evolution, such as the relationship between rate of evolution and functional
importance. The rise of the neutral theory marked synthesis of evolutionary biology and molecular biology—
though an incomplete one.[23]
With their work on firmer theoretical footing, in 1971 Emile Zuckerkandl and other molecular
evolutionists founded the Journal of Molecular Evolution.
[edit] The neutralist-selectionist debate and near-neutrality

The critical responses to the neutral theory that soon appeared marked the beginning of the
neutralist-selectionist debate. In short, selectionists viewed natural selection as the primary or only cause of
evolution, even at the molecular level, while neutralists held that neutral mutations were widespread and that
genetic drift was a crucial factor in the evolution of proteins. Kimura became the most prominent defender of
the neutral theory—which would be his main focus for the rest of his career. With Ohta, he refocused his
arguments on the rate at which drift could fix new mutations in finite populations, the significance of constant
protein evolution rates, and the functional constraints on protein evolution that biochemists and molecular
biologists had described. Though Kimura had initially developed the neutral theory partly as an outgrowth of
the classical position within the classical/balance controversy (predicting high genetic load as a consequence
of non-neutral mutations), he gradually deemphasized his original argument that segregational load would be
impossibly high without neutral mutations (which many selectionists, and even fellow neutralists King and
Jukes, rejected).[24]
From the 1970s through the early 1980s, both selectionists and neutralists could explain the
observed high levels of heterozygosity in natural populations, by assuming different values for unknown
parameters. Early in the debate, Kimura's student Tomoko Ohta focused on the interaction between natural
selection and genetic drift, which was significant for mutations that were not strictly neutral, but nearly so. In
such cases, selection would compete with drift: most slightly deleterious mutations would be eliminated by
natural selection or chance; some would move to fixation through drift. The behavior of this type of mutation,
described by an equation that combined the mathematics of the neutral theory with classical models, became
the basis of Ohta's nearly neutral theory of molecular evolution.[25]
In 1973, Ohta published a short letter in Nature[26] suggesting that a wide variety of molecular
evidence supported the theory that most mutation events at the molecular level are slightly deleterious rather
than strictly neutral. Molecular evolutionists were finding that while rates of protein evolution (consistent with
the molecular clock) were fairly independent of generation time, rates of noncoding DNA divergence were
inversely proportional to generation time. Noting that population size is generally inversely proportional to
generation time, Tomoko Ohta proposed that most amino acid substitutions are slightly deleterious while
noncoding DNA substitutions are more neutral. In this case, the faster rate of neutral evolution in proteins
expected in small populations (due to genetic drift) is offset by longer generation times (and vice versa), but
in large populations with short generation times, noncoding DNA evolves faster while protein evolution is
retarded by selection (which is more significant than drift for large populations).[27]
Between then and the early 1990s, many studies of molecular evolution used a "shift model" in which
the negative effect on the fitness of a population due to deleterious mutations shifts back to an original value
when a mutation reaches fixation. In the early 1990s, Ohta developed a "fixed model" that included both
beneficial and deleterious mutations, so that no artificial "shift" of overall population fitness was necessary.
[28] According to Ohta, however, the nearly neutral theory largely fell out of favor in the late 1980s, because
the mathematically simpler neutral theory for the widespread molecular systematics research that flourished
after the advent of rapid DNA sequencing. As more detailed systematics studies started to compare the
evolution of genome regions subject to strong selection versus weaker selection in the 1990s, the nearly
neutral theory and the interaction between selection and drift have once again become an important focus of
research.[29]
[edit] Microbial phylogeny

While early work in molecular evolution focused on readily sequenced proteins and relatively recent
evolutionary history, by the late 1960s some molecular biologists were pushing further toward the base of the
tree of life by studying highly conserved nucleic acid sequences. Carl Woese, a molecular biologist whose
earlier work was on the genetic code and its origin, began using small subunit ribosomal RNA to reclassify
bacteria by genetic (rather than morphological) similarity. Work proceeded slowly at first, but accelerated as
new sequencing methods were developed in the 1970s and 1980s. By 1977, Woese and George Fox
announced that some bacteria, such as methanogens, lacked the rRNA units that Woese's phylogenetic
studies were based on; they argued that these organisms were actually distinct enough from conventional
bacteria and the so-called higher organisms to form their own kingdom, which they called archaebacteria.
Though controversial at first (and challenged again in the late 1990s), Woese's work became the basis of the
modern three-domain system of Archaea, Bacteria, and Eukarya (replacing the five-domain system that had
emerged in the 1960s).[30]
Work on microbial phylogeny also brought molecular evolution closer to cell biology and origin of life
research. The differences between archaea pointed to the importance of RNA in the early history of life. In his
work with the genetic code, Woese had suggested RNA-based life had preceded the current forms of DNA-
based life, as had several others before him—an idea that Walter Gilbert would later call the "RNA world". In
many cases, genomics research in the 1990s produced phylogenies contradicting the rRNA-based results,
leading to the recognition of widespread lateral gene transfer across distinct taxa. Combined with the
probable endosymbiotic origin of organelle-filled eukarya, this pointed to a far more complex picture of the
origin and early history of life, one which might not be describable in the traditional terms of common
ancestry.[31]
[edit] Notes
1. ^ Dietrich, "Paradox and Persuasion", pp. 90-91; Zuckerkandl, "On the Molecular
Evolutionary Clock", p. 34
2. ^ Dietrich, "Paradox and Persuasion", pp. 90-91; Morgan, "Emile Zuckerkandl, Linus Pauling,
and the Molecular Evolutionary Clock", pp. 161-162.
3. ^ Hagen, "Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution", pp.
335-339
4. ^ Dietrich, "The Origins of the Neutral Theory of Molecular Evolution", pp. 25-28
7. ^ Hubby J. L. (1963). "Protein Differences in Drosophila. I. Drosophila melanogaster".
Genetics 48 (6): 871–879. PMID 17248176.
8. ^ Hubby, J. L.; Lewontin, R. C. (1966). "A Molecular Approach to the Study of Genic
Heterozygosity in Natural Populations. I. The Number of Alleles at Different Loci in Drosophila
pseudoobscura". Genetics 54: 546–595. ; and Lewontin, R. C.; Hubby, J. L. (1966). "A Molecular
Approach to the Study of Genic Heterozygosity in Natural Populations. II. Amount of Variation and
Degree of Heterozygosity in Natural Populations of Drosophila pseudoobscura". Genetics 54 (2):
595–609. PMID 5968643.
10.^ Hagen, "Naturalists, Molecular Biologists, and the Challenge of Molecular Evolution", pp.
323-325
11.^ Zuckerkandl, "On the Molecular Evolutionary Clock", pp. 34-35
12.^ Dietrich, "Paradox and Persuasion", pp. 91-94
14.^ Wilson, Naturalist, pp. 219-237
15.^ Mayr's first published argument for the proximate/ultimate distinction was: Mayr Ernst
(1961). "Cause and Effect in Biology". Science 134: 1501–1506. PMID 14471768.
16.^ Hagen, "Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution", pp.
333-335
17.^ Dietrich, "Paradox and Persuation", pp. 100-103. Dobzhansky's famous phrase appears in
the first page of: Theodosius Dobzhansky, "Biology, Molecular and Organismic", American Zoologist,
volume 4 (1964), pp 443-452.
18.^ Dietrich, "Paradox and Persuation", pp. 95-98; Hagen, "Naturalists, Molecular Biologists,
and the Challenges of Molecular Evolution", pp. 330-332
19.^ Motoo Kimura, [Evolutionary Rate at the Molecular Level", Nature, Vol. 217 (1968), pp.
624-626
20.^ Dietrich, "The Origins of the Neutral Theory of Molecular Evolution", pp. 46-50
21.^ King, Jack L.; Jukes, Thomas (1969). "Non-Darwinian Evolution". Science 164 (881): 788–
798. doi:10.1126/science.164.3881.788. PMID 5767777.
23.^ Dietrich, "The Origins of the Neutral Theory of Molecular Evolution", pp. 54, 57-58
25.^ Ohta, "The current significance and standing of neutral and nearly neutral theories", pp.
673-674
26.^ Ohta, Tomoko (1973-11-09). "Slightly Deleterious Mutant Substitutions in Evolution".
Nature 246 (5428): 96–98. doi:10.1038/246096a0. PMID 4585855.
27.^ Ohta, Tomoko; John H. Gillespie (1996-04). "Development of Neutral and Nearly Neutral
Theories". Theoretical Population Biology 49 (2): 128–42. doi:10.1006/tpbi.1996.0007.
PMID 8813019. , pp 130-131
28.^ Ohta and Gillispie, "Development of Neutral and Nearly Neutral Theories", pp. 135-136
29.^ Ohta, "The current significance and standing of neutral and nearly neutral theories", p. 674
30.^ Sapp, Genesis, pp. 224-228
[edit] References
• Dietrich, Michael R. "The Origins of the Neutral Theory of Molecular Evolution." Journal of
the History of Biology, Vol. 27, No. 1 (Spring 1994), pp 21–59
• Dietrich, Michael R. (1998). "Paradox and Persuasion: Negotiating the Place of Molecular
Evolution within Evolutionary Biology". Journal of the History of Biology 31 (1): 85–111.
doi:10.1023/A:1004257523100. PMID 11619919.
• Crow, James F. "Motoo Kimura, 13 November 1924 - 13 November 1994." Biographical
Memoirs of Fellows of the Royal Society, Vol. 43 (November 1997), pp 254–265
• Hagen, Joel B. (1999). "Naturalists, Molecular Biologists, and the Challenge of Molecular
Evolution". Journal of the History of Biology 32 (2): 321–341. doi:10.1023/A:1004660202226.
PMID 11624208.
• Kreitman, Martin. "The neutralist-selectionist debate: The neutral theory is dead. Long live
the neutral theory", BioEssays, Vol. 18, No. 8 (1996), pp. 678–684
• Morgan, Gregory J. (1998). "Emile Zuckerkandl, Linus Pauling, and the Molecular
Evolutionary Clock, 1959-1965". Journal of the History of Biology 31 (2): 155–178.
doi:10.1023/A:1004394418084. PMID 11620303.
• Ohta, Tomoko. "The neutralist-selectionist debate: The current significance and standing of
neutral and nearly neutral theories", BioEssays, Vol. 18, No. 8 (1996), pp. 673–677
• Sapp, Jan. Genesis: The Evolution of Biology. New York: Oxford University Press, 2003.
ISBN 0-19-515618-8
• Wilson, Edward O. Naturalist. Warner Books, 1994. ISBN 0-446-67199-1
• Zuckerkandl, Emile (1987). "On the Molecular Evolutionary Clock". Journal of Molecular
Evolution 26 (1-2): 34–46. doi:10.1007/BF02111280. PMID 3125336.

• Perspectives on Molecular Evolution - maintained by historian of science Michael R. Dietrich
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W000
Dawkins vs. Gould


Dawkins vs. Gould
First edition cover
Author Kim Sterelny
Subject(s) Evolutionary biology, philosophy of biology
Publisher Icon Books
Publication date 2007
Pages 205
ISBN ISBN 1-84046-780-0 ISBN 978-1840467-80-2
OCLC Number 76936307
Preceded by Thought in a Hostile World: The evolution of human cognition (2003)

Followed by What is Biodiversity (2008)
Dawkins vs. Gould: Survival of the Fittest is a book by philosopher of biology Kim Sterelny about the
differing views of biologists Richard Dawkins and Stephen Jay Gould. When first published in 2001 it became
an international bestseller. A new edition was published in 2007 to include Gould's The Structure of
Evolutionary Theory finished shortly before his death in 2002, and more recent works by Dawkins. The
synopsis below is from the 2007 publication.[1]
Contents
[hide]
• 1 Synopsis
• 1.1 Part I - Battle Joined
• 1.2 Part II - Dawkins' World
• 1.3 Part III - The View from Harvard
• 1.4 Part IV - The State of Play
• 1.5 Suggested Reading
• 2 See also
• 3 Notes
• 4 References
[edit] Synopsis
[edit] Part I - Battle Joined
In the introductory chapter the author points out that there have been many conflicts in biology. Still,
few have been as public or as polemical as the one between Dawkins and Gould. Dawkins sees evolution as
a competition between gene lineages, where organisms are vehicles for those genes. Gould, a paleontologist
in the tradition of George Gaylord Simpson, has a different perspective. For example, he sees chance as
very important, and views organisms as being more important than genes. Their broader world views also
differ, for instance they have very different beliefs about the relationship between religion and science.
[edit] Part II - Dawkins' World

This begins with a discussion on genes and gene lineages (chapter 2). Dawkins' view on the nature
of evolution, as outlined in The Selfish Gene, has genes as the units of selection, both in the first replicators
and in more complex organisms, where alliances of genes are formed (and sometimes broken). He then
discusses in chapter 3, Dawkins' view of heritability, with genes as difference makers that satisfy replicator
principles and have phenotypic power, increasing the likelihood of phenotypic expression, depending on
environmental context. In chapter 4, he discusses aspects of genomes and genetic replication, using various
examples. He notes that in a story about magpie aggression, "Dawkins' story will be about genes and
vehicles", whereas Gould and others will describe it in terms of phenotypic fitness(p. 39). He discusses ways
in which genes "lever their way into the next generation", including genes which are loners, or 'Outlaws', and
which promote their own replication at the expense of other genes in their organism's genome. He then
discusses the role of extended phenotypes, in which genotypes that influence their environment further
increase the like likelihood of replication (chapter 4). Chapter 5 explores selfish genes and the selection
within the animal kingdom of cooperation as opposed to altruism, levels of selection, and the evolution of
evolvability itself. Sterelny notes that on the issue of high-level selection, "Dawkins and Gould are less sharp
than they once were" (p. 65).
In chapter 6, Sterelny notes that "despite the heat of some recent rhetoric, the same is true of the role
of selection in generating evolutionary change"(p. 67), and naive adaptationism. "Everyone accepts that
many characteristics of organisms are not the direct result of selection", as in the example of redness of
blood, which is a by-product of its oxygen-carrying properties (p. 70). Numerous general truths are
uncontroversial "though their application to particular cases may be. Nor is there disagreement between
Gould and Dawkins on core cases", such as echolocation in bats, which "everyone agrees is an adaptation"
(p. 71). They do however differ on the relative role of selection and variation. For example, they have different
emphases on development. Developmental constraints are fundamental to Gould's approach. Dawkins gives
this less weight, and has been more interested in enhanced possibilities open to lineages as a result of
developmental revolutions. For example, the evolution of segmentation increases variation possibilities. He
discusses this in Climbing Mount Improbable, and "returns to similar themes at the end of The Ancestor's
Tale: major transitions in evolution are developmental transitions, transitions which make new variants
possible, and hence new adaptive complexes possible" (pp. 77–78).
"Gould, on the other hand, is inclined to bet that the array of possibilities open to a lineage is tightly
restricted, often to minor variants of its current state" (p. 78). Gould sees morphological stability as "probably
explained by constraints on the supply of variation to selection" (p. 78). But whereas in his earlier work Gould
considered variation supply as a brake on evolutionary change, in The Structure of Evolutionary Theory he
carefully notes that it can also enhance possibilities for change. "So while both Dawkins and Gould recognise
the central role of developmental biology in an explanation of evolutionary change, they make different bets
as to what the role will be. Gould but not Dawkins thinks that one of these roles is as a brake", damping down
change possibilities (p. 78). Another difference is Dawkins conception of evolutionary biology's central
problem as the explanation of adaptive complexity, whereas Gould has largely focused on the existence of
large-scale patterns in the history of life which are not explained by natural selection. "A further disagreement
concerns the existence and importance of these patterns" (p. 79), which leads on to Part III.
[edit] Part III - The View from Harvard

In discussing Gould's perspective, Sterelny begins with two fundamental distinctions which Gould
saw between his viewpoint and that of the Dawkins camp. Firstly, Gould thought that gene selectionists
misrepresent the role of genes in microevolution, ascribing a causal role in evolution, rather than by-product
record of evolutionary change. Moreover, evolutionary biologists have often neglected non-selective
possibilities when formulating hypotheses about microevolutionary change. For example, contemporary sex
differences in human males and females need not be adaptations, but could be evolutionary vestiges of a
greater sexual dimorphism in ancestral species.
But Gould's main target is 'extrapolationism', concerning the relationship between evolutionary
processes occurring within species and those of large-scale life histories. In this view, the evolution of
species lineages is an aggregate of events at the local population scale, with major changes being the
additive result of minor changes over successive generations. While not disputing the relevance of this,
Gould argued that it is not the whole truth. "Indeed, it is not much of an exaggeration to say that Gould's
professional life has been one long campaign against the idea that this history of life is nothing but the long,
long accumulation of local events" (p. 86). Sterelny offers four highlights to illustrate this.
Firstly, punctuated equilibrium, in which new species arise by a split in a parental species, followed
by geologically rapid speciation of one or both of the fragments. A period of stasis then occurs until the
species either becomes extinct or splits again. Gould argued that punctuated equilibrium challenges the
gradual change expected by extrapolationists. In the case of Hominid evolution, and the evolutionary trend of
marked increase in brain size. To Gould, this trend was the result of species sorting, in which species with
relatively larger brains were more likely to appear, or to survive.
Secondly, in his Natural History writings, Gould often argued that the history of life was profoundly
affected by mass extinctions caused by environmental catastrophes such as an asteroid impact causing the
Cretaceous/Tertiary extinction which wiped out pterosaurs, large marine reptiles and non-avian dinosaurs 65
million years ago. Such a mass extinction would be sudden at not just the larger geological time-scale, but
also the more ephemeral ecological one. "The properties that are visible to selection and evolution in local
populations - the extent to which an organism is suited to life here and now" become irrelevant to survival
prospects in mass extinction times. "Survival or extinction in mass extinction episodes determines the large-
scale shape of the tree of life". Massive culling of synapsids at the end of the Permian "gave the dinosaurs
their chance. The death of the dinosaurs opened the door for the radiation of mammals" (p. 89).
Thirdly, in Wonderful Life, Gould descries the Burgess Shale fauna, which is known in detail due to
fortuitous preservation of both hard and soft tissue around 505 million years ago. Gould argues that the
Burgess Shale fauna demonstrate both diversity of species and disparity of body plans. He accepts that
diversity has probably increased over the last few million years, but argues that disparity of animal life
peaked early in evolutionary history, with very little disparity generated since the Cambrian, and profound
conservatism in surviving lineages. For example, despite diversity in beetle species their body plans follow
the same general pattern. He argues that survival has been contingent, and that if the tape of life was
replayed from the earliest Cambrian, with small alterations in the initial conditions, a different set of survivors
may have evolved.
Fourth, in The Spread of Excellence, "Gould argues that evolutionary trends are not the scaled-up
consequences of competitive interactions among organisms" (p. 90). For example, morphological changes in
horses are not the cumulative result of the competitive success of horses better adapted to grazing. "Rather,
Gould argues that this trend is really a change in the spread of variation within the horse lineage", which used
to be species rich with a wide range of lifestyles and sizes. "But only a very few species survived, and those
few happen to be largish horses. The average horse is larger now only because almost all horse species
went extinct, and the few survivors happened to be somewhat atypical", and there is no evolutionary 'trend'
towards increased size (p. 91). Similarly with complexity. While complexity has increased over time, it is
misleading to see this simply as a trend towards increased complexity, from simple organisms such as
bacteria to complex organisms such as us. Rather, the distance from the least to the most complex living
organism has increased. "The real phenomenon to be explained is this increase in variation rather than an
upward trend in average complexity. There is, Gould argues, no such trend" (p. 92).
Sterelny notes two issues arising from consideration of Gould's case against extrapolationism. "Are
the patterns in life's history that he claims to detect real? And do these patterns really show the existence of
evolutionary mechanisms other than those operating at the scale of local populations?" (p. 92).
Sterelny then outlines in chapter 8 Gould and Eldredge's punctuated equilibrium hypothesis. They
argued that the appearance of stability in species evolution is not a mere effect of the gappiness and
impperfection of the fossil record. Rather, it is the result of discontinuous tempos of change in the process of
speciation and the deployment of species in geological time. Sterelny notes that this hypothesis has been
misunderstood in two important ways. First, in some early discussions of the idea, the contrast between
geological and ecological time was blurred, with Gould and Eldredge interpreted as claiming that species
originate more or less overnight in a single step. However, Gould and Eldredge were referring to geological
time, in which speciation taking 50,000 years would seem instantaneous relative to a species existence over
millions of years. A second misunderstanding relates to further evolutionary change following speciation.
They are not claiming that there is no generational change at all. "Lineages do change. But the change
between generations does not accumulate. Instead, over time, the species wobbles about its phenotypic
mean. Jonathan Weiner's The Beak of the Finch describes this very process" (p. 96). Sterelny notes that
despite the fact that the fossil record represents, for several reasons, a biased sample, "the consensus
seems to be shifting Gould's way: the punctuated equilibrium pattern is common, perhaps even
predominant". Yet even if stasis is common "why suppose that this is bad news for the extrapolationist
orthodoxy?" (p. 97). He notes that "the problem is not stasis but speciation. How can events in a local
population generate a new species?" (p. 98). In discussing this issue, he notes "any solution to the speciation
problemwill take us beyond events in local populations observable on human timescales", and "it is likely that
whatever explains the occasional transformation of a population into a species will rely on large-scale but
rare climactic, biological, geographic or geological events; events which isolate populations until local change
is entrenched" (p. 99).[a] He notes that speciation is not just the accumulation of events in a local population,
but dependant the population's embeddedness into a larger whole. "There is a break with a strong version of
extrapolationism, but it is not a radical break. Dawkins could, should, and probably would accept it; in The
Ancestor's Tale, he has an inclusive view of speciation mechanisms" (p. 100). Thus, while "Gould somewhat
overstates the adherence of orthodoxy to strict extrapolationism", punctuated equilibrium is more important
than some of the more "ungenerous treatment" that has been meted out (pp. 100–101).
In chapter 9, Sterelny discusses mass extinction, and notes Gould's hypothesis that mass extinctions
are more frequent, rapid, intense and different in their effects than has been supposed (p. 108). Moreover,
Gould argues that during such extinctions, there are evolutionary principles that would enable the prediction
of winners and losers. "The game has rules. But they are different rules from those of normal times...Species
survival is not random, but the properties on which survival depends are not adaptations to the danger mass
extinction threatens. If a meteor impact caused a nuclear winter, then the ability to lie dormant would have
improved your chances. But dormancy is not an adaptation to the danger of meteor impacts" (p. 110).
Similarly, "species with broad geographical ranges, species with broad habitat tolerances, species whose
lifecycle does not tie them too closely to a particular type of community all would have had a better chance of
making it" (p. 110), and this amounts to species selection. However as Gould concedes, there are no well-
worked-out case studies. "In short, Gould's case for the importance of mass extinction depends n the view
that there is a qualitative difference between mass extinction and background extinction, and that major
groups have disappeared that would otherwise have survived". (p. 113). A plausible but difficult to prove
claim, as is the claim that mass extinction regimes are species selection regimes.
In chapter 10, Sterelny discusses the fossil evidence of Cambrian fauna, and how this provides the
basis for Gould's challenge to gradualistic orthodoxy. About 543 million years ago, at the base of the
Cambrian, the Ediacaran fauna, characterised by small shelly fossils, fossilised tracks, and burrows,
apparently disappeared. From available evidence, diversity of fauna was very limited at the beginning of the
Cambrian Period. "By the middle of the Cambrian, about 520 million years ago, animal life was rich and
diverse" (p. 116), as demonstrated by the Maotianshan Shales fossils, in Chengjiang, China, which "are as
spectacular as the Burgess Shale fauna, and significantly older" (p. 116). "Thus the fossil record seems to
show that most of the major animal groups appeared simulatenously. In the 'Cambrian explosion', we find
segmented worms, velvet worms, starfish and their allies, molluscs (bivalves, snails, squid and their
relatives), sponges, brachiopods and other shelled animals appearing all at once, with their basic
organisation, organ systems and sensory mechanisms already operational" (p. 116). "This explosive
evolutionary radiation of the Cambrian seems to be unique. Plants seem to have arisen somewhat more
gradually...nor was there a similar radiation when animals invaded the land...the colonisation of the land saw
no new ways of making an animal" (p. 117). Despite adaptations, the basic body plans remain recognisable.
One possibility is that the 'Cambrian explosion' is "an illusion generated by the failure of earlier Precambrian
fossils to survive to our times," (p. 117) that there is a long history of hidden evolution preceding the
appearance of multi-celled animals in the fossil record. "This remains a live option. There are fossil embryos
of animals from China dating to about 570 million years ago" (p. 120), and there are many animal lineages for
which there is no fossil record, possibly due to being small and soft-bodied, so leaving no detectable traces.
Certainly Precambrian animal life is evidenced by the Ediacaran fossils, but the relationship between fauna
from these two periods remains unclear. Gould was inclined to support the view that the Ediacaran fauna
became wholly extinct prior to the Cambrian, thus were not Cambrian ancestors, "hence their existence does
not extend the timeframe f animal evolution into the Precambrian." (p. 120).
However, the development of methods of calibrating rates of change in DNA sequences has given
the ability to estimate the last common ancestor of various lineages. It also allows the obtaining of molecular
clock dates for lineages without a fossil record, which shows that zero-fossil phyla are also ancient. Such
information comes with important caveats in relation to methodology, including the underlying assumptions of
each method. "However, even the youngest dates from molecular clocks place the origins of the deepest
branches in the tree of animal life - where the sponges and jellyfish branch off from the other early animals -
over 600 million years ago, and so quite deep in the Precambrian." (p. 125). Gould accepted this, but noted
that this does not negate the Cambrian Explosion. Molecular clocks date origins, while fossils date
geographical spread and morphology. Molecular clock data cannot decide between gradual morphological
change and rapid evolutionary bursts after initial species divergence. "Moreover, Gould argues that the fossil
record supports the model in which the lineage splits much earlier than the distinctive morphologies evolve.
For that explains why we find no Precambrian proto-arthropod fossils. In short, the 'hidden history' hypothesis
remains an open option, but so does Gould's guess that the Cambrian explosion was genuinely explosive
rather than an illusion generated by incomplete preservation." (pp. 125–126).
Of relevance to the explosive radiation hypothesis are the findings from the Cambrian sites: the
Burgess (~505 myr), the Chengjiang (~522 myr), and the Sirius Passet formation in Greenland, which is
dated at about 518 million years Before Present. Sterelny describes the distinction between disparity and
diversity, and then explores Gould's claim that since the Cambrian, diversity has increased, but disparity has
decreased. Since the Cambrian, not just species within phyla, but whole phyla themselves have become
extinct. The major subdivisions of animal life are phyla, each of which is a distinctive way of building an
animal. Gould's claim is that "the Cambrian phylum count was larger, maybe much larger, than the
contemporary count. No new phyla have appeared, and many have gone. That count, in turn, is a reasonable
measure of disparity. So Cambrian disparity was considerably larger than current disparity. The history of
animal life is not a history of gradually increasing differentiation. It is a history of exuberant initial proliferation
followed by much loss; perhaps sudden loss" (p. 129). Gould doubted that selection played much role in
either the early burst of disparity, the post-Cambrian conservativeness of evolution, or the roster of loss and
survival.
To Gould, there is a conservative pattern of history indicated by a reduction in disparity as measured
by both the lack of new body plans and the lack of any major modifications of old ones. Given that evolution
in general has not ceased in the past 500 million years, this poses a number of questions. However, Dawkins
and more so his former student Mark Ridley think Gould's basic claim about history's pattern is incorrect.
Central to Ridley's approach is cladistics, in which the purpose of biological systematics is to discover and
represent genealogical relationships between species. Biological classifications are thus evolutionary
genealogies, where only monophyletic groups (e.g. genera, families, orders, classes, phyla) are recognised
and named. To cladists, similarity and dissimilarity are not objective features of the living world; they are
products of human perceptions. Thus, whereas some morphological and physiological differences are more
salient to us, and more striking or surprising, this is a fact about us, not the history of life. Conversely,
genealogical reconstructions - who is related to whom - are objective facts independent of the observer's
perception. Sterelny discusses how both cladists and Dawkins think that Gould overestimates Cambrian
disparity, and he notes that while the distinction between disparity and diversity is very plausible, in the
absence of a good account of the nature of disparity, and objective measures, "the existence of Gould's
puzzling pattern remains conjectural" (p. 141).
Finally, in chapter 11, Sterelny discusses the "evolutionary escalator", or the tendency over time for
life on earth to show a progressive increase both in compexity and adaptivity. While Gould does not outright
reject this, he thinks it is a misleading way to think about the history of life. As above, with the example of
horses, Gould argues that there has been no directional trend, but rather, a massive extinction in the horse
lineage, with the surviving remnants happening to be largish grazers. So the appearance of a trend is
generated by a reduction in heterogeneity. "A trend which is hostage to one switch between life and death is
no trend at all" (p. 146). At the scale of complexity, the same applies. "What we think of as a progressive
increase in complexity is a change in the difference between the least and the most complex organism. It is a
change in the spread of complexity" (p. 146). Life starts in the simplest form that the constraints of chemistry
and physics will allow, with bacteria probably close to that limit. "So life starts at the minimum level of
complexity. Since even now nearly everything that is alive is a bacterium, for the most part life has stayed
that way" (p. 146). But occasionally life builds a lineage that becomes more complex over time. There are no
global evolutionary mechanisms that either prevent more complex organisms evolving from simpler ones, or
that make it more likely to occur. Complexity tends to drift up because the point of life's origin is close to the
physical lower bound. Such complex creatures are relatively less than bacteria, which still dominate life, but
the difference between the simplest and most complex organisms tends to become greater over time. So the
increased range is wholly undirected. Displayed as a frequency distribution curve or histogram, the shape
would be skewed to the right (i.e. positively skewed), with the mode near the left. Over time, the range would
increase as average complexity drifts upwards. But the mode would remain at left, with the curve spreading
to the right, because there is a wall imposed by the laws of the physical sciences to the left, but not to the
right.
To Gould, this upward drift in complexity is not the same as directional progress. 'Replaying the tape'
of life's history would not guarantee the same outcomes, especially as mass extinction events make history
utterly unpredictable. Conversely, Dawkins and Simon Conway Morris think that the course of evolutionary
history is more predictable than does Gould. They argue that "convergent evolution is such a ubiquitous
feature of evolution that the broad outline of evolution is highly predictable. Evolutionary pathways are
constrained by both opportunity and possibility. There are not many ways of building working organisms, and
so we can predict that evolution will move along this small set of pathways. Many of the most distinctive
features of living systems have evolved more than once. Some of them (like eyes) have evolved many times'
(p. 149). Also, Dawkins thinks that evolution is progressive, not in an anthropocentric sense, but because
over time life is becoming better adapted, although not in every aspect, as when local conditions change and
organisms must move or readapt. "There is no reason to suppose that there is any arrow of overall
improvement here" (p. 150).
However, Dawkins thinks that relationships between organisms and their enemies, such as predator-
prey, or parasite-host relationships, are locked into a permanent arms race, and such lineages generate
progressive change. "Both predator and prey will become absolutely more efficient in hunting and avoiding
hunters, though their relative success with respect to one another may not change at all over time" (p. 151).
Thus progress is real though partial and intermittent. "Partial because it is generated only when selective
regimes are both directional and stable: selecting for the same kind of phenotypic change over long periods,
as in arms races...intermittent because every arms race will ultimately be disrupted by large-scale
environmental changes" (p. 151). However, while they were in progress, each lineage was objectively
improving.
To Sterelny, Gould overstates his case, and "there is more to the history of life's complexity than a
gradual increase in variance" (p. 151). He cites the 1995 work The Major Transitions in Evolution by John
Maynard Smith and Eors Szathmary, in which life's history involves a series of major transitions and hence
inherent directionality, with each transition facilitating possibilities for the evolution of more complex
organisms. Dawkins pursues a similar, though less detailed, argument*[2] in discussing the evolution of
evolvability, in which a series of 'watershed events' make new life forms possible. These watersheds in
evolvability comprise the evolution of sex, of multi-celled life together with a life cycle that takes large
organisms through a single-celled reproduction stage, and the evolution of a modular mode of the
development and construction of bodies. "Segmentation, for Dawkins, is a special case of modularity; of
building a creature out of relatively discrete chunks. For once a chunk has been invented by evolution, it can
be modified or redeployed without stuffing up the rest of the organism" (p. 152).
While Gould too is interested in evolvability, the crucial difference between Gould's view, and that of
Maynard Smith, Szathmary and Dawkins, is in how they see the spread of complexity. To Gould, complexity
drifts upward, having a lower boundary or wall to the left, "but no upper bound, and these features of
complexity are fixed by biochemistry, not the course of evolutionary history" (p. 153). Maynard Smith and
Szathmary consider that evolutionary history has had upper bounds, or walls to the right. For example, until
eukaryotic life evolved, there was an upper bound of complexity set by the intrinsic limits on the size and
structural complexity of prokaryotes, and for "perhaps 2 billion years, bacterial evolution ws confined between
these two limits" (p. 153). Similarly, until a series of evolutionary innovations facilitated the evolution of multi-
celled organisms, eukaryotic complexity was set by the limits on a single eukaryotic cell. "Maynard Smith and
Szathmary argue that social existence, too, has evolutionary preconditions. Until these are met, a wall
remains to the right" (p. 153). Whereas to Gould, there are unchanging boundaries set by physics and
chemistry, Maynard Smith, Szathmary and Dawkins view evolution as irreversibly transforming these
boundaries. "The eukaryotic cell, sexual reproduction and cellular differentiation all change the nature of
evolutionary possibility. These possibilities have changed over time in a direction that increases the
maximum attainable complexity. In short, over time the rules of evolution change" (pp. 153–154). So
evolvability has changed, with developmental mechanisms determining the variation available to selection.
Gould claims that bacteria dominate every age, including this one.*[3] They are the world's most numerous
organisms, have the most disparate metabolic pathways, and may constitute most of the world's biomass.
"All this is true and important", with Dawkins making similar observations.*[4] "But it is not the whole truth. We
live in an age in which many biological structures are now possible that were once not possible. That too is
true, and important" (p. 153).
[edit] Part IV - The State of Play

In Chapter 12, Sterelny notes that "Dawkins and his allies really do have a different conception of
evolution from that embraced by Eldredge, Lewontin and other collaborators of Gould", but that this does not
explain the undercurrent of hostility generated in the debate, as illustrated by a series of exchanges in the
New York Review of Books. But the issues pertain mostly to matters internal to evolutionary theory, and apart
from banal psychological explanations pertaining to human reaction to public criticism, Sterelny thinks that at
core is their different attitudes to science itself. To Dawkins, science is not just a light in the dark, but "by far
our best, and perhaps our only, light" (p. 158). While not infallible, the natural sciences are society's one
great engine for producing objective knowledge about the world, not just one knowledge system among
many, and certainly not a socially constructed reflection of contemporary dominant ideology. Dawkins
accepts that science cannot say what we should accept and reject, "but does not think of values as a special
kind of fact that can be studied non-scientifically", notwithstanding that values are a kind of fact that
anthropologists can and do study. "Least of all does he think religion has any special authority on values"
(p. 158).
Gould's perspective is more ambiguous, in which some important questions are outside the scope of
science, falling into the domain of religion. "On this issue, Dawkins' views are simple. He is an atheist.
Theisms of all varieties are just bad ideas about how the world works, and science can prove that those ideas
are bad. What is worse, as he sees it, these bad ideas have mostly had socially unfortunate consequences"
(pp. 158–159). In contrast, Gould thought theism is irrelevant to religion. "He interprets religion as a system of
moral belief. Its essential feature is that it makes moral claims on how we ought to live. In Gould's view,
science is irrelevant to moral claims. Science and religion are concerned with independent domains" (p. 159).
Sterelny considers Gould's views on religion "doubly strange" (p. 159). First, various religions make
innumerable factual claims about the history of the world and how it works, and those claims are often the
basis of moral injunctions. Second, Gould's conception of ethics seems strange. "Does he think that there are
genuine ethical truths? Is there genuine moral knowledge?" (p. 159). Recent ethical thinking has two
approaches to this question, with perhaps the main contemporary argument being the 'expressivist' view that
moral claims express the speaker's attitude towards some act or individual. In this view "when, for instance, I
call someone a scumbag, I do not describe a particular moral property of that person. Rather, I express my
distaste for that person and their doings" (pp. 159–160). The main alternative is 'naturalism', in which moral
claims are based on facts, albeit complex, about human welfare. Gould seems to deny both options. "If
'expressivism' is right, there is no independent domain of moral knowledge to which religion contributes", with
moral utterances reflecting not objective features of the world, but attitudes and opinions of the speakers.
Conversely, "if naturalism is right, science is central to morality. For it discovers conditions under which we
prosper" (p. 159).
Gould thinks that there are important domains of human understanding where science has no role,
and moreover he is skeptical about science's role within its 'proper' domain. Nevertheless, he rejects extreme
versions of postmodern relativism. Evolution is an objective fact, containing objective facts, and those facts
are not just aspects of a Western creation myth reflecting the dominant ideology, or an element of the current
paleontological paradigm. "So to some extent[b] Gould shares with Dawkins the view that science delivers
objective knowledge about the world as it is" (p. 161). But while science reflects objective evidence and is not
a mere socio-cultural construction "Gould argues that science is very deeply influenced by the cultural and
social matrix in which it develops", (p. 161) with many of his writings[c] illustrating the influence of social
context on science, and its ultimate sensitivity to evidence. These writings "began as reflections on natural
history; they ended as reflections on the history of natural history" (p. 161). Gould's Time's Arrow, Time's
Cycle (first published in 1987) "locates the development of our conception of deep history in its cultural and
intellectual context without any suggestion that that cultural context perverted the development of geology",
whereas "in Wonderful Life, Gould argued that the Burgess Shale fauna were misunderstood because they
were interpreted through the ideology of their discoverer" (p. 162). The Mismeasure of Man is Gould's most
famous work on the themes of socio-cultural interests leading to bad science, pseudo-science, racist and
sexist science, where "a particular ideological context led to a warped and distorted appreciation of the
evidence on human difference" (p. 162).
Thus, "one sharp contrast between Dawkins and Gould is on the application of science in general,
and evolutionary biology in particualr, to our species" (p. 162). Yet paradoxically, Dawkins' most systematic
writings on human evolution explore the differences between human evolution and that of most other
organisms, in which humans pass on their values through ideas and skills which Dawkins calls memes. To
Dawkins, ideas are often like pathogens or parasites, replicating throughout human populations, sometimes
quite virulently, with evangelical religion being a salient example[d]. Doubts about the reliability and accuracy
of idea replication suggest Dawkins' own view of cultural evolution may not work. But his general approach
has gained some popularity, as illustrated by works which explore the interaction between cultural and
biological evolution, such as Peter Richerson and Robert Boyd's Not By Genes Alone,[e]. as well as Eytan
Avital and Eva Jablonka's Animal Traditions. "So though Dawkins approaches human behaviour using
different tools to those of standard sociobiologists and evolutionary psychologists, he is fully committed to the
idea that we can understand ourselves only in an evolutionary framework" (pp. 164–165). This contrasts with
Gould. While "Of course" he accepts that humans are an evolved species, "Everything that Gould does not
like in contemporary evolutionary thinking comes together in human sociobiology and its descendant,
evolutionary psychology. The result has been a twenty-year campaign of savage polemic against
evolutionary theories of human behaviour. Gould hates sociobiology". And "It is true that some evolutionary
psychology does seem simple-minded," such as Randy Thornhill's "unconvincing" attempt to argue that a
tendency towards rape is an evolutionary adaptation (p. 165). However, contemporary evolutionary
psychologists, and especially biological anthropologists, have accepted the need for caution in testing
adaptationist hypotheses (p. 165). However, even the most disciplined sociobiological approaches reflect
different approaches to evolution to that exemplified by Gould. They "tend not to emphasise the importance
of development and history in imposing constraints on adaptation, the problems in translating
microevolutionary change into species-level change, the role of contingency and mass extinction in
reshaping evolving lineages, or the importance of paleobiology to evolutionary biology" (p. 166), which likely
played a part in Gould's hostility. But Sterelny suspects more most of all, Gould thought "these ideas are
dangerous and ill-motivated as well as wrong. They smack of hubris, of science moving beyond its proper
domain, and incautiously at that". Conversely, to Dawkins, knowledge of evolutionary underpinnings to
human behaviour is potentially liberating, and "might even help us to escape the poisoned chalice of religion"
(p. 166).
Finally, in chapter 13, Sterelny summarises the fundamental contrasts between the views of Dawkins
and Gould. In Dawkins' argument, selection acts on lineages of replicators, which are mostly but not
exclusively genes. Ideas and skills are the replicators in animals capable of social learning, and " the earliest
replicators were certainly not genes" (p. 167). Genetic competition occurs through vehicle-building alliances,
with selection dependant on repeatable influences on those vehicles. Other genetic replication strategies
include Outlaws, the prospects of which are enhanced at the expense of vehicle adaptiveness. And extended
phenotype genes advantageously enhance their environment. The vehicles of Dawkins replicators need not
be individuals, but can also be groups, although animal cooperation is not sufficient to claim group selection.
Evolution's central explanatory imperative is the existence of complex adaptation, which can only be
explained by natural selection. This complex adaptation evolves gradually, with occasional replication errors
resulting in large but survivable phenotypic change. Humans are unusual species in that they are vehicles for
memes as well as genes, although humans are not exempt from evolutionary biological explanations.
Extrapolationism is a sound working theory, with most evolutionary patterns the result of microevolutionary
change over vast geological time. Major animal lineages are the result of ordinary speciation processes,
although possibility-expanding changes may result in some form of lineage-level selection.
In contrast, Gould sees selection as usually acting on organisms in a local population, although in
theory and practice, it can occur at many levels, with change at one level often affecting future options at
other levels. Selection can occur at the group level, with some species lineages having characteristics which
make extinction less likely, or speciation more likely. And while rare, selection can occur on genes within an
organism. While selection is important, and requires understanding, it is just one of many factors explaining
microevolutionary events and macroevolutionary patterns. Further, complex adaptations are but one
phenomenon explanations in evolutionary biology. Extrapolationism is not a good theory, with large-scale
patterns in the history of life not explainable by extrapolating from measurable events in local populations.
Evolutionary biology needs a theory of variation, explaining the effect of variation supply on change
potentiality. While humans are evolved animals, attempts to explain human behaviour using techniques from
evolutionary biology have largely failed, "vitiated by one-sided understanding of evolutionary biology. They
have often been biologicallly naive" (p. 170).
Sterelny notes that these debates remain alive and developing, with no final abjudication possible as
yet. "But we can say something about how the argument has developed" (p. 170). He claims that "the idea
that gene-selectionist views of evolution are tacitly dependent on reductionism and genetic determinism is a
mistake. Dawkins and the other gene selectionists do not think that nothing happens in evolution but changes
in gene frequency" (p. 170). They do not deny the significance of the organism or phenotype, which they see
as vehicles of selection, or 'survival machines', which interact with other survival machines and with the
environment in ways replication of the genes whose vehicles they are. But there are other replication-
enhancing strategies apart from organism construction. Extended phenotypes, as exemplified by parasitic
species, are common and important, with probably all parasitic gene pools including "genes whose adaptive
effects are on host organisms" (p. 171). And "the outlaw count is unknown, but it is growing all the time", and
may transpire to be more common than thought.
Sterelny notes that "gene selectionism is not determinism. No gene selectionist thinks that there is
typically a simple relationship between carrying a particular gene and having a particular phenotype". While
they exist, such as the sickle-cell haemoglobin gene, they are the exception not the rule. Gene-selectionist
ideas are compatible with context dependence of gene action, but they do assume some reasonabl regular
relationship between a specific gene in an organism's genotype, and some aspect of the organism's
phenotypic expression. The assume that within gene lineages, the effect on their vehicles will be fairly
similar. "So while gene selectionists are not genetic determinists, they are making a bet n developmental
biology. Whe revitalised to reoccurring features of context, gene action will turn out to be fairly systematic.
There is no reason to suppose that this hunch is false, but it is, not known to be true" (p. 172).
Developmental biology is relevant to this debate in another important way: "The role of selection in
evolution. Gould is betting that when the facts of developmental biology are in, it will turn out that the
evolutionary possibiities of most lineages are highly constrained", with some characteristics "frozen" into their
respective lineages. "They are developmentally entrenched. That is, these basic organisational features are
connected in development to most aspects of the organism's phenotype, and that makes them hard to
change" (p. 172). And "since variation in these frozen-in features is unlikely, selection is not likely to be
important in explaining their persistence" (p. 173), and Gould thinks 'frozen accidents' are important in
explanations of evolutionary patterns found in the fossil record. Conversely, Dawkins thinks that over time,
selection can alter the range of a lineage's evolutionary possibilities. "So he thinks both that selection has a
larger range of variation with which to work, and that when patterns do exist over long periods...selection will
have played a stabilising role" (p. 173). The integration of evolution and development "is the hottest of hot
topics in contemporary evolutionary theory, and this issue is still most certainly open". In discussing the
effects of mutations, Sterelny's "best current guess is that developmental biology probably does generate
biases in the variation that is available to selection, and hence that evolutionary trajectories will often depend
both on selection and these biases in supply" (173), vindicating Gould's view that developmental biology is
crucial to explaining evolutionary patterns (p. 174).
"But it is harder to see how to resolve some of Gould's other claims about the large-scale history of
life. Despite the plausibility of the distinction between disparity and diversity, we are not close to constructing
a good account of disparity and its measurement" (p. 174). Further, convergent evolution belies the
unpredictability that Gould supposes. However, "most examples of convergence are not independent of
evolutionary experiments. For they concern lineages with an enormous amount of shared history, and hence
shared developmental potential", as in "the standard example of streamlining in marine reptiles, sharks,
pelagic bony fish like the tuna, and dolphins" (p. 175). Further, "the scale is not large enough. The fact that
eyes have often evolved does not show that had, say, the earliest chordates succumbed to a bit of bad luck
(and become extinct), then vertebrate-like organisms wold have evolved again" (p. 175). Moreover, Gould's
main concern is not with adaptive complexes, which are the source of the above, oft-cited examples, "but
with body plans - basic ways of assembling organisms." Sterelny thinks that "we have to score Gould's
contingency claims as: 'Don't know; and at this stage don't know how to find out'" (p. 175).
Gould seems right that mass extinctions played a role in shaping evolutionary history, and "is
probably rignt that extinction works by different rules n mass extinction regimes" (p. 176). Some ideas are
difficult to asses, such as whether mass extinctions filter out the features of species or of individuals
comprising species. It is also difficult to tell the how fundamental is the disagreement between Gould and
Dawkins on this. But Sterelny's bet is that Gould may be right in thinking that survival or extinction in mass
extinction depends on species properties. "However, it has proved hard to find really clear, empirically well-
founded examples to back up this hunch" (p. 176). It was once thought that sexual reproduction was
maintained by species selection, which Sterelny outlines. He notes however that "this idea has recently fallen
on hard times", with new individual-based ideas being developed. Further, species-level maintenance of
sexual reproduction "has a problem: sex does not always promote evolvability", breaking up as well as
creating advantageous gene combinations (p. 177).
"So it has been hard to find really convincing examples of species-level properties that are built by
species-level selection. The problem is to find: (i) traits that are aspects of species, not the organisms making
up the species; (ii) traits that are relevant to extinction and survival; and (iii) traits that are transmitted to
daughter species, granddaughter species and so forth". And "transmission to daughter species is especially
problematic" (p. 177). In the end, Sterelny states his own views are much closer to Dawkins than to Gould's,
especially regarding microevolution - change within local populations. "But macroevolution is not just
microevolution scaled up. Gould's paleontological perspective offers real insights into mass extinction and its
consequences, and, perhaps, the nature of species and speciation". And Gould is right to expand the
explanatory agenda of evolutionary biology to include large-scale patterns in life's history. "So, Dawkins is
right about evolution on local scales, but maybe Gould is right about the relationship between events on a
local scale, and those on the vast scale of paleontological time" (p. 178).
[edit] Suggested Reading

The Suggested Reading section for each chapter is an extension of the chapter, aimed at pointing
the reader in the direction of material that may assist their understanding of the issues under discussion.
This section of Sterelny's book contains, chapter by chapter, a comprehensive list of recommended
reading, covering all of the main publications by Dawkins, Gould, and their respective proponents, along with
many lesser known publications by them, with accompanying commentary on either the authors, the
publications, or both. Also, the readability of the various publications, and the relevance of the publications to
the issues under discussion, as well as the relationship of the publications to each other, such as authors
responding to each other through their publications, or supporting the stance of other authors, etc. He also
tries to further clarify some points in the process.
[edit] See also

• Evolutionary biology
• Dawkins, Richard (1976). The Selfish Gene. New York, New York: Oxford University Press.
ISBN 0192860925.
• Dawkins, Richard (2004). The Ancestor's Tale: A Pilgrimage To the Dawn of Life. London:
• Dennett, Daniel (1995), Darwin's Dangerous Idea, Simon & Schuster, ISBN 0-684-82471-X .
Dennett's book explores the significance and power of natural selection. He supports Dawkins' views
on evolution, and is at times quite critical of Gould's approach.
• Gould, Stephen Jay (2002). The Structure of Evolutionary Theory. Cambridge: The Belknap
Press of Harvard University Press. ISBN 0-674-00613-5.
[edit] Notes
^
a. Sterelny cites the Milankovich cycles as one such isolating mechanism.
b. ^ Italics in the quoted text.
c. ^ Chiefly in his Natural History essays, which were published in the collected volumes of his
popular science books.
d. ^ In drawing on Viruses of the Mind, from Dawkins' book A Devil's Chaplain, Sterelny contrasts
evangelical religions with non-evangelical ones such as Judaism, which he describes as "mostly a family
affair", in which the religious views are primarily inherited socially from parents (p. 164).
e. ^ There are no Wikipedia articles specifically dealing with Richerson, Boyd, or their works. But their
approach is captured in the article on Dual inheritance theory, which cites their works, including the book
cited by Sterelny.
[edit] References
1. ^ Sterelny, K. (2007). Dawkins Vs Gould: Survival of the Fittest. Cambridge, U.K.: Icon
Books. ISBN 1-84046-780-0. Also ISBN 978-1840467-80-2
2. ^ Dawkins, Richard (2004). The Ancestor's Tale: A Pilgrimage To the Dawn of Life. London:
Weidenfeld & Nicolson. p. 503. ISBN 0-297-82503-8.
3. ^ Gould, Stephen Jay (1996). Full House: The Spread of Excellence from Plato to Darwin .
New York: Harmony Books. ISBN 0-517-70394-7.
4. ^ Dawkins, Richard (2004), chapter 39.
[hide]v · d · eRichard Dawkins
The Selfish Gene (1976) · The Extended Phenotype (1982) · The Blind
Watchmaker (1986) · River Out of Eden (1995) · Climbing Mount Improbable
Books (1996) · Unweaving the Rainbow (1998) · A Devil's Chaplain (2003) · The
Ancestor's Tale (2004) · The God Delusion (2006) · The Greatest Show on Earth:
The Evidence for Evolution (2009) · List of publications
Growing Up in the Universe (1991) · Dawkins vs. Gould (2001) · Beyond

Related works Belief (2006) · Richard Dawkins: How a Scientist Changed the Way We Think
(2006) · The Oxford Book of Modern Science Writing (2008)
Nice Guys Finish First (1987) · Break the Science Barrier (1996) · The
Documentaries Atheism Tapes (2004) · The Root of All Evil? (2006) · The Enemies of Reason
(2007) · The Genius of Charles Darwin (2008) · Faith School Menace (2010)
Meme · Out Campaign · Gerin oil · Foundation for Reason and Science ·
See also Ultimate Boeing 747 gambit · Lalla Ward · Frameshift · Weasel program · Marian
Stamp Dawkins · Middle World · Go God Go · The Courtier's Reply
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W000
Komodo dragon

Komodo dragon[1]
Conservation status
Vulnerable (IUCN 3.1)

Kingdom: Animalia
Phylum: Chordata
Class: Reptilia
Order: Squamata
Suborder: Lacertilia
Family: Varanidae
Genus: Varanus
Subgenus: V. (Varanus)
Species: V. komodoensis
Binomial name
Varanus komodoensis
Ouwens, 1912[2]
Komodo dragon distribution
The Komodo dragon (Varanus komodoensis) is a large species of lizard found in the Indonesian
islands of Komodo, Rinca, Flores, and Gili Motang.[3] A member of the monitor lizard family (Varanidae), it is
the largest living species of lizard, growing to an average length of 2 to 3 metres (6.6 to 9.8 ft) and weighing
around 70 kilograms (150 lb). Their unusual size has been attributed to island gigantism, since there are no
other carnivorous animals to fill the niche on the islands where they live.[4][5] However, recent research
suggests that the large size of komodo dragons may be better understood as representative of a relic
population of very large varanid lizards that once lived across Indonesia and Australia, most of which, along
with other megafauna,[6] died out after contact with modern humans. Fossils very similar to V. komodoensis
have been found in Australia dating to greater than 3.8 million years ago, and its body size remained stable
on Flores, one of the handful of Indonesian islands where it is currently found, ever since Flores (along with
neighboring islands) were isolated by rising sea levels approximately 900,000 years ago.[6] As a result of
their size, these lizards dominate the ecosystems in which they live.[7] Although Komodo dragons eat mostly
carrion, they will also hunt and ambush prey including invertebrates, birds, and mammals.
Mating begins between May and August, and the eggs are laid in September. About twenty eggs are
deposited in abandoned megapode nests and incubated for seven to eight months, hatching in April, when
insects are most plentiful. Young Komodo dragons are vulnerable and therefore dwell in trees, safe from
predators and cannibalistic adults. They take around three to five years to mature, and may live as long as
fifty years. They are among the rare vertebrates capable of parthenogenesis, in which females may lay viable
eggs if males are absent, producing only male offspring.[8]
Komodo dragons were first recorded by Western scientists in 1910.[9] Their large size and fearsome
reputation make them popular zoo exhibits. In the wild their range has contracted due to human activities and
they are listed as vulnerable by the IUCN. They are protected under Indonesian law, and a national park,
Komodo National Park, was founded to aid protection efforts.
Contents
[hide]
• 1 Etymology
• 3 Description
• 3.1 Senses
• 4 Ecology
• 4.1 Diet
• 4.2 Saliva
• 4.4 Parthenogenesis
• 5 History
• 5.1 Discovery by the Western world
• 5.2 Studies
• 6 Danger to humans
• 7 Conservation
• 7.1 In captivity
• 8 See also
• 9 References
[edit] Etymology
The Komodo dragon is also known as the Komodo monitor or the Komodo Island monitor in scientific
literature, although this is not very common.[1] To the natives of Komodo Island, it is referred to as ora, buaya
darat (land crocodile) or biawak raksasa (giant monitor).[10][11]

The evolutionary development of the Komodo dragon started with the Varanus genus, which
originated in Asia about 40 million years ago and migrated to Australia. Around 15 million years ago, a
collision between Australia and Southeast Asia allowed the varanids to move into what is now the Indonesian
archipelago, extending their range as far east as the island of Timor. The Komodo dragon was believed to
have differentiated from its Australian ancestors 4 million years ago. However, recent fossil evidence from
Queensland suggests that the Komodo dragon evolved in Australia before spreading to Indonesia.[6][12]
Dramatic lowering of sea level during the last glacial period uncovered extensive stretches of continental
shelf that the Komodo dragon colonized, becoming isolated in their present island range as sea levels rose
afterwards.[6][11]
[edit] Description
Closeup of a Komodo dragon's skin

In the wild, an adult Komodo dragon usually weighs around 70 kilograms (150 lb),[13] although
captive specimens often weigh more. The largest verified wild specimen was 3.13 metres (10.3 ft) long and
weighed 166 kilograms (370 lb), including undigested food.[11] The Komodo dragon has a tail as long as its
body, as well as about 60 frequently replaced serrated teeth that can measure up to 2.5 cm (1 inch) in length.
Its saliva is frequently blood-tinged, because its teeth are almost completely covered by gingival tissue that is
naturally lacerated during feeding.[14] This creates an ideal culture for the virulent bacteria that live in its
mouth.[15] It also has a long, yellow, deeply forked tongue.[11]
[edit] Senses
The Komodo dragon does not have a particularly acute sense of hearing, despite its visible earholes,
and is only able to hear sounds between 400 and 2000 hertz.[11][16] It is able to see as far away as
300 metres (980 ft), but because its retinas only contain cones, it is thought to have poor night vision. The
Komodo dragon is able to see in color, but has poor visual discrimination of stationary objects.[17]
A Komodo dragon on Komodo Island uses its tongue to sample the air
The Komodo dragon uses its tongue to detect, taste, and smell stimuli, as with many other reptiles,
with the vomeronasal sense using a Jacobson's organ, a sense that aids navigation in the dark.[15] With the
help of a favorable wind and its habit of swinging its head from side to side as it walks, Komodo dragons may
be able to detect carrion from 4–9.5 kilometres (2.5–6 mi) away.[14][17] The dragon's nostrils are not of great
use for smelling, as the animal does not have a diaphragm.[14][18] It only has a few taste buds in the back of
its throat.[15] Its scales, some of which are reinforced with bone, have sensory plaques connected to nerves
that facilitate its sense of touch. The scales around the ears, lips, chin, and soles of the feet may have three
or more sensory plaques.[14]
The Komodo dragon was formerly thought to be deaf when a study reported no agitation in wild
Komodo dragons in response to whispers, raised voices, or shouts. This was disputed when London
Zoological Garden employee Joan Proctor trained a captive specimen to come out to feed at the sound of her
voice, even when she could not be seen.[19]
[edit] Ecology
Close-up of a Komodo dragon's foot and tail

The Komodo dragon prefers hot and dry places, and typically lives in dry open grassland, savanna,
and tropical forest at low elevations. As an ectotherm, it is most active in the day, although it exhibits some
nocturnal activity. Komodo dragons are largely solitary, coming together only to breed and eat. They are
capable of running rapidly in brief sprints up to 20 kilometres per hour (12.4 mph), diving up to 4.5 metres
(15 ft), and climbing trees proficiently when young through use of their strong claws.[13] To catch prey that is
out of reach, the Komodo dragon may stand on its hind legs and use its tail as a support.[19] As the Komodo
dragon matures, its claws are used primarily as weapons, as its great size makes climbing impractical.[14]
For shelter, the Komodo dragon digs holes that can measure from 1–3 metres (3–10 ft) wide with its
powerful forelimbs and claws.[20] Because of its large size and habit of sleeping in these burrows, it is able
to conserve body heat throughout the night and minimize its basking period the morning after.[21] The
Komodo dragon typically hunts in the afternoon, but stays in the shade during the hottest part of the day.[22]
These special resting places, usually located on ridges with a cool sea breeze, are marked with droppings
and are cleared of vegetation. They also serve as a strategic location from which to ambush deer.[23]
[edit] Diet
Komodo dragons on Rinca

Komodo dragons are carnivores. Although they eat mostly carrion,[4] they will also ambush live prey
with a stealthy approach. When suitable prey arrives near a dragon's ambush site, it will suddenly charge at
the animal and go for the underside or the throat.[14] It is able to locate its prey using its keen sense of smell,
which can locate a dead or dying animal from a range of up to 9.5 kilometers (6 miles).[14] Komodo dragons
have also been observed knocking down large pigs and deer with their strong tail, as well as deliberately
harassing pregnant goats and deer in the hopes of inducing a miscarriage they can consume.[24][25]
Komodo dragons eat by tearing large chunks of flesh and swallowing them whole while holding the
carcass down with their forelegs. For smaller prey up to the size of a goat, their loosely articulated jaws,
flexible skull, and expandable stomach allow it to swallow its prey whole. The vegetable contents of the
stomach and intestines are typically avoided.[23] Copious amounts of red saliva that the Komodo dragons
produce help to lubricate the food, but swallowing is still a long process (15–20 minutes to swallow a goat).
Komodo dragons may attempt to speed up the process by ramming the carcass against a tree to force it
down its throat, sometimes ramming so forcefully that the tree is knocked down.[23] To prevent itself from
suffocating while swallowing, it breathes using a small tube under the tongue that connects to the lungs.[14]
After eating up to 80 percent of its body weight in one meal,[7] it drags itself to a sunny location to speed
digestion, as the food could rot and poison the dragon if left undigested for too long. Because of their slow
metabolism, large dragons can survive on as little as 12 meals a year.[14] After digestion, the Komodo
dragon regurgitates a mass of horns, hair, and teeth known as the gastric pellet, which is covered in
malodorous mucus. After regurgitating the gastric pellet, it rubs its face in the dirt or on bushes to get rid of
the mucus, suggesting that it, like humans, does not relish the scent of its own excretions.[14]
A young Komodo dragon photographed on Rinca feeding on a water buffalo carcass
The largest animals generally eat first, while the smaller ones follow a hierarchy. The largest male
asserts his dominance and the smaller males show their submission by use of body language and rumbling
hisses. Dragons of equal size may resort to "wrestling". Losers usually retreat though they have been known
to be killed and eaten by victors.[14]
Komodo excrement is mostly white as the stomach is not capable of digesting the calcium found in
the bones of the animals they eat.
The Komodo dragon's diet is wide-ranging, and includes invertebrates, other reptiles (including
smaller Komodo dragons), birds, bird eggs, small mammals, monkeys, wild boar, goats, deer, horses, and
water buffalo.[26] Young Komodos will eat insects, eggs, geckos, and small mammals.[4] Occasionally they
consume humans and human corpses, digging up bodies from shallow graves.[19] This habit of raiding
graves caused the villagers of Komodo to move their graves from sandy to clay ground and pile rocks on top
of them to deter the lizards.[23] The Komodo dragon may have evolved to feed on the extinct dwarf elephant
Stegodon that once lived on Flores, according to evolutionary biologist Jared Diamond.[27]
Because the Komodo dragon does not have a diaphragm, it cannot suck water when drinking, nor
can it lap water with its tongue. Instead, it drinks by taking a mouthful of water, lifting its head, and letting the
water run down its throat.[14]
[edit] Saliva
A sleeping Komodo dragon. Its large, curved claws are used in fighting and eating.
Auffenberg described the Komodo dragon as having septic pathogens in its saliva, specifically the
bacteria: E. coli, Staphylococcus sp., Providencia sp., Proteus morgani and P. mirabilis.[28] He noted that
while these pathogens can be found in the mouths of wild Komodo dragons, they disappear from the mouths
of captive animals, due to a cleaner diet and the use of antibiotics.[28][29] This was verified by taking
mucous samples from the external gum surface of the upper jaw of two freshly captured individuals.[28][29]
Saliva samples were analyzed by researchers at the University of Texas who found 57 different strains of
bacteria growing in the mouths of three wild Komodo dragons including Pasteurella multocida.[11][30] The
rapid growth of these bacteria was noted by Fredeking: "Normally it takes about three days for a sample of P.
multocida to cover a petri dish; ours took eight hours. We were very taken aback by how virulent these
strains were".[31] This study supported the observation that wounds inflicted by the Komodo dragon are often
associated with sepsis and subsequent infections in prey animals.[30] How the Komodo dragon is unaffected
by these virulent bacteria remains a mystery.[31]
In late 2005, researchers at the University of Melbourne speculated that the perentie (Varanus
giganteus), other species of monitor, and agamids may be somewhat venomous. The team believes that the
immediate effects of bites from these lizards were caused by mild envenomation. Bites on human digits by a
lace monitor (V. varius), a Komodo dragon, and a spotted tree monitor ( V. scalaris) all produced similar
effects: rapid swelling, localized disruption of blood clotting, and shooting pain up to the elbow, with some
symptoms lasting for several hours.[32]
In 2009, the same researchers published further evidence demonstrating that Komodo dragons
possess a venomous bite. MRI scans of a preserved skull showed the presence of two venom glands in the
lower jaw. They extracted one of these glands from the head of a terminally ill specimen in the Singapore
Zoological Gardens, and found that it secreted a venom containing several different toxic proteins. The
known functions of these proteins include inhibition of blood clotting, lowering of blood pressure, muscle
paralysis, and the induction of hypothermia, leading to shock and loss of consciousness in envenomated
prey.[33][34] As a result of the discovery, the previous theory that bacteria were responsible for the deaths of
komodo victims was disputed.[35]
Kurt Schwenk, an evolutionary biologist at the University of Connecticut finds the discovery of these
glands intriguing, but considers most of the evidence for venom in the study to be "meaningless, irrelevant,
incorrect or falsely misleading". Even if the lizards have venomlike proteins in their mouths, Schwenk argues,
they may be using them for a different function, and he doubts that venom is necessary to explain the effect
of a Komodo dragon bite, arguing that shock and blood loss are the primary factors.[36][37]
[edit] Reproduction
Mating occurs between May and August, with the eggs laid in September.[11] During this period,
males fight over females and territory by grappling with one another upon their hind legs with the loser
eventually being pinned to the ground. These males may vomit or defecate when preparing for the fight.[19]
The winner of the fight will then flick his long tongue at the female to gain information about her receptivity.[7]
Females are antagonistic and resist with their claws and teeth during the early phases of courtship.
Therefore, the male must fully restrain the female during coitus to avoid being hurt. Other courtship displays
include males rubbing their chins on the female, hard scratches to the back, and licking.[38] Copulation
occurs when the male inserts one of his hemipenes into the female's cloaca.[17] Komodo dragons may be
monogamous and form "pair bonds", a rare behavior for lizards.[19]
A Komodo dragon with its long tail and claws fully visible
The female lays her eggs in burrows cut into the side of a hill or in the abandoned nesting mounds of
the Orange-footed Scrubfowl (a moundbuilder or megapode), with a preference for the abandoned mounds.
[39] Clutches contain an average of 20 eggs which have an incubation period of 7–8 months.[19] The female
lies on the eggs to incubate and protect them until they hatch around April, at the end of the rainy season
when insects are plentiful. Hatching is an exhausting effort for the pups, who break out of their eggshells with
an egg tooth that falls off soon after. After cutting out the hatchlings may lie in their eggshells for hours before
starting to dig out of the nest. They are born quite defenseless, and many are eaten by predators.[14]
Young Komodo dragons spend much of their first few years in trees, where they are relatively safe
from predators, including cannibalistic adults, who make juvenile dragons 10% of their diet.[19] According to
David Attenborough, the habit of cannibalism may be advantageous in sustaining the large size of adults, as
medium-sized prey on the islands is rare.[24] When the young must approach a kill, they roll around in fecal
matter and rest in the intestines of eviscerated animals to deter these hungry adults.[19] Komodo dragons
take about three to five years to mature, and may live for up to 50 years.[20]
[edit] Parthenogenesis
Main article: Parthenogenesis
A parthenogenetic baby Komodo dragon, Chester Zoo, England

A Komodo dragon at London Zoo named Sungai laid a clutch of eggs in late 2005 after being
separated from male company for more than two years. Scientists initially assumed that she had been able to
store sperm from her earlier encounter with a male, an adaptation known as superfecundation.[40] On
December 20, 2006, it was reported that Flora, a captive Komodo dragon living in the Chester Zoo in
England, was the second known Komodo dragon to have laid unfertilized eggs: she laid 11 eggs, and 7 of
them hatched, all of them male.[41] Scientists at Liverpool University in England performed genetic tests on
three eggs that collapsed after being moved to an incubator, and verified that Flora had never been in
physical contact with a male dragon. After Flora's eggs' condition had been discovered, testing showed that
Sungai's eggs were also produced without outside fertilization.[42] On January 31, 2008, the Sedgwick
County Zoo in Wichita, Kansas became the first zoo in the Americas to document parthenogenesis in
Komodo dragons. The zoo has two adult female Komodo dragons, one of which laid about 17 eggs on May
19–20, 2007. Only two eggs were incubated and hatched due to space issues; the first hatched on January
31, 2008 while the second hatched on February 1. Both hatchlings were males.[43][44]
Komodo dragons have the ZW chromosomal sex-determination system, as opposed to the
mammalian XY system. Male progeny prove that Flora's unfertilized eggs were haploid (n) and doubled their
chromosomes later to become diploid (2n) (by being fertilized by a polar body, or by chromosome duplication
without cell division), rather than by her laying diploid eggs by one of the meiosis reduction-divisions in her
ovaries failing. When a female Komodo dragon (with ZW sex chromosomes) reproduces in this manner, she
provides her progeny with only one chromosome from each of her pairs of chromosomes, including only one
of her two sex chromosomes. This single set of chromosomes is duplicated in the egg, which develops
parthenogenetically. Eggs receiving a Z chromosome become ZZ (male); those receiving a W chromosome
become WW and fail to develop.[45][46]
It has been hypothesized that this reproductive adaptation allows a single female to enter an isolated
ecological niche (such as an island) and by parthenogenesis produce male offspring, thereby establishing a
sexually reproducing population (via reproduction with her offspring that can result in both male and female
young).[45] Despite the advantages of such an adaptation, zoos are cautioned that parthenogenesis may be
detrimental to genetic diversity.[47]
[edit] History
[edit] Discovery by the Western world
Komodo dragon coin, issued by Indonesia

Komodo in the emblem of East Nusa Tenggara province
Komodo dragons were first documented by Europeans in 1910, when rumors of a "land crocodile"
reached Lieutenant van Steyn van Hensbroek of the Dutch colonial administration.[48] Widespread notoriety
came after 1912, when Peter Ouwens, the director of the Zoological Museum at Bogor, Java, published a
paper on the topic after receiving a photo and a skin from the lieutenant, as well as two other specimens from
a collector.[2] Later, the Komodo dragon was the driving factor for an expedition to Komodo Island by W.
Douglas Burden in 1926. After returning with 12 preserved specimens and 2 live ones, this expedition
provided the inspiration for the 1933 movie King Kong.[49] It was also Burden who coined the common name
"Komodo dragon."[22] Three of his specimens were stuffed and are still on display in the American Museum
of Natural History.[50]
[edit] Studies
The Dutch, realizing the limited number of individuals in the wild, outlawed sport hunting and heavily
limited the number of individuals taken for scientific study. Collecting expeditions ground to a halt with the
occurrence of World War II, not resuming until the 1950s and 1960s, when studies examined the Komodo
dragon's feeding behavior, reproduction, and body temperature. At around this time, an expedition was
planned in which a long-term study of the Komodo dragon would be undertaken. This task was given to the
Auffenberg family, who stayed on Komodo Island for 11 months in 1969. During their stay, Walter Auffenberg
and his assistant Putra Sastrawan captured and tagged more than 50 Komodo dragons.[31] The research
from the Auffenberg expedition would prove to be enormously influential in raising Komodo dragons in
captivity.[3] Research after the Auffenberg family has shed more light on the nature of the Komodo dragon,
with biologists such as Claudio Ciofi continuing to study the creatures.[51]
[edit] Danger to humans

Although attacks are very rare, Komodo dragons have been known to attack humans; on June 4,
2007 a Komodo dragon attacked an eight-year-old boy on Komodo Island. The boy later died of massive
bleeding from his wounds. It was the first recorded fatal attack in 33 years.[52] Locals blamed the attack on
environmentalists outside the island prohibiting goat sacrifices. This denied the Komodo dragons their
expected food source, causing them to wander into human civilization in search of food. A belief held by
many natives of Komodo Island is that Komodo dragons are actually the reincarnation of fellow kinspeople
and should thus be treated with reverence.[53][54]
On March 24, 2009, two Komodo Dragons attacked and killed fisherman Muhamad Anwar on
Komodo. Anwar was attacked after he fell out of a sugar-apple tree and was left bleeding badly from bites to
his hands, body, legs, and neck. He was taken to a clinic on the neighboring island of Flores where he was
pronounced dead on arrival.[55]
In a bizarre incident in June 2001, Phil Bronstein, Executive Editor of the San Francisco Chronicle
newspaper, was given a special tour of the Komodo dragons at the Los Angeles Zoo for a Father's Day
present by his wife, the actress Sharon Stone. Bronstein and Stone were benefactors of the zoo. While
barefooted and petting one of the dragons, Bronstein's foot was seriously bitten and required extensive
surgery.[56][57]
[edit] Conservation
A basking Komodo dragon photographed at Disney's Animal Kingdom

The Komodo dragon is a vulnerable species and is found on the IUCN Red List.[58] There are
approximately 4,000 to 5,000 living Komodo dragons in the wild. Their populations are restricted to the
islands of Gili Motang (100), Gili Dasami (100), Rinca (1,300), Komodo (1,700), and Flores (perhaps 2,000).
[3] However, there are concerns that there may presently be only 350 breeding females.[10] To address
these concerns, the Komodo National Park was founded in 1980 to protect Komodo dragon populations on
islands including Komodo, Rinca, and Padar.[59] Later, the Wae Wuul and Wolo Tado Reserves were
opened on Flores to aid with Komodo dragon conservation.[51] There is evidence that Komodo dragons
became accustomed to human presence, as they were often fed animal carcasses at several feeding
stations by tourists and sacrifices from natives before a hunt.[4][53] As these practices have been outlawed,
attacks on humans by the lizards has increased.[53]
Volcanic activity, earthquakes, loss of habitat, fire (the population at Padar was almost destroyed
because of a wildfire, and has since mysteriously disappeared),[14][51] loss of prey, tourism, and poaching
have all contributed to the vulnerable status of the Komodo dragon. Under Appendix I of CITES (the
Convention on International Trade in Endangered Species), commercial trade of skins or specimens is
illegal.[18][60]
[edit] In captivity
A Komodo dragon at Smithsonian National Zoological Park. Despite the visible earholes, Komodo
dragons cannot hear very well.
Komodo dragons have long been great zoo attractions, where their size and reputation make them
popular exhibits. They are, however, rare in zoos because they are susceptible to infection and parasitic
disease if captured from the wild, and do not readily reproduce.[10] In May 2009, there were 13 European, 2
African, 35 North American, 1 Singaporean, and 2 Australian institutions that keep Komodo dragons.[61]
The first Komodo dragon was exhibited in 1934 at the Smithsonian National Zoological Park, but it
lived for only two years. More attempts to exhibit Komodo dragons were made, but the lifespan of these
creatures was very short, averaging five years in the National Zoological Park. Studies done by Walter
Auffenberg, which were documented in his book The Behavioral Ecology of the Komodo Monitor, eventually
allowed for more successful managing and reproducing of the dragons in captivity.[3]
It has been observed in captive dragons that many individuals display relatively tame behavior within
a short period of time in captivity. Many occurrences are reported where keepers have brought the animals
out of their enclosures to interact with zoo visitors, including young children, to no harmful effect.[62][63]
Dragons are also capable of recognizing individual humans. Ruston Hartdegen of the Dallas Zoo reported
that their Komodo dragons reacted differently when presented with their regular keeper, a less familiar
keeper, or a completely unfamiliar keeper.[64]
Research with captive Komodo dragons has also provided evidence that they engage in play. One
study concerned an individual who would push a shovel left by its keeper, apparently attracted to the sound
of it scraping across the rocky surface. A young female dragon at the National Zoo in Washington, D.C.
would grab and shake various objects including statues, beverage cans, plastic rings and blankets. She
would also insert her head into boxes, shoes, and other objects. She did not confuse these objects with food,
as she would only swallow them if they were covered in rat blood. This social play has led to a striking
comparison with mammalian play.[7]
Komodo dragons at Toronto Zoo. Komodo dragons in captivity often grow fat, especially in their tails,
due to regular feeding.
Another documentation of play in Komodo dragons comes from the University of Tennessee, where
a young Komodo dragon named "Kraken" interacted with plastic rings, a shoe, a bucket, and a tin can by
nudging them with her snout, swiping at them, and carrying them around in her mouth. She treated all of
them differently from her food, prompting leading researcher Gordon Burghardt to conclude that they
disprove the view of object play being "food-motivated predatory behavior." Kraken was the first Komodo
dragon hatched in captivity outside of Indonesia, born in the National Zoo on September 13, 1992.[11][65]
Even seemingly docile dragons may become aggressive unpredictably, especially when the animal's
territory is invaded by someone unfamiliar. In June 2001, a Komodo dragon seriously injured Phil Bronstein—
executive editor of the San Francisco Chronicle—when he entered its enclosure at the Los Angeles Zoo after
being invited in by its keeper. Bronstein was bitten on his bare foot, as the keeper had told him to take off his
white shoes, which could have potentially excited the Komodo dragon.[66][67] Although he escaped, he
needed to have several tendons in his foot reattached surgically.[68]
[edit] See also

Amphibians and Reptiles portal
Indonesia portal
• Dragon
• Papua monitor (Varanus salvadorii) – A monitor lizard often asserted to be the longest lizard
• Toxicofera – A hypothetical clade encompassing all venomous reptiles, including the Komodo
dragon
• Varanus priscus (formerly known as Megalania prisca) – A huge extinct varanid lizard of
Pleistocene Australia
• Whiptail lizards – Lizards widely studied for their parthenogenesis
[edit] References
1. ^ a b "Varanus komodoensis". Integrated Taxonomic Information System.
http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=202168.
Retrieved 19 June 2007.
2. ^ a b Ouwens, P.A. (1912). "On a large Varanus species from the island of Komodo". Bull.
Jard. Bot. Buit. 2 (6): 1–3.
3. ^ a b c d Trooper Walsh; Murphy, James Jerome; Claudio Ciofi; Colomba De LA Panouse
(2002). Komodo Dragons: Biology and Conservation (Zoo and Aquarium Biology and Conservation
Series). Washington, D.C.: Smithsonian Books. ISBN 1-58834-073-2.
4. ^ a b c d Chris Mattison, (1989 & 1992). Lizards of the World. New York: Facts on File. pp. 16,
57, 99, 175. ISBN 0-8160-5716-8.
5. ^ Burness G, Diamond J, Flannery T (Dec 2001). "Dinosaurs, dragons, and dwarfs: the
evolution of maximal body size" (Free full text). Proc Natl Acad Sci USA 98 (25): 14518–23.
doi:10.1073/pnas.251548698. ISSN 0027-8424. PMID 11724953. PMC 64714.
6. ^ a b c d Hocknull SA, Piper PJ, van den Bergh GD, Due RA, Morwood MJ, Kurniawan I
(September 2009). "Dragon's paradise lost: palaeobiogeography, evolution and extinction of the
largest-ever terrestrial lizards (Varanidae)" (Free full text). PLoS ONE 4 (9): e7241.
doi:10.1371/journal.pone.0007241. PMID 19789642. PMC 2748693.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007241.
7. ^ a b c d Tim Halliday (Editor), Kraig Adler (Editor) (2002). Firefly Encyclopedia of Reptiles
and Amphibians. Hove: Firefly Books Ltd. pp. 112, 113, 144, 147, 168, 169. ISBN 1-55297-613-0.
8. ^ This article in Nature (magazine) reports a female who reproduced parthenogenetically for
one batch of eggs, and subsequently was impregnated by a male in a normal process. Nature.com
9. ^ Mampam.com
10.^ a b c "Endangered! Ora". American Museum of Natural History.
http://www.amnh.org/nationalcenter/Endangered/ora/ora.html. Retrieved 2007-01-15.
11.^ a b c d e f g h Ciofi, Claudio. "The Komodo Dragon". Scientific American.
http://www.sciam.com/article.cfm?id=the-komodo-dragon. Retrieved 2006-12-21.
12.^ "Australia was 'hothouse' for killer lizards", ABC, September 30, 2009. Retrieved on
September 30, 2009.
13.^ a b Burnie, David; Don E. Wilson (2001). Animal. New York, New York: DK Publishing, Inc..
pp. 417, 420. ISBN 0-7894-7764-5.
14.^ a b c d e f g h i j k l m n Tara Darling (Illustrator). Komodo Dragon: On Location (Darling,
Kathy. on Location.). Lothrop, Lee and Shepard Books. ISBN 0-688-13777-6.
15.^ a b c "Komodo Dragon". Singapore Zoological Gardens. Archived from the original on 2006-
11-27. http://web.archive.org/web/20061127173608/http://www.szgdocent.org/resource/rr/c-
komodo.htm. Retrieved 2006-12-21.
16.^ "Komodo Conundrum". bbc.co.uk. Archived from the original on 2006-11-16.
http://web.archive.org/web/20061116030327/http://www.bbc.co.uk/nature/animals/features/336featur
e1.shtml. Retrieved 2007-11-25.
17.^ a b c "Komodo Dragon Fact Sheet". National Zoo.
http://nationalzoo.si.edu/Animals/ReptilesAmphibians/Facts/FactSheets/Komododragon.cfm.
18.^ a b "Zipcodezoo: Varanus komodoensis (Komodo Dragon, Komodo Island Monitor, Komodo
Monitor)". BayScience Foundation, Inc.. http://zipcodezoo.com/Animals/V/Varanus_komodoensis.
19.^ a b c d e f g h text by David Badger; photography by John Netherton (2002). Lizards: A
Natural History of Some Uncommon Creatures, Extraordinary Chameleons, Iguanas, Geckos, and
More. Stillwater, MN: Voyageur Press. pp. 32, 52, 78, 81, 84, 140–145, 151. ISBN 0-89658-520-4.
20.^ a b consultant editors, Harold G. Cogger & Richard G. Zweifel; illustrations by David
Kirshner (1998). Encyclopedia of Reptiles & Amphibians. Boston: Academic Press. pp. 132, 157–8.
ISBN 0-12-178560-2.
21.^ Eric R. Pianka and Laurie J. Vitt; with a foreword by Harry W. Greene (2003). Lizards:
Windows to the Evolution of Diversity. Berkeley: University of California Press. p. 244. ISBN 0-520-
23401-4.
22.^ a b "Komodo National Park Frequently Asked Questions". Komodo Foundation.
http://www.komodo-gateway.org/faq1.html. Retrieved 2007-10-25.
23.^ a b c d Alison Ballance; Morris, Rod (2003). South Sea Islands: A Natural History. Hove:
Firefly Books Ltd. ISBN 1-55297-609-2.
24.^ a b Attenborough, David (2008). Life in Cold Blood. Princeton, N.J: Princeton University
Press. ISBN 0-691-13718-8.
25.^ Auffenberg, Walter (1981). The Behavioral Ecology of the Komodo Monitor. Gainesville,
Florida: University Presses of Florida. ISBN 0-8130-0621-X.
26.^ Vidal, John (2008-06-12). "The terrifying truth about Komodo dragons". London:
guardian.co.uk. http://www.guardian.co.uk/world/2008/jun/12/indonesia. Retrieved 2008-06-19.
27.^ Diamond, Jared M. (1987). "Did Komodo dragons evolve to eat pygmy elephants?". Nature
326 (6116): 832. doi:10.1038/326832a0.
28.^ a b c Auffenberg, Walter (1981). The Behavioral Ecology of the Komodo Monitor.
Gainesville: University Presses of Florida. pp. 406. ISBN 0-8130-0621-X.
29.^ a b Balsai, Michael Joseph (2001). The phylogenetic position of Palaeosaniwa and the
early evolution of the Platynotan (Varanoid) anguimorphs (January 1, 2001). University of
Pennsylvania - Electronic Dissertations. Paper AAI3031637. UPENN.edu
30.^ a b Montgomery; D Gillespie, P Sastrawan, TM Fredeking, and GL Stewart (2002). "Aerobic
salivary bacteria in wild and captive Komodo dragons". Journal of Wildlife Diseases (Wildlife Disease
Association) 38 (3): 545–551. PMID 12238371. http://www.jwildlifedis.org/cgi/reprint/38/3/545.pdf.
31.^ a b c Cheater, Mark (August/September 2003). "Chasing the Magic Dragon". National
Wildlife Magazine (National Wildlife Federation) 41 (5).
http://www.nwf.org/nationalwildlife/article.cfm?articleId=810&issueId=63.
32.^ Fry, BG; Vidal, N; Norman, JA; Vonk, FJ; Scheib, H; Ramjan, SF; Kuruppu, S; Fung, K et
al. (February 2006). "Early evolution of the venom system in lizards and snakes" (PDF). Nature 439
(7076): 584–588. doi:10.1038/nature04328. ISSN 0028-0836. PMID 16292255.
http://www.nature.com/nature/journal/v439/n7076/abs/nature04328.html.
33.^ Scientists discover deadly secret of Komodo's bite, Yahoo news from May 18th 2009
34.^ Bryan G. Fry, Stephen Wroec, Wouter Teeuwissed, et al., (University of Melbourne):
PNAS, publisched online, doi:10.1073/pnas.0810883106, A central role for venom in predation by
Varanus komodoensis (Komodo Dragon) and the extinct giant Varanus (Megalania) priscus'
35.^ Staff. "Komodo dragons kill with venom, not bacteria, study says." CNN. May 20, 2009.
Retrieved on May 25, 2009.
36.^ Zimmer, Carl (May 2009), "Venom Might Boost Dragons Bite", San diego Tribune,
http://www3.signonsandiego.com/stories/2009/may/25/1c25komodo183628-venom-may-be-boost-
dragons-bite/?uniontrib, retrieved 2009-09-26
37.^ Anthony Bartkewicz (May 2009), "Study:Komodo Dragons Kill With Venom", Fox News
Service,
http://www.myfoxdfw.com/dpp/news/weird/dpgo_Study_Komodo_Dragons_Kill_With_Venom_SAB_0
5192009_2497449, retrieved 2009-09-26
38.^ "Komodo Dragon, Varanus komodoensis". San Diego Zoo.
http://library.sandiegozoo.org/factsheets/komodo_dragon/komodo.htm. Retrieved 2009-10-27.
39.^ Jessop, Tim S., et al.. "Distribution, Use and Selection of Nest Type by Komodo Dragons"
(PDF). Elsevier. Archived from the original on 2007-08-29.
http://web.archive.org/web/20070829154723/http://www.komododragon.biz/uploads/downloads/jesso
p+et+al+2004e.pdf. Retrieved 2008-03-13.
40.^ Morales, Alex. "Komodo Dragons, World's Largest Lizards, Have Virgin Births". Bloomberg
Television. http://www.bloomberg.com/apps/news?
pid=20601082&sid=apLYpeppu8ag&refer=canada. Retrieved 2008-03-28.
41.^ Notice by her cage in Chester Zoo in England
42.^ Henderson, Mark (2006-12-21). "Wise men testify to Dragon's virgin birth". London: The
Times. http://www.timesonline.co.uk/tol/news/uk/article759338.ece. Retrieved 2007-11-26.
43.^ "Recent News - Sedgwick County Zoo". Sedgwick County Zoo. Archived from the original
on 2008-02-11. http://web.archive.org/web/20080211184900/http://www.scz.org/n_recent.html.
44.^ "Komodo dragons hatch with no male involved". MSNBC.
http://www.msnbc.msn.com/id/23058689/. Retrieved 2008-02-12.
45.^ a b "Virgin births for giant lizards". BBC News. 2006-12-20.
http://news.bbc.co.uk/2/hi/science/nature/6196225.stm. Retrieved 2008-03-13.
46.^ "Strange but True: Komodo Dragons Show that "Virgin Births" Are Possible: Scientific
American". Scientific American. http://www.sciam.com/article.cfm?id=strange-but-true-komodo-d.
47.^ Watts PC, Buley KR, Sanderson S, Boardman W, Ciofi C, Gibson R (Dec 2006).
"Parthenogenesis in Komodo Dragons". Nature 444 (7122): 1021–2. doi:10.1038/4441021a.
ISSN 0028-0836. PMID 17183308.
48.^ Daily Mail - Should we really be scared of the Komodo dragon?
49.^ Rony, Fatimah Tobing (1996). The third eye: race, cinema, and ethnographic spectacle .
Durham, N.C: Duke University Press. p. 164. ISBN 0-8223-1840-7.
50.^ "American Museum of Natural History: Komodo Dragons". American Museum of Natural
History.
http://www.amnh.org/exhibitions/expeditions/treasure_fossil/Treasures/Komodo_Dragons/komodo.ht
ml?aa. Retrieved 2007-06-07.
51.^ a b c "Trapping Komodo Dragons for Conservation". National Geographic.
http://news.nationalgeographic.com/news/2003/01/0129_030129_komodo.html. Retrieved 2007-11-
08.
52.^ "Komodo dragon kills boy in Indonesia". MSNBC.
53.^ a b c Trofimov, Yaroslav (2008-08-25). "When Good Lizards Go Bad: Komodo Dragons
Take Violent Turn". Wall Street Journal. http://online.wsj.com/article/SB121963304805268235.html?
mod=djemBestOfTheWeb. Retrieved 2008-08-29.
54.^ "Dangerous Encounters – Dragon Hunt – Photos: Komodo with transmitter". National
Geographic Channel. http://channel.nationalgeographic.com/series/dangerous-
encounters/3395/Photos#tab-Overview. Retrieved 2009-03-24.
55.^ "Komodo dragons kill Indonesian Fisherman". cnn.com (cnn.com). 2009-03-24.
http://edition.cnn.com/2009/WORLD/asiapcf/03/24/komodo.dragon/index.html. Retrieved 2009-03-
24.
56.^ Cagle, Jess (2001-06-23). "Transcript: Sharon Stone vs. the Komodo Dragon". TIME.
http://www.time.com/time/sampler/article/0,8599,133163,00.html. Retrieved 2010-02-12.
57.^ "Lizard bites Sharon Stone's husband". BBC News. 2001-06-11.
http://news.bbc.co.uk/2/hi/entertainment/1382755.stm. Retrieved 2010-02-12.
58.^ World Conservation Monitoring Centre (1996). Varanus komodoensis. 2006. IUCN Red List
of Threatened Species. IUCN 2006. www.iucnredlist.org. Retrieved on 11 May 2006.
59.^ "The official website of Komodo National Park, Indonesia.". Komodo National Park.
http://www.komodonationalpark.org/. Retrieved 2007-02-02.
60.^ "Appendices I, II and III". CITES. http://www.cites.org/eng/app/appendices.shtml. Retrieved
2008-03-24.
61.^ "ISIS Abstracts". ISIS. http://app.isis.org/abstracts/Abs50024.asp. Retrieved 2009-01-04.
62.^ Procter, J.B. (October 1928). "On a living Komodo Dragon Varanus komodoensis Ouwens,
exhibited at the Scientific Meeting". Proc. Zool. Soc. London: 1017–1019.
63.^ Lederer, G. (1931). "Erkennen wechselwarme Tiere ihren Pfleger?". Wochenschr. Aquar.-
Terrarienkunde 28: 636–638.
64.^ Murphy, J.; T. Walsh (2006). "Dragons and Humans" (PDF). Herpetological Review 37 (3):
269–275. http://zoohistory.co.uk/html/modules/Downloads/files/HRkomododragons.pdf.
65.^ "Such jokers, those Komodo dragons". Science News 78 (1): 78. August 2002.
66.^ Cagle, Jess (2001-06-23). "Transcript: Sharon Stone vs. the Komodo Dragon". Time.
http://www.time.com/time/sampler/article/0,8599,133163,00.html. Retrieved 2008-03-20.
67.^ Phillip T. Robinson (2004). Life at the Zoo: Behind the Scenes with the Animal Doctors.
New York: Columbia University Press. p. 79. ISBN 0-231-13248-4.
68.^ Pence, Angelica (2001-06-11). "Editor stable after attack by Komodo dragon / Surgeons
reattach foot tendons of Chronicle's Bronstein in L.A.". San Francisco Chronicle.
http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2001/06/11/MN204069.DTL. Retrieved 2008-03-23.

Wikimedia Commons has media related to: Varanus komodoensis
Wikispecies has information related to: Varanus komodoensis
• Attenborough, David (1957). Zoo Quest for a Dragon. London: Lutterworth Press.
• Auffenberg, Walter (1981). The Behavioral Ecology of the Komodo Monitor. Gainesville:
University Presses of Florida. ISBN 0-8130-0621-X.
• Burden, W. Douglas (1927). Dragon Lizards of Komodo: An Expedition to the Lost World of
the Dutch East Indies. Kessinger Publishing. ISBN 0-7661-6579-5.
• Eberhard, Jo; King, Dennis; Green, Brian; Knight, Frank; Keith Newgrain (1999). Monitors:
The Biology of Varanid Lizards. Malabar, Fla: Krieger Publishing Company. ISBN 1-57524-112-9.
• Lutz, Richard L; Lutz, Judy Marie (1997). Komodo: The Living Dragon. Salem, Or: DiMI
Press. ISBN 0-931625-27-0.
[hide]v · d · eVaranoidea
Kingdom: Animalia · Phylum: Chordata · Class: Reptilia · Order: Squamata
[hide] Extant species
Helodermatidae Beaded lizard · Gila Monster
Argus monitor · Black tree monitor · Bengal monitor · Black-spotted

Ridge-tailed Monitor · Crocodile monitor · Desert Monitor · Dumeril's monitor ·
Emerald tree monitor · Gray's monitor · Kimberley Rock Monitor · Komodo
dragon · Lace monitor · Mangrove monitor · Mertens' Water Monitor · Nile
Varanidae
monitor · Peacock monitor · Peach Throat monitor · Perentie · Rock monitor ·
Pilbara monitor · Rennell Island Monitor · Rosenberg's Monitor · Short-tailed
monitor · Spiny-tailed monitor · Timor tree monitor · Turquoise monitor · Sand
goanna · Savannah monitor · Water monitor · Yellow Monitor
Related
Monitor lizards · Cretaceous lizards · Helodermas · Mosasaurs
categories
[hide] Fossil species
Aigialosauridae Aigialosaurus · Carsosaurus · Judeasaurus · Kaganaias
Dolichosauridae Adriosaurus · Dolichosaurus · Acteosaurus
Helodermatidae Estesia
Mosasauridae Halisaurinae · Mosasaurinae · Plioplatecarpinae · Tylosaurinae
Varanidae Megalania · Palaeosaniwa
Retrieved from "http://en.wikipedia.org/wiki/Komodo_dragon"
Categories: IUCN Red List vulnerable species | Monitor lizards | Reptiles of Indonesia | Vertebrate
parthenogenesis | Megafauna of Eurasia | Venomous animals | Komodo National Park | Animals described in
1912
W000
W000
Multicellular organism

In this image, a wild-type Caenorhabditis elegans is stained to highlight the nuclei of its cells.
Multicellular organisms are organisms that consist of more than one cell, in contrast to single-celled
organisms. Most life that can be seen with the naked eye is multicellular, as are all animals (except for
specialized organisms such as Myxozoa) and land plants.
Contents
[hide]
• 2 Hypotheses for origin
• 2.1 The Symbiotic Theory
• 2.2 The Cellularization (Syncytial) Theory
• 2.3 The Colonial Theory
• 3 See also
• 4 References

Early life was most probably single celled. Multicellularity has evolved independently dozens of times
in the history of Earth, for example in plants and animals[1]. Multicellularity exists in both prokaryotes and
eukaryotes, and first appeared several billion years ago in cyanobacteria. In order to reproduce, true
multicellular organisms must solve the problem of regenerating a whole organism from germ cells (i.e. sperm
and egg cells), an issue that is studied in developmental biology. Therefore, the development of sexual
reproduction in unicellular organisms during the Mesoproterozoic is thought to have precipitated the
development and rise of multicellular life.[citation needed]
Multicellular organisms, especially long-living animals, also face the challenge of cancer, which
occurs when cells fail to regulate their growth within the normal program of development. Changes in tissue
morphology can be observed during this process.
[edit] Hypotheses for origin

There are various mechanisms by which multicellularity could have evolved. For now, there's little
evidence to support choosing one of them as the first to evolve.
One hypothesis is that a group of function-specific cells aggregated into a slug-like mass called a
grex, which moved as a multicellular unit. This is essentially what slime molds do. Another hypothesis is that
a primitive cell underwent nucleus division, thereby becoming a syncytium. A membrane would then form
around each nucleus (and the cellular space and organelles occupied in the space), thereby resulting in a
group of connected cells in one organism (this mechanism is observable in Drosophila). A third hypothesis is
that, as a unicellular organism divided, the daughter cells failed to separate, resulting in a conglomeration of
identical cells in one organism, which could later develop specialized tissues. This is what animal and plant
embryos do and also what colonial choanoflagellates apparently do [2].
Because the first multicellular organisms were simple, soft organisms lacking bone, shell or other
hard body parts, they are not well preserved in the fossil record[3]. One exception may be the demosponge,
which may have left a chemical signature in ancient rocks. The earliest fossils of multicellular organisms
include the contested Grypania spiralis and the fossils of the black shales of the Palaeoproterozoic
Francevillian Group Fossil B Formation in Gabon.[4]
Until recently phylogenetic reconstruction has been through anatomical (particularly embryological)
similarities. This is inexact, as living multicellular organisms such as animals and plants are more than 500
million years removed from their single-celled ancestors. Such a passage of time allows both divergent and
convergent evolution time to mimic similarities and accumulate differences between groups of modern and
extinct ancestral species. Modern phylogenetics uses sophisticated techniques such as alloenzymes,
satellite DNA and other molecular markers to describe traits that are shared between distantly related
lineages.
The evolution of multicellularity could have occurred in three ways:
[edit] The Symbiotic Theory

This theory suggests that the first multicellular organisms occurred from symbiosis (cooperation) of
different species of single celled organisms, each with different roles. Over time these organisms would
become so dependent on each other they would not be able to survive independently, eventually leading to
their genomes being incorporated into one, multicellular, organism[5]. Each respective organism would
become a separate lineage of differentiated cells within the newly created species.
This kind of severely co-dependent symbiosis can be seen frequently, such as in the relationship
between clown fish and Riterri sea anemones. In these cases it is extremely doubtful if either species would
survive very long if the other became extinct. However, the problem with this theory is that it is still not known
how each organism's DNA could be incorporated into one single genome to constitute them as a single
species. Although such symbiosis is theorized to have occurred (e.g. mitochondria and chloroplasts in animal
and plant cells - endosymbiosis) it has only happened extremely rarely and, even then, the genomes of the
endosymbionts have retained an element of distinction, separately replicating their DNA during mitosis of the
host species. For instance, the two or three symbiotic organisms forming the composite lichen, while
dependent on each other for survival, have to separately reproduce and then re-form to create one individual
organism once more.
[edit] The Cellularization (Syncytial) Theory

This theory states that a single unicellular organism could have developed internal membrane
partitions around each of its nuclei[6] Many protists such as the ciliates or slime moulds can have several
nuclei, lending support to this hypothesis. However, simple presence of multiple nuclei is not enough to
support the theory. Multiple nuclei of ciliates are dissimilar and have clear differentiated functions: the
macronucleus serves the organism's needs while the micronucleus is used for sexual-like reproduction with
exchange of genetic material. Slime molds syncitia form from individual amoeboid cells, like syncitial tissues
of some multicellular organisms, not the other way round. To be deemed valid, this theory needs a
demonstrable example and mechanism of generation of a multicellular organism from a pre-existing
syncytium.
[edit] The Colonial Theory

The third explanation of multicellularisation is the Colonial Theory proposed by Haeckel in 1874. This
theory claims that the symbiosis of many organisms of the same species (unlike the symbiotic theory, which
suggests the symbiosis of different species) led to a multicellular organism. At least some, presumably land-
evolved, multicellularity occurs by cells separating and then rejoining (e.g., cellular slime molds) whereas for
the majority of multicellular types (those that evolved within aquatic environments), multicellularity occurs as
a consequence of cells failing to separate following division[7]. The mechanism of this latter colony formation
can be as simple as incomplete cytokinesis, though multicellularity is also typically considered to involve
cellular differentiation[8]
The advantage of the Colonial Theory hypothesis is that it has been seen to occur independently
numerous times (in 16 different protoctistan phyla). For instance, during food shortages the amoeba
Dictyostelium groups together in a colony that moves as one to a new location. Some of these amoeba then
slightly differentiate from each other. Other examples of colonial organisation in protozoa are Volvocaceae,
such as Eudorina and Volvox (the latter of which consists of up to 500 — 50,000 cells (depending on the
species), only a fraction of which reproduce[9] (in one species 25 — 35, 8 asexually and around 15 — 25
sexually). However, it can often be hard to separate colonial protists from true multicellular organisms, as the
two concepts are not distinct. This problem plagues most hypotheses of how multicellularisation could have
occurred.
However, most scientists accept that multicellular organisms, from all phyla, evolved by the colonial
mechanism.
[edit] See also

• Cellular differentiation
• Organogenesis
• Embryogenesis
• Eukaryote
• Bacterial colony
• Nicole King, a biologist studying the evolution of multicellularity
[edit] References
1. ^ Bonner, John Tyler (1998). "The Origins of Multicellularity" (PDF, 0.2 MB). Integrative
Biology: Issues, News, and Reviews 1 (1): 27–36. doi:10.1002/(SICI)1520-6602(1998)1:1<27::AID-
INBI4>3.0.CO;2-6. ISSN 1093-4391. http://courses.cit.cornell.edu/biog1101/outlines/Bonner%20-
Origin%20of%20Multicellularity.pdf.
2. ^ In a Single-Cell Predator, Clues to the Animal Kingdom’s Birth by Sean B. Carroll
http://www.nytimes.com/2010/12/14/science/14creatures.html?scp=1&sq=In%20a%20Single-Cell
%20Predator,%20Clues%20to%20the%20Animal%20Kingdom’s%20Birth&st=cse
3. ^ A H Knoll, 2003. Life on a Young Planet. Princeton University Press. ISBN 0-691-00978-3
(hardcover), ISBN 0-691-12029-3 (paperback). An excellent book on the early history of life, very
accessible to the non-specialist; includes extensive discussions of early signatures, fossilization, and
organization of life.
4. ^ El Albani, Abderrazak; A, Bengtson S, Canfield DE, Bekker A, Macchiarelli R, Mazurier A,
Hammarlund EU, Boulvais P, Dupuy JJ, Fontaine C, Fürsich FT, Gauthier-Lafaye F, Janvier P,
Javaux E, Ossa FO, Pierson-Wickmann AC, Riboulleau A, Sardini P, Vachard D, Whitehouse M,
Meunier A. (1 July 2010). "Large colonial organisms with coordinated growth in oxygenated
environments 2.1 Gyr ago". Nature 466 (7302): 100–104. doi:10.1038/nature09166. ISSN 0028-0836.
PMID 20596019.
5. ^ Margulis, Lynn (1998). Symbiotic Planet: A New Look at Evolution. New York: Basic Books.
pp. 160. ISBN 9780465072729. http://www.questia.com/PM.qst?a=o&d=96971657.
6. ^ Hickman CP, Hickman FM (8 July 1974). Integrated Principles of Zoology (5th ed.). Mosby.
pp. 112. ISBN 9780801621840.
7. ^ Wolpert, L.; Szathmáry, E. (2002). "Multicellularity: Evolution and the egg". Nature 420
(6917): 745. doi:10.1038/420745a. PMID 12490925. edit
8. ^ Kirk, D. L. (2005). "A twelve-step program for evolving multicellularity and a division of
labor". BioEssays 27 (3): 299–310. doi:10.1002/bies.20197. PMID 15714559. edit
9. ^ AlgaeBase. Volvox Linnaeus, 1758: 820.

• Tree of Life Eukaryotes
Processes of
Population genetic
Evolutionary Canalisation · Inversion · Modularity · Phenotypic plasticity

developmental
biology (Evo-devo)
concepts

Modes of

Retrieved from "http://en.wikipedia.org/wiki/Multicellular_organism"

Categories: Developmental biology | Evolutionary biology
W000
Race (classification of humans)

This is the latest accepted revision, accepted on 1 February 2011.

This article may be too long to read and navigate comfortably. Please consider
splitting content into sub-articles and using this article for a summary of the key points of the
subject. (May 2009)
A series of articles on
Race
Main topics
Race and genetics
Human genetic clustering
Human genetic variation
Health
Ancestry and health
Ethnicity and health
Population groups in biomedicine
Race and intelligence
Social
Historical definitions
Race in Brazil
Race in the United States

Social interpretations of race
The Race Question (1950)

Related
Ethnic group
Genetics
Human evolution
Racism topics
Category: Race
This box: view · talk · edit

Race refers to classifications of humans into relatively large and distinct populations or groups often
based on factors such as appearance based on heritable phenotypical characteristics or geographic
ancestry, but also often influenced by and correlated with traits such as culture, ethnicity and socio-economic
status.[1] As a biological term, race denotes genetically divergent human populations that can be marked by
common phenotypic traits.[2] This sense of race is often used by forensic anthropologists when analyzing
skeletal remains, in biomedical research, and in race-based medicine.[3] The study of shared traits among
peoples is also conducted along ethnic lines, involving the endogamic history of groups. Racial groupings
may correspond with patterns of social stratification, helping social scientists to understand the underlying
disparities among racially defined groups of people.[4] Additionally, law enforcement utilizes race to create
profiles of wanted suspects in an expeditious manner.
While scientists use the concept of race to make practical distinctions among fuzzy sets of traits, the
scientific community feels that the idea of race is often used by the general public[5] in a naïve[6] or simplistic
way, erroneously designating wholly discrete types of individuals. Among humans, race has no cladistic
significance—all people belong to the same hominid subspecies, Homo sapiens sapiens.[7][8] Regardless of
the extent to which race exists, the word "race" is problematic and may carry negative connotations.[9] Social
conceptions and groupings of races vary over time, involving folk taxonomies[10][11][12] that define essential
types of individuals based on perceived sets of traits. Scientists consider biological essentialism obsolete,[13]
and generally discourage racial explanations for collective differentiation in both physical and behavioral
traits.[6][14]
As people define and put about different conceptions of race, they actively create contrasting social
realities through which racial categorization is achieved in varied ways.[15] In this sense, races are said to be
social constructs.[16][17] These constructs can develop within various legal,[15][18] economic,[18] and
sociopolitical[19][20] contexts, and at times may be the effect, rather than the cause, of major social
situations.[19] Socioecomonic factors,[19][21][22][23][24] in combination with early but enduring[25] views of
race, have led to considerable suffering amongst the disadvantaged racial groups. Scholars continue to
debate the degrees to which racial categories are biologically warranted[9][26] and socially constructed, as
well as the extent to which the realities[27] of race must be acknowledged in order for society to comprehend
and address racism adequately.[15][26]
Contents
[hide]
• 1 Early modern concepts of race
• 2 Modern debate
• 2.1 Models of human evolution
• 2.2 Race as subspecies
• 2.2.1 Morphological subspecies
• 2.2.2 Subspecies as genetically
differentiated populations
• 2.2.3 Subspecies as clade
• 2.3 Population genetics
• 2.3.1 Clines
• 2.3.2 Populations
• 2.4 Summary of different biological definitions of
race
• 2.5 Current views across disciplines
• 2.6 Races as social constructions
• 2.6.1 In the United States
• 2.6.2 In Brazil
• 2.6.3 Marketing of race: genetic lineages as
social lineages
• 2.7 Race and intelligence
Early modern concepts of race
See also: Historical definitions of race
Ethnographic Map from Meyers Konversationslexikon of 1885-90, listing Caucasian races (Aryans,
Hamites, Semites), Mongolian races (northern Mongolian, Chinese and Indo-Chinese, Japanese and
Korean, Tibetan, Malayan, Polynesian, Maori, Micronesian, Eskimo, American Indian), and Negroid races
(African, Hottentots, Melanesians/Papua, "Negrito", Australian Aborigine, Dravidians, Sinhalese) The word
"race," denoting lineage, comes from a French translation of haras (silent "h") into the Italian razza — which in
Italian of that time applied to animals, not people. This points to current English and Italian usage being
derived and adapted, respectively, from the French. (Italians, around the time of Marco Polo's
characterization of the Persians, used schiatta to denote race; that use of schiatta continues today).[28]
While race used to describe peoples, nations or ethnic groups is several centuries old—Marco Polo in
his 13th-century travels, for example, describes the Persian race[29]—the 19th- and 20th-century concepts of
its meaning and modern sensibilities about how society views race date back only to the 17th century.[30]
The word "race", along with many of the ideas now associated with the term, were products of
European imperialism and colonization during the age of exploration.[31] As Europeans encountered people
from different parts of the world, they speculated about the physical, social, and cultural differences among
various human groups. The rise of the Atlantic slave trade, which gradually displaced an earlier trade in
slaves from throughout the world, created a further incentive to categorize human groups in order to justify
the subordination of African slaves.[32] Drawing on Classical sources and upon their own internal
interactions — for example, the hostility between the English and Irish was a powerful influence on early
thinking about the differences between people[33] — Europeans began to sort themselves and others into
groups associated with physical appearance and with deeply ingrained behaviors and capacities. A set of folk
beliefs took hold that linked inherited physical differences between groups to inherited intellectual,
behavioral, and moral qualities.[34] Although similar ideas can be found in other cultures,[35] they appear not
to have had as much influence upon their social structures as was found in Europe and the parts of the world
colonized by Europeans. However, often brutal conflicts between ethnic groups have existed throughout
history and across the world.[36]
The first post-Classical published classification of humans into distinct races seems to be François
Bernier's Nouvelle division de la terre par les différents espèces ou races qui l'habitent ("New division of
Earth by the different species or races which inhabit it"), published in 1684. In the 18th century, the
differences among human groups became a focus of scientific investigation.[37] Initially, scholars focused on
cataloguing and describing "The Natural Varieties of Mankind," as Johann Friedrich Blumenbach entitled his
1775 text (which established the five major divisions of humans still reflected in some racial classifications,
i.e., the Caucasoid race, Mongoloid race, Ethiopian race (later termed the Negroid race), American Indian
race, and Malayan race). From the 17th through the 19th centuries, the merging of folk beliefs about group
differences with scientific explanations of those differences produced what one scholar has called an
"ideology of race".[31] According to this ideology, races are primordial, natural, enduring and distinct. It was
further argued that some groups may be the result of mixture between formerly distinct populations, but that
careful study could distinguish the ancestral races that had combined to produce admixed groups.[36]
Modern debate
The lay concept of race does not correspond to the variation that exists in nature.
— Joseph L. Graves, Jr.[5]
Models of human evolution

See also: Multiregional hypothesis and Recent single origin hypothesis
In a 1995 article, Leonard Lieberman and Fatimah Jackson suggested that any new support for a
biological concept of race will likely come from another source, namely, the study of human evolution. They
therefore ask what, if any, implications current models of human evolution may have for any biological
conception of race.[38]
Today, all humans are classified as belonging to the species Homo sapiens and sub-species Homo
sapiens sapiens. However, this is not the first species of hominids: the first species of genus Homo, Homo
habilis, are theorized to have evolved in East Africa at least 2 million years ago, and members of this species
populated different parts of Africa in a relatively short time. Homo erectus is theorized to have evolved more
than 1.8 million years ago, and by 1.5 million years ago had spread throughout Europe and Asia. Virtually all
physical anthropologists agree that Homo sapiens evolved out of Homo erectus.
Anthropologists have been divided as to whether Homo sapiens evolved as one interconnected
species from H. erectus (called the Multiregional Model, or the Regional Continuity Model), or evolved only in
East Africa, and then migrated out of Africa and replaced H. erectus populations throughout Europe and Asia
(called the Out of Africa Model or the Complete Replacement Model). Anthropologists continue to debate
both possibilities, and the evidence is technically open to debate as to which model is correct, although most
anthropologists currently favor the Out of Africa model.
Lieberman and Jackson argued that while advocates of both the Multiregional Model and the Out of
Africa Model use the word race and make racial assumptions, none define the term.[38] They conclude that
"Each model has implications that both magnify and minimize the differences between races. Yet each model
seems to take race and races as a conceptual reality. The net result is that those anthropologists who prefer
to view races as a reality are encouraged to do so" and conclude that students of human evolution would be
better off avoiding the word race, and instead describe genetic differences in terms of populations and clinal
gradations.[38]
Race as subspecies
Further information: Race (biology), Species, Subspecies, Systematics, Phylogenetics, and
Cladistics.
With the modern evolutionary synthesis in the early 20th century, many biologists sought to use
evolutionary models and populations genetics in an attempt to formalise taxonomy. The Biological Species
Concept (BSC) is the most widely used system for describing species; this concept defines a species as a
group of organisms that interbreed in their natural environment and produce viable offspring. In practice,
species are not classified according to the BSC but according to typology by the use of a holotype, due to the
difficulty of determining whether all members of a group of organisms do or can in practice potentially
interbreed.[39] BSC species are routinely classified on a subspecific level, though this classification is
conducted differently for different taxons, for mammals the normal taxonomic unit below the species level is
usually the subspecies.[40]
More recently the Phylogenetic Species Concept (PSC) has gained a substantial following. The PSC
is based on the idea of a least-inclusive taxonomic unit (LITU), in phylogenetic classification no subspecies
can exist because they would automatically constitute a LITU (any monophyletic group). Technically species
cease to exist as do all hierarchical taxa, a LITU is effectively defined as any monophyletic taxon,
phylogenetics is strongly influenced by cladistics which classifies organisms based on evolution rather than
similarities between groups of organisms.[39] In biology the term "race" is used with caution because it can
be ambiguous, "'Race' is not being defined or used consistently; its referents are varied and shift depending
on context. The term is often used colloquially to refer to a range of human groupings. Religious, cultural,
social, national, ethnic, linguistic, genetic, geographical and anatomical groups have been and sometimes
still are called 'races'".[7] Generally when it is used it is synonymous with subspecies.[41] One main obstacle
to identifying subspecies is that, while it is a recognised taxonomic term, it has no precise definition.[42]
Species of organisms that are monotypic (i.e., form a single subspecies) display at least one of these
properties:
• All members of the species are very similar and cannot be sensibly divided into biologically
significant subcategories.
• The individuals vary considerably but the variation is essentially random and largely
meaningless so far as genetic transmission of these variations is concerned (many plant species fit
into this category, which is why horticulturists interested in preserving, say, a particular flower color
avoid propagation from seed, and instead use vegetative methods like propagation from cuttings).
• The variation among individuals is noticeable and follows a pattern, but there are no clear
dividing lines among separate groups: they fade imperceptibly into one another. Such clinal variation
displays a lack of allopatric partition between groups (i.e., a clearly defined boundary demarcating
the subspecies), which is usually required before they are recognised as subspecies.[43]
A polytypic species has two or more subspecies. These are separate populations that are more
genetically different from one another and that are more reproductively isolated, gene flow between these
populations is much reduced leading to genetic differentiation.
Morphological subspecies
Traditionally subspecies are seen as geographically isolated and genetically differentiated
populations.[42] Or to put it another way "the designation 'subspecies' is used to indicate an objective degree
of microevolutionary divergence"[7] One objection to this idea is that it does not identify any degree of
differentiation. Therefore, any population that is somewhat biologically different could be considered a
subspecies, even to the level of a local population. As a result it is necessary to impose a threshold on the
level of difference that is required for a population to be designated a subspecies.[42]
This effectively means that populations of organisms must have reached a certain measurable level
of difference to be recognised as subspecies. Dean Amadon proposed in 1949 that subspecies would be
defined according to the seventy-five percent rule which means that 75% of a population must lie outside
99% of the range of other populations for a given defining morphological character or a set of characters. The
seventy-five percent rule still has defenders but other scholars argue that it should be replaced with ninety or
ninety-five percent rule.[44]
In 1978, Sewall Wright suggested that human populations that have long inhabited separated parts
of the world should, in general, be considered different subspecies by the usual criterion that most individuals
of such populations can be allocated correctly by inspection. It does not require a trained anthropologist to
classify an array of Englishmen, West Africans, and Chinese with 100% accuracy by features, skin color, and
type of hair despite so much variability within each of these groups that every individual can easily be
distinguished from every other. However, it is customary to use the term race rather than subspecies for the
major subdivisions of the human species as well as for minor ones.[45]
On the other hand in practice subspecies are often defined by easily observable physical
appearance, but there is not necessarily any evolutionary significance to these observed differences, so this
form of classification has become less acceptable to evolutionary biologists.[7][42] Likewise this typological
approach to race is generally regarded as discredited by biologists and anthropologists.
Because of the difficulty in classifying subspecies morphologically, many biologists have found the
concept problematic, citing issues such as:[7]
• Visible physical differences do not always correlate with one another, leading to the
possibility of different classifications for the same individual organisms.
• Parallel evolution can lead to the existence of the appearance of similarities between groups
of organisms that are not part of the same species.
• Isolated populations within previously designated subspecies have been found to exist.
• The criteria for classification may be arbitrary if they ignore gradual variation in traits.
Subspecies as genetically differentiated populations
Another way to look at differences between populations is to measure genetic differences rather than
physical differences. The Human Genome Project found only gradations in genetic variation, not sharp lines
which would naturally define notions of race or ethnicity. "People who have lived in the same geographic
region for many generations may have some alleles in common, but no allele will be found in all members of
one population and in no members of any other."[46]
Genetic differences between populations of organisms can be measured using the fixation index of
Sewall Wright, which is often abbreviated to FST. This statistic is used to compare differences between any
two given populations and can be used to measure genetic differences between populations for individual
genes, or for many genes simultaneously.[47] For example it is often stated that the fixation index for humans
is about 0.15. This means that about 85% of the variation measured in the human population is within any
population, and about 15% of the variation occurs between populations, or that any two individuals from
different populations are almost as likely to be more similar to each other than either is to a member of their
own group.[7][42]
It is often stated that human genetic variation is low compared to other mammalian species, and it
has been claimed that this should be taken as evidence that there is no natural subdivision of the human
population.[36][48] Wright himself believed that a value of 0.25 represented great genetic variation and that
an FST of 0.15-0.25 represented moderate variation. It should, however, be noted that about 5% of human
variation occurs between populations within continents, and therefore the F ST between continental groups of
humans (or races) is as low as 0.1 (or possibly lower).[47]
In their 2003 paper "Human Genetic Diversity and the Nonexistence of Biological Races"[49] Jeffrey
Long and Rick Kittles give a long critique of the application of F ST to human populations. They find that the
figure of 85% is misleading because it implies that all human populations contain on average 85% of all
genetic diversity. They claim that this does not correctly reflect human population history, because it treats all
human groups as independent. A more realistic portrayal of the way human groups are related is to
understand that some human groups are parental to other groups and that these groups represent
paraphyletic groups to their descent groups. For example, under the recent African origin theory the human
population in Africa is paraphyletic to all other human groups because it represents the ancestral group from
which all non-African populations derive, but more than that, non-African groups only derive from a small
non-representative sample of this African population.
This means that all non-African groups are more closely related to each other and to some African
groups (probably east Africans) than they are to others, and further that the migration out of Africa
represented a genetic bottleneck, with much of the diversity that existed in Africa not being carried out of
Africa by the emigrating groups. This view produces a version of human population movements that do not
result in all human populations being independent; but rather, produces a series of dilutions of diversity the
further from Africa any population lives, each founding event representing a genetic subset of its parental
population. Long and Kittles find that rather than 85% of human genetic diversity existing in all human
populations, about 100% of human diversity exists in a single African population, whereas only about 70% of
human genetic diversity exists in a population derived from New Guinea. Long and Kittles make the
observation that this still produces a global human population that is genetically homogeneous compared to
other mammalian populations.[49]
Wright's F statistics are not used to determine whether a group can be described as a subspecies or
not, though the statistic is used to measure the degree of differentiation between populations, the degree of
genetic differentiation is not a marker of subspecies status.[47] Generally taxonomists prefer to use
phylogenetic analysis to determine whether a population can be considered a subspecies. Phylogenetic
analysis relies on the concept of derived characteristics that are not shared between groups, usually applying
to populations that are allopatric (geographically separated) and therefore discretely bounded. This would
make a subspecies, evolutionarily speaking, a clade - a group with a common evolutionary ancestor
population.[42] The smooth gradation of human genetic variation in general rules out any idea that human
population groups can be considered monophyletic (cleanly divided) as there appears to always have been
considerable gene flow between human populations.[42]
Subspecies as clade
By the 1970s many evolutionary scientists were avoiding the concept of "subspecies" as a taxonomic
category for four reasons:
• very few data indicate that contiguous subspecies ever become species[ citation needed]
• geographically disjunct groups regarded as subspecies usually can be demonstrated to
actually be distinct species[citation needed]
• subspecies had been recognized on the basis of only 2-5 phenotypic characters, which often
were adaptations to local environments but which did not reflect the evolutionary differentiation of
populations as a whole[citation needed]
• with the advent of molecular techniques used to get a better handle on genetic introgression
(gene flow), the picture afforded by looking at genetic variation was often at odds with the phenotypic
variation (as is the case with looking at genes versus percentage of epidermal melanin in human
populations)[citation needed]
These criticisms have coincided with the rise of cladistics
A clade is a taxonomic group of organisms consisting of a single common ancestor and all the
descendants of that ancestor. Every creature produced by sexual reproduction has two immediate lineages,
one maternal and one paternal.[50] Whereas Carolus Linnaeus established a taxonomy of living organisms
based on anatomical similarities and differences, cladistics seeks to establish a taxonomy—the phylogenetic
tree—based on genetic similarities and differences and tracing the process of acquisition of multiple
characteristics by single organisms. Some researchers have tried to clarify the idea of race by equating it to
the biological idea of the clade. Often mitochondrial DNA or Y chromosome sequences are used to study
ancient human migration paths. These single-locus sources of DNA do not recombine and are inherited from
a single parent. Individuals from the various continental groups tend to be more similar to one another than to
people from other continents, and tracing either mitochondrial DNA or non-recombinant Y-chromosome DNA
explains how people in one place may be largely derived from people in some remote location.
Most evolutionary scientists have rejected the identification of races with clades for two reasons.
First, as Rachel Caspari (2003) argued, clades are by definition monophyletic groups (a taxon that includes
all descendants of a given ancestor) since no groups currently regarded as races are monophyletic, none of
those groups can be clades.
For anthropologists Lieberman and Jackson, however, there are more profound methodological and
conceptual problems with using cladistics to support concepts of race. They emphasize that "the molecular
and biochemical proponents of this model explicitly use racial categories in their initial grouping of samples".
For example, the large and highly diverse macroethnic groups of East Indians, North Africans, and
Europeans are presumptively grouped as Caucasians prior to the analysis of their DNA variation.
This limits and skews interpretations, obscures other lineage relationships, deemphasizes the impact
of more immediate clinal environmental factors on genomic diversity, and can cloud our understanding of the
true patterns of affinity. They argue that however significant the empirical research, these studies use the
term race in conceptually imprecise and careless ways. They suggest that the authors of these studies find
support for racial distinctions only because they began by assuming the validity of race.
For empirical reasons we prefer to place emphasis on clinal variation, which recognizes the
existence of adaptive human hereditary variation and simultaneously stresses that such
variation is not found in packages that can be labeled races.[38]
Indeed, recent research reports evidence for smooth, clinal genetic variation even in regions
previously considered racially homogeneous, with the apparent gaps turning out to be artifacts of sampling
techniques (Serre & Pääbo 2004). These scientists do not dispute the importance of cladistic research, only
its retention of the word race, when reference to populations and clinal gradations are more than adequate to
describe the results.
Population genetics
At the beginning of the 20th century, anthropologists accepted, and taught, the belief that biologically
distinct races are isomorphic with distinct linguistic, cultural, and social groups, while popularly applying that
belief to the field of eugenics, in conjunction with a practice that is now called scientific racism.[51]
Charles Darwin's theory of evolution was co-opted by the budding eugenics movement as a
justification for systematic population and racial planning in the early 20th century.
Following the horrific consequences of the Nazi eugenics program to achieve and ensure "race
purity", racial essentialism lost scientific credibility. Race anthropologists were pressured to acknowledge
findings coming from studies of culture and population genetics, and to revise their conclusions about the
sources of phenotypic variation.[52] Most modern anthropologists and biologists came to view race as an
invalid genetic or biological designation.[53]
The first to challenge the concept of race on empirical grounds were anthropologists Franz Boas,
who demonstrated phenotypic plasticity due to environmental factors,[54] and Ashley Montagu who relied on
evidence from genetics.[55] E. O. Wilson then challenged the concept from the perspective of general animal
systematics, and further rejected the claim that "races" were equivalent to "subspecies".[56]
Clines
One crucial innovation in reconceptualizing genotypic and phenotypic variation was anthropologist C.
Loring Brace's observation that such variations, insofar as it is affected by natural selection, migration, or
genetic drift, are distributed along geographic gradations or clines.[57] In part this is due to isolation by
distance. This point called attention to a problem common to phenotype-based descriptions of races (for
example, those based on hair texture and skin color): they ignore a host of other similarities and differences
(for example, blood type) that do not correlate highly with the markers for race. Thus, anthropologist Frank
Livingstone's conclusion, that since clines cross racial boundaries, "there are no races, only clines".[58]
In a response to Livingstone, Theodore Dobzhansky argued that when talking about race one must
be attentive to how the term is being used: "I agree with Dr. Livingstone that if races have to be 'discrete
units,' then there are no races, and if 'race' is used as an 'explanation' of the human variability, rather than
vice versa, then the explanation is invalid." He further argued that one could use the term race if one
distinguished between "race differences" and "the race concept." The former refers to any distinction in gene
frequencies between populations; the latter is "a matter of judgment." He further observed that even when
there is clinal variation, "Race differences are objectively ascertainable biological phenomena… but it does
not follow that racially distinct populations must be given racial (or subspecific) labels."[58] In short,
Livingstone and Dobzhansky agree that there are genetic differences among human beings; they also agree
that the use of the race concept to classify people, and how the race concept is used, is a matter of social
convention. They differ on whether the race concept remains a meaningful and useful social convention.
In 1964, biologists Paul Ehrlich and Holm pointed out cases where two or more clines are distributed
discordantly—for example, melanin is distributed in a decreasing pattern from the equator north and south;
frequencies for the haplotype for beta-S hemoglobin, on the other hand, radiate out of specific geographical
points in Africa.[59] As anthropologists Leonard Lieberman and Fatimah Linda Jackson observed,
"Discordant patterns of heterogeneity falsify any description of a population as if it were genotypically or even
phenotypically homogeneous".[38]
Patterns such as those seen in human physical and genetic variation as described above, have led
to the consequence that the number and geographic location of any described races is highly dependent on
the importance attributed to, and quantity of, the traits considered. For example, if only skin color and a "two
race" system of classification were used, then one might classify Indigenous Australians in the same race as
Black people, and Caucasians in the same race as East Asian people, but biologists and anthropologists
would dispute that these classifications have any scientific validity. Scientists discovered a skin-lighting
mutation that partially accounts for the appearance of Light skin in humans (people who migrated out of
Africa northward into what is now Europe) which they estimate occurred 20,000 to 50,000 years ago. The
East Asians owe their relatively light skin to different mutations.[60] On the other hand, the greater the
number of traits (or alleles) considered, the more subdivisions of humanity are detected, since traits and
gene frequencies do not always correspond to the same geographical location. Or as Ossorio & Duster
( 2005) put it:
Anthropologists long ago discovered that humans' physical traits vary gradually, with groups that
are close geographic neighbors being more similar than groups that are geographically
separated. This pattern of variation, known as clinal variation, is also observed for many alleles
that vary from one human group to another. Another observation is that traits or alleles that vary
from one group to another do not vary at the same rate. This pattern is referred to as
nonconcordant variation. Because the variation of physical traits is clinal and nonconcordant,
anthropologists of the late 19th and early 20th centuries discovered that the more traits and the
more human groups they measured, the fewer discrete differences they observed among races
and the more categories they had to create to classify human beings. The number of races
observed expanded to the 30s and 50s, and eventually anthropologists concluded that there
were no discrete races.[61] Twentieth and 21st century biomedical researchers have discovered
this same feature when evaluating human variation at the level of alleles and allele frequencies.
Nature has not created four or five distinct, nonoverlapping genetic groups of people.
More recent genetic studies indicate that skin color may change radically over as few as 100
generations, or about 2,500 years, given the influence of the environment.[62]
Populations
Population geneticists have debated as to whether the concept of population can provide a basis for
a new conception of race. In order to do this, a working definition of population must be found. Surprisingly,
there is no generally accepted concept of population that biologists use. It has been pointed out that the
concept of population is central to ecology, evolutionary biology and conservation biology, but also that most
definitions of population rely on qualitative descriptions such as "a group of organisms of the same species
occupying a particular space at a particular time"[63] Waples and Gaggiotti identify two broad types of
definitions for populations; those that fall into an ecological paradigm, and those that fall into an evolutionary
paradigm. Examples of such definitions are:
• Ecological paradigm: A group of individuals of the same species that co-occur in space and
time and have an opportunity to interact with each other.
• Evolutionary paradigm: A group of individuals of the same species living in close-enough
proximity that any member of the group can potentially mate with any other member.[63]
Richard Lewontin, claiming that 85 percent of human variation occurs within populations and not
among populations, argued that neither "race" nor "subspecies" were appropriate or useful ways to describe
populations.[64] Nevertheless, barriers—which may be cultural or physical— between populations can limit
gene flow and increase genetic differences. Recent work by population geneticists conducting research in
Europe suggests that ethnic identity can be a barrier to gene flow.[65] Others, such as Ernst Mayr, have
argued for a notion of "geographic race".[66] Some researchers report the variation between racial groups
(measured by Sewall Wright's population structure statistic FST) accounts for as little as 5% of human genetic
variation. Sewall Wright himself commented that if differences this large were seen in another species, they
would be called subspecies.[45] In 2003 A. W. F. Edwards argued that cluster analysis supersedes
Lewontin's arguments (see below).
These empirical challenges to the concept of race forced evolutionary sciences to reconsider their
definition of race. Mid-century, anthropologist William C. Boyd defined race as:
A population which differs significantly from other populations in regard to the frequency of one
or more of the genes it possesses. It is an arbitrary matter which, and how many, gene loci we choose
to consider as a significant "constellation".[67]
Lieberman & Kirk (1995) have pointed out that "the weakness of this statement is that if one gene
can distinguish races then the number of races is as numerous as the number of human couples
reproducing." Moreover, anthropologist Stephen Molnar has suggested that the discordance of clines
inevitably results in a multiplication of races that renders the concept itself useless.[68]
The distribution of many physical traits resembles the distribution of genetic variation within and
between human populations.[69][70] For example, ~90% of the variation in human head shapes occurs
within every human group, and ~10% separates groups, with a greater variability of head shape among
individuals with recent African ancestors.[71]
Conversely, in the paper "Genetic similarities within and between human populations" Witherspoon
et al. (2007) show that even when individuals can be reliably assigned to specific population groups, it is still
possible for two randomly chosen individuals from different populations/clusters to be more similar to each
other than to a randomly chosen member of their own cluster. This is because multi locus clustering relies on
population level similarities, rather than individual similarities, so that each individual is classified according
to their similarity to the typical genotype for any given population. The paper claims that this masks a great
deal of genetic similarity between individuals belonging to different clusters. Or in other words, two
individuals from different clusters can be more similar to each other than to a member of their own cluster,
while still both being more similar to the typical genotype of their own cluster than to the typical genotype of a
different cluster.[72]
When differences between individual pairs of people are tested, Witherspoon et al. found that the
answer to the question "How often is a pair of individuals from one population genetically more dissimilar
than two individuals chosen from two different populations?" is not adequately addressed by multi locus
clustering analyses. They found that even for just three population groups separated by large geographic
ranges (European, African and East Asian) the inclusion of many thousands of loci is required before the
answer can become "never". On the other hand, the accurate classification of the global population must
include more closely related and admixed populations, which will increase this above zero, so they state "In a
similar vein, Romualdi et al. (2002) and Serre & Pääbo (2004) have suggested that highly accurate
classification of individuals from continuously sampled (and therefore closely related) populations may be
impossible". Witherspoon et al. conclude "The fact that, given enough genetic data, individuals can be
correctly assigned to their populations of origin is compatible with the observation that most human genetic
variation is found within populations, not between them. It is also compatible with our finding that, even when
the most distinct populations are considered and hundreds of loci are used, individuals are frequently more
similar to members of other populations than to members of their own population"[72]
Summary of different biological definitions of race

Biological definitions of race (Long & Kittles 2003)
Concept Reference Definition
"A great division of mankind, characterized as a group

by the sharing of a certain combination of features, which have
Hooton
Essentialist been derived from their common descent, and constitute a
(1926)
vague physical background, usually more or less obscured by
individual variations, and realized best in a composite picture."
"A subspecies is an aggregate of phenotypically similar

populations of a species, inhabiting a geographic subdivision of
Taxonomic Mayr (1969)
the range of a species, and differing taxonomically from other
populations of the species."
"Races are genetically distinct Mendelian populations.

Dobzhansky
Population They are neither individuals nor particular genotypes, they
(1970)
consist of individuals who differ genetically among themselves."
"A subspecies (race) is a distinct evolutionary lineage
within a species. This definition requires that a subspecies be
Templeton genetically differentiated due to barriers to genetic exchange
Lineage
(1998) that have persisted for long periods of time; that is, the
subspecies must have historical continuity in addition to current
genetic differentiation."
Current views across disciplines

One result of debates over the meaning and validity of the concept of race is that the current
literature across different disciplines regarding human variation lacks consensus, though within some fields,
such as biology, there is strong consensus. Some studies use the word race in its early essentialist
taxonomic sense. Many others still use the term race, but use it to mean a population, clade, or haplogroup.
Others eschew the concept of race altogether, and use the concept of population as a less problematic unit
of analysis.
Since 1932, an increasing number of college textbooks introducing physical anthropology have
rejected race as a valid concept: from 1932 to 1976, only seven out of thirty-two rejected race; from 1975 to
1984, thirteen out of thirty-three rejected race; from 1985 to 1993, thirteen out of nineteen rejected race.
According to one academic journal entry, where 78 percent of the articles in the 1931 Journal of Physical
Anthropology employed these or nearly synonymous terms reflecting a bio-race paradigm, only 36 percent
did so in 1965, and just 28 percent did in 1996.[73] The Statement on "Race" (1998) composed by a select
committee of anthropologists and issued by the executive board of the American Anthropological Association
as a statement they "believe [...] represents generally the contemporary thinking and scholarly positions of a
majority of anthropologists", declares:[74]}}
With the vast expansion of scientific knowledge in this century, ... it has become clear that
human populations are not unambiguous, clearly demarcated, biologically distinct groups. [...]
Given what we know about the capacity of normal humans to achieve and function within any
culture, we conclude that present-day inequalities between so-called "racial" groups are not
consequences of their biological inheritance but products of historical and contemporary social,
economic, educational, and political circumstances.
In an ongoing debate, some geneticists[who?] argue that race is neither a meaningful concept nor a
useful heuristic device,[75] and even that genetic differences among groups are biologically meaningless,[76]
because more genetic variation exists within such races than among them, and that racial traits overlap
without discrete boundaries.[77] Other geneticists, in contrast, argue that categories of self-identified
race/ethnicity or biogeographic ancestry are both valid and useful,[78] that these categories correspond to
clusters inferred from multilocus genetic data,[79] and that this correspondence implies that genetic factors
might contribute to unexplained phenotypic variation between groups.[80]
In February, 2001, the editors of the medical journal Archives of Pediatrics and Adolescent Medicine
asked authors to no longer use race as an explanatory variable and not to use obsolescent terms. Some
other peer-reviewed journals, such as the New England Journal of Medicine and the American Journal of
Public Health, have made similar endeavours.[81] Furthermore, the National Institutes of Health recently
issued a program announcement for grant applications through February 1, 2006, specifically seeking
researchers who can investigate and publicize among primary care physicians the detrimental effects on the
nation's health of the practice of medical racial profiling using such terms. The program announcement
quoted the editors of one journal as saying that, "analysis by race and ethnicity has become an analytical
knee-jerk reflex."[82]
A survey, taken in 1985 (Lieberman et al. 1992), asked 1,200 American scientists how many
disagree with the following proposition: "There are biological races in the species Homo sapiens." The
responses were:
• biologists 16%
• developmental psychologists 36%
• physical anthropologists 41%
• cultural anthropologists 53%[83]
The figure for physical anthropologists at PhD granting departments was slightly higher, rising from
41% to 42%, with 50% agreeing. This survey, however, did not specify any particular definition of race
(although it did clearly specify biological race within the species Homo sapiens); it is difficult to say whether
those who supported the statement thought of race in taxonomic or population terms.
The same survey, taken in 1999,[84] showed the following changing results for anthropologists:
• physical anthropologists 69%
• cultural anthropologists 80%
On May 17, 1998 The American Anthropological Association produced a "Statement on 'Race'":[85]
In the United States both scholars and the general public have been conditioned to viewing
human races as natural and separate divisions within the human species based on visible
physical differences. With the vast expansion of scientific knowledge in this century, however, it
has become clear that human populations are not unambiguous, clearly demarcated,
biologically distinct groups. Evidence from the analysis of genetics (e.g., DNA) indicates that
most physical variation, about 94%, lies within so-called racial groups. Conventional geographic
"racial" groupings differ from one another only in about 6% of their genes. This means that there
is greater variation within "racial" groups than between them. In neighboring populations there is
much overlapping of genes and their phenotypic (physical) expressions. Throughout history
whenever different groups have come into contact, they have interbred. The continued sharing
of genetic materials has maintained all of humankind as a single species.
In Poland the race concept was rejected by only 25 percent of anthropologists in 2001, although:
"Unlike the U.S. anthropologists, Polish anthropologists tend to regard race as a term without taxonomic
value, often as a substitute for population."[86]
In the face of these issues, some evolutionary scientists have simply abandoned the concept of race
in favor of "population." What distinguishes population from previous groupings of humans by race is that it
refers to a breeding population (essential to genetic calculations) and not to a biological taxon. Other
evolutionary scientists have abandoned the concept of race in favor of cline (meaning, how the frequency of
a trait changes along a geographic gradient). (The concepts of population and cline are not, however,
mutually exclusive and both are used by many evolutionary scientists.)
According to Jonathan Marks,[87]
By the 1970s, it had become clear that (1) most human differences were cultural; (2) what was
not cultural was principally polymorphic - that is to say, found in diverse groups of people at
different frequencies; (3) what was not cultural or polymorphic was principally clinal - that is to
say, gradually variable over geography; and (4) what was left - the component of human
diversity that was not cultural, polymorphic, or clinal - was very small.
A consensus consequently developed among anthropologists and geneticists that race as the
previous generation had known it - as largely discrete, geographically distinct, gene pools - did
not exist.
In the face of this rejection of race by evolutionary scientists, many social scientists have replaced
the word race with the word "ethnicity" to refer to self-identifying groups based on beliefs concerning shared
culture, ancestry and history. Alongside empirical and conceptual problems with "race," following the Second
World War, evolutionary and social scientists were acutely aware of how beliefs about race had been used to
justify discrimination, apartheid, slavery, and genocide. This questioning gained momentum in the 1960s
during the U.S. civil rights movement and the emergence of numerous anti-colonial movements worldwide.
They thus came to believe that race itself is a social construct, a concept that was believed to correspond to
an objective reality but which was believed in because of its social functions.[88]
Races as social constructions

Main articles: Social interpretations of race and Racialism
Even as the idea of race was becoming a powerful organizing principle in many societies, some
observers criticized the concept. In Europe, the gradual transition in appearances from one group to adjacent
groups suggested to Blumenbach that "one variety of mankind does so sensibly pass into the other, that you
cannot mark out the limits between them".[87] As anthropologists and other evolutionary scientists have
shifted away from the language of race to the term population to talk about genetic differences, historians,
cultural anthropologists and other social scientists re-conceptualized the term "race" as a cultural category or
social construct—a particular way that some people talk about themselves and others.
Craig Venter and Francis Collins of the National Institute of Health jointly made the announcement of
the mapping of the human genome in 2000. Upon examining the data from the genome mapping, Venter
realized that although the genetic variation within the human species is on the order of 1-3% (instead of the
previously assumed 1%), the types of variations do not support notion of genetically defined races. Venter
said, "Race is a social concept. It's not a scientific one. There are no bright lines (that would stand out), if we
could compare all the sequenced genomes of everyone on the planet." "When we try to apply science to try
to sort out these social differences, it all falls apart."[89]
Stephan Palmié asserted that race "is not a thing but a social relation";[90] or, in the words of Katya
Gibel Mevorach, "a metonym," "a human invention whose criteria for differentiation are neither universal nor
fixed but have always been used to manage difference."[91] As such, the use of the term "race" itself must be
analyzed. Moreover, they argue that biology will not explain why or how people use the idea of race: History
and social relationships will.
In the United States

Main article: Race in the United States
See also: Admixture in the United States
The immigrants to the Americas came ultimately from every region of Europe, Africa, and Asia.
Throughout America the immigrants mixed among themselves and with the indigenous inhabitants of the
continent. In the United States, for example, most people who self-identify as African–American have some
European ancestors—in one analysis of genetic markers that have differing frequencies between continents,
European ancestry ranged from an estimated 7% for a sample of Jamaicans to ∼23% for a sample of African–
Americans from New Orleans.[92] Similarly, many people who identify as European American have some
African or Amerindian ancestors, either through openly interracial marriages or through the gradual inclusion
of people with mixed ancestry into the majority population. In a survey of college students who self-identified
as white in a northeastern U.S. university, ∼30% were estimated to have less than 90% European ancestry.
[93]
Since the early history of the United States, Amerindians, African–Americans, and European
Americans have been classified as belonging to different races. For nearly three centuries, the criteria for
membership in these groups were similar, comprising a person’s appearance, his fraction of known non-
White ancestry, and his social circle.2 But the criteria for membership in these races diverged in the late 19th
century. During Reconstruction, increasing numbers of Americans began to consider anyone with "one drop"
of known "Black blood" to be Black, regardless of appearance. 3 By the early 20th century, this notion of
invisible blackness was made statutory in many states and widely adopted nationwide. 4 In contrast,
Amerindians continue to be defined by a certain percentage of "Indian blood" (called blood quantum), due in
large part to American slavery ethics. Finally, to be White one had to have perceived "pure" White ancestry.
Efforts to sort the increasingly mixed population of the United States into discrete categories
generated many difficulties.[94] Efforts to track mixing between groups led to a proliferation of categories,
such as mulatto and octoroon, and blood quantum distinctions that became increasingly untethered from self-
reported ancestry. A person's racial identity can change over time, and self-ascribed race can differ from
assigned race (Kressin et al. 2003).
The difference between how Amerindian and Black identities are defined today (blood quantum
versus one-drop rule) has demanded explanation. According to anthropologists such as Gerald Sider, the
goal of such racial designations was to concentrate power, wealth, privilege and land in the hands of Whites
in a society of White hegemony and privilege (Sider 1996; see also Fields 1990). The differences have little
to do with biology and far more to do with the history of racism and specific forms of White supremacy (the
social, geopolitical and economic agendas of dominant Whites vis-à-vis subordinate Blacks and Native
Americans), especially the different roles Blacks and Amerindians occupied in White-dominated 19th century
America.
The theory suggests that the blood quantum definition of Native American identity enabled Whites to
acquire Amerindian lands, while the one-drop rule of Black identity enabled Whites to preserve their
agricultural labor force. The contrast presumably emerged because, as peoples transported far from their
land and kinship ties on another continent, Black labor was relatively easy to control, thus reducing Blacks to
valuable commodities as agricultural laborers. In contrast, Amerindian labor was more difficult to control;
moreover, Amerindians occupied large territories that became valuable as agricultural lands, especially with
the invention of new technologies such as railroads; thus, the blood quantum definition enhanced White
acquisition of Amerindian lands in a doctrine of Manifest Destiny that subjected them to marginalization and
multiple episodic localized campaigns of extermination.
The political economy of race had different consequences for the descendants of aboriginal
Americans and African slaves. The 19th century blood quantum rule meant that it was relatively easier for a
person of mixed Euro-Amerindian ancestry to be accepted as White. The offspring of only a few generations
of intermarriage between Amerindians and Whites likely would not have been considered Amerindian at all
(at least not in a legal sense). Amerindians could have treaty rights to land, but because an individual with
one Amerindian great-grandparent no longer was classified as Amerindian, they lost any legal claim to
Amerindian land. According to the theory, this enabled Whites to acquire Amerindian lands. The irony is that
the same individuals who could be denied legal standing because they were "too White" to claim property
rights, might still be Amerindian enough to be considered "breeds", stigmatized for their Native American
ancestry.
The one-drop rule, on the other hand, made it relatively difficult for anyone of known Black ancestry
to be accepted as White during the 20th century. The child of a Black sharecropper and a White person was
considered Black. And, significantly, in terms of the economics of sharecropping, such a person also would
likely be a sharecropper as well, thus adding to the employer's labor force. However, some people with hints
of African ancestry had light enough skin and other features to pass as "white". This did not happen for many
people though. Many African–Americans today still possess small traces of European ancestry because of
this mixing of races.
In short, this theory suggests that in a 20th century economy that benefited from sharecropping, it
was useful to have as many Blacks as possible. Conversely, in a 19th century nation bent on westward
expansion, it was advantageous to diminish the numbers of those who could claim title to Amerindian lands
by simply defining them out of existence.
It must be mentioned, however, that although some scholars of the Jim Crow period agree that the
20th century notion of invisible Blackness shifted the color line in the direction of paleness, thereby swelling
the labor force in response to Southern Blacks' Great Migration northwards, others (Joel Williamson, C. Vann
Woodward, George M. Fredrickson, Stetson Kennedy) see the one-drop rule as a simple consequence of the
need to define Whiteness as being pure, thus justifying White-on-Black oppression. In any event, over the
centuries when Whites wielded power over both Blacks and Amerindians and widely believed in their
inherent superiority over people of color, it is no coincidence that the hardest racial group in which to prove
membership was the White one.
In the United States, social and legal conventions developed over time that forced individuals of
mixed ancestry into simplified racial categories (Gossett 1997). An example is the aforementioned one-drop
rule implemented in some state laws that treated anyone with a single known African–American ancestor as
black (Davis 2001). The decennial censuses conducted since 1790 in the United States also created an
incentive to establish racial categories and fit people into those categories.[20] In other countries in the
Americas where mixing among groups was overtly more extensive, social categories have tended to be more
numerous and fluid, with people moving into or out of categories on the basis of a combination of
socioeconomic status, social class, ancestry, and appearance.[95]
The term "Hispanic" as an ethnonym emerged in the 20th century with the rise of migration of
laborers from American Spanish-speaking countries to the United States. Today, the word "Latino" is often
used as a synonym for "Hispanic". The definitions of both terms are non-race specific, and include people
who consider themselves to be of distinct races (Black, White, Amerindian, Asian, and mixed groups).[96] In
contrast to "Latino" or "Hispanic", "Anglo" refers to non-Hispanic White Americans or non-Hispanic European
Americans, most of whom speak the English language but are not necessarily of English descent.
In Brazil
Main article: Race in Brazil
This section does not cite any references or sources.
Please help improve this article by adding citations to reliable sources. Unsourced material
may be challenged and removed. (May 2009)
Compared to 19th century United States, 20th century Brazil was characterized by a perceived
relative absence of sharply defined racial groups. According to anthropologist Marvin Harris, this pattern
reflects a different history and different social relations. Basically, race in Brazil was "biologized," but in a way
that recognized the difference between ancestry (which determines genotype) and phenotypic differences.
There, racial identity was not governed by rigid descent rule, such as the one-drop rule, as it was in the
United States. A Brazilian child was never automatically identified with the racial type of one or both parents,
nor were there only a very limited number of categories to choose from.[97]
Over a dozen racial categories would be recognized in conformity with all the possible combinations
of hair color, hair texture, eye color, and skin color. These types grade into each other like the colors of the
spectrum, and no one category stands significantly isolated from the rest. That is, race referred preferentially
to appearance, not heredity. The complexity of racial classifications in Brazil reflects the extent of
miscegenation in Brazilian society, a society that remains highly, but not strictly, stratified along color lines.
Henceforth, the Brazilian narrative of a perfect "post-racist" country, must be met with caution, as sociologist
Gilberto Freyre demonstrated in 1933 in Casa Grande e Senzala.
Marketing of race: genetic lineages as social lineages

New research in molecular genetics, and the marketing of genetic identities through the analysis of
one's Y chromosome, mtDNA or autosomal DNA, has reignited the debate surrounding race. Most of the
controversy surrounds the question of how to interpret these new data, and whether conclusions based on
existing data are sound. Although the vast majority of researchers endorse the view that continental groups
do not constitute different subspecies, and molecular geneticists generally reject the identification of mtDNA
and Y chromosomal lineages or allele clusters with "races", some anthropologists have suggested that the
marketing of genetic analysis to the general public in the form of "Personalized Genetic Histories" (PGH) is
leading to a new social construction of race.
Typically, a consumer of a commercial PGH service sends in a sample of DNA which is analyzed by
molecular biologists and is sent a report, of which the following is a sample
"African DNA Ancestry Report"
The subject's likely haplogroup L2 is associated with the so-called Bantu expansion from West
and Central sub-Saharan Africa east and south, dated 2,000-4,000 years ago ... Between the
15th and 19th centuries C.E, the Atlantic slave trade resulted in the forced movement of
approximately 13 million people from Africa, mainly to the Americas. Only approximately 11
million survived the passage and many more died in the early years of captivity. Many of these
slaves were traded to the West African Cape Verde ports of embarkation through Portuguese
and Arab middlemen and came from as far south as Angola. Among the African tribal groups, all
Bantu-speaking, in which L2 is common are: Hausa, Kanuri, Fulfe, Songhai, Malunjin (Angola),
Yoruba, Senegalese, Serer and Wolof.
Although no single sentence in such a report is technically wrong, through the combination of these
sentences, anthropologists and others have argued, the report is telling a story that connects a haplotype
with a language and a group of tribes. This story is generally rejected by research scientists because an
individual receives his or her Y chromosome or mtDNA from only one ancestor in every generation;
consequently, with every generation one goes back in time, the percentage of one's ancestors it represents
halves; if one goes back hundreds (let alone thousands) of years, it represents only a tiny fragment of one's
ancestry. As Mark Shriver and Rick Kittles recently remarked,
For many customers of lineage-based tests, there is a lack of understanding that their maternal
and paternal lineages do not necessarily represent their entire genetic make-up. For example,
an individual might have more than 85% Western European 'genomic' ancestry but still have a
West African mtDNA or NRY lineage.[98]
Nevertheless, they acknowledge, such stories are increasingly appealing to the general public.[98]
Through these kinds of reports, new advances in molecular genetics are being used to create or
confirm stories have about social identities. Although these identities are not racial in the biological sense,
they are in the cultural sense in that they link biological and cultural identities. Nadia Abu el-Haj has argued
that the significance of genetic lineages in popular conceptions of race owes to the perception that while
genetic lineages, like older notions of race, suggests some idea of biological relatedness, unlike older notions
of race they are not directly connected to claims about human behaviour or character. Abu el-Haj has thus
argued that "postgenomics does seem to be giving race a new lease on life." Nevertheless, Abu el-Haj
argues that to understand what it means to think of race in terms of genetic lineages or clusters, one must
understand that
Race science was never just about classification. It presupposed a distinctive relationship
between "nature" and "culture," understanding the differences in the former to ground and to
generate the different kinds of persons ("natural kinds") and the distinctive stages of cultures
and civilizations that inhabit the world.
Abu el-Haj argues that genomics and the mapping of lineages and clusters liberates "the new racial
science from the older one by disentangling ancestry from culture and capacity." As an example, she refers
to recent work by Hammer et al., which aimed to test the claim that present-day Jews are more closely
related to one another than to neighbouring non-Jewish populations. Hammer et al. found that the degree of
genetic similarity among Jews shifted depending on the locus investigated, and suggested that this was the
result of natural selection acting on particular loci. They therefore focused on the non-recombining Y
chromosome to "circumvent some of the complications associated with selection".[99]
As another example she points to work by Thomas et al., who sought to distinguish between the Y
chromosomes of Jewish priests (Kohanim), (in Judaism, membership in the priesthood is passed on through
the father's line) and the Y chromosomes of non-Jews.[100] Abu el-Haj concluded that this new "race
science" calls attention to the importance of "ancestry" (narrowly defined, as it does not include all ancestors)
in some religions and in popular culture, and people's desire to use science to confirm their claims about
ancestry; this "race science," she argues, is fundamentally different from older notions of race that were used
to explain differences in human behaviour or social status:
As neutral markers, junk DNA cannot generate cultural, behavioural, or, for that matter, truly
biological differences between groups ... mtDNA and Y-chromosome markers relied on in such
work are not "traits" or "qualities" in the old racial sense. They do not render some populations
more prone to violence, more likely to suffer psychiatric disorders, or for that matter, incapable
of being fully integrated - because of their lower evolutionary development - into a European
cultural world. Instead, they are "marks," signs of religious beliefs and practices… it is via
biological noncoding genetic evidence that one can demonstrate that history itself is shared, that
historical traditions are (or might well be) true."[101]
On the other hand, there are tests that do not rely on molecular lineages, but rather on correlations
between allele frequencies, often when allele frequencies correlate these are called clusters. Clustering
analyses are less powerful than lineages because they cannot tell a historical story, they can only estimate
the proportion of a person's ancestry from any given large geographical region. These sorts of tests use
informative alleles called Ancestry-informative marker (AIM), which although shared across all human
populations vary a great deal in frequency between groups of people living in geographically distant parts of
the world.
These tests use contemporary people sampled from certain parts of the world as references to
determine the likely proportion of ancestry for any given individual. In a recent Public Service Broadcasting
(PBS) programme on the subject of genetic ancestry testing the academic Henry Louis Gates: "wasn’t thrilled
with the results (it turns out that 50 percent of his ancestors are likely European)".[102] Charles Rotimi, of
Howard University's National Human Genome Center, is one of many who have highlighted the
methodological flaws in such research—that "the nature or appearance of genetic clustering (grouping) of
people is a function of how populations are sampled, of how criteria for boundaries between clusters are set,
and of the level of resolution used" all bias the results—and concluded that people should be very cautious
about relating genetic lineages or clusters to their own sense of identity.[103]
Thus, in analyses that assign individuals to groups it becomes less apparent that self-described
racial groups are reliable indicators of ancestry. One cause of the reduced power of the assignment of
individuals to groups is admixture. For example, self-described African Americans tend to have a mix of West
African and European ancestry. Shriver et al. (2003) found that on average African Americans have ~80%
African ancestry. Also, in a survey of college students who self-identified as "white" in a northeastern U.S.
university, ~30% of whites had less than 90% European ancestry.[36] The cited source, Shriver et al. (2003),
however, does not give this number for the sample, instead identifying "less than 5% estimated non-
European admixture in the State College sample."[93]
Stephan Palmié has responded to Abu el-Haj's claim that genetic lineages make possible a new,
politically, economically, and socially benign notion of race and racial difference by suggesting that efforts to
link genetic history and personal identity will inevitably "ground present social arrangements in a time-
hallowed past," that is, use biology to explain cultural differences and social inequalities.[104]

Main article: Race and intelligence
Researchers have reported differences in the average IQ test scores of various ethnic groups. The
interpretation, causes, accuracy and reliability of these differences are highly controversial. Some
researchers, such as Arthur Jensen, Richard Herrnstein, and Richard Lynn, have argued that such
differences are at least partially genetic. Others, for example Thomas Sowell, argue that the differences
largely owe to social and economic inequalities. Still others such as Stephen Jay Gould and Richard
Lewontin have argued that categories such as "race" and "intelligence" are both cultural constructs the
definitions of which are wholly subject to the particular socio-political contexts in which they are used, which
in turn renders any attempt to explain variation in one in terms of the other a meaningless exercise of circular
reasoning.
Political and practical uses

In biomedicine
Main articles: Population groups in biomedicine and Ancestry and health
See also: Pharmacogenomics, Race and health, and Ethnicity and health
In the United States, policy makers use racially categorized data to identify and address health
disparities between racial or ethnic groups.[105] In clinical settings, race has long been considered in the
diagnosis and treatment of medical conditions, because some medical conditions are more prevalent in
certain racial or ethnic groups than in others. Recent interest in race-based medicine, or race-targeted
pharmacogenomics, has been fueled by the proliferation of human genetic data which followed the decoding
of the human genome in the early 2000s. There is an active debate among biomedical researchers about the
meaning and importance of race in their research. Some researchers strongly support the continued use of
racial categorizations in biomedical research and clinical practice.[106] They argue that race may correlate,
albeit imperfectly, with the presence of specific genetic variants associated with disease:[106] Insofar as race
"provides a sufficiently precise proxy for human genetic variation",[107] the concept may be medically viable.
In addition, knowledge of a person's race may provide a cost-effective way to assess susceptibility to
genetically influenced medical conditions.[106]
Detractors of race-based medicine acknowledge that race is sometimes useful in clinical medicine,
but encourage minimizing its use. They suggest that medical practices should maintain their focus on the
individual rather than an individual's membership to any group. They argue that overemphasizing genetic
contributions to health disparities carries various risks such as reinforcing stereotypes, promoting racism or
ignoring the contribution of non-genetic factors to health disparities.[108] Some researchers in the field have
been accused "of using race as a placeholder during the 'meantime' of pharmacogenomic development".
[109] Conversely, it is argued that in the early stages of the field's development, researchers must consider
race-related factors if they are to ascertain the clinical potentials of ongoing scholarship.[107][110]
In law enforcement
may be challenged and removed. (January 2010)
In the U.S., the FBI identifies fugitives to categories they define as sex, physical features, occupation,
nationality, and race. From left to right, the FBI assigns the above individuals to the following races: White,
Black, White (Hispanic), Asian. Top row males, bottom row females.[111]
Main article: Racial profiling
See also: Race and crime in the United States
In an attempt to provide general descriptions that may facilitate the job of law enforcement officers
seeking to apprehend suspects, the United States FBI employs the term "race" to summarize the general
appearance (skin color, hair texture, eye shape, and other such easily noticed characteristics) of individuals
whom they are attempting to apprehend. From the perspective of law enforcement officers, it is generally
more important to arrive at a description that will readily suggest the general appearance of an individual than
to make a scientifically valid categorization by DNA or other such means. Thus, in addition to assigning a
wanted individual to a racial category, such a description will include: height, weight, eye color, scars and
other distinguishing characteristics.
British Police use a classification based in the ethnic background of British society: W1 (White-
British), W2 (White-Irish), W9 (Any other white background); M1 (White and black Caribbean), M2 (White and
black African), M3 (White and Asian), M9 (Any other mixed background); A1 (Asian-Indian), A2 (Asian-
Pakistani), A3 (Asian-Bangladeshi), A9 (Any other Asian background); B1 (Black Caribbean), B2 (Black
African), B3 (Any other black background); O1 (Chinese), O9 (Any other). Some of the characteristics that
constitute these groupings are biological and some are learned (cultural, linguistic, etc.) traits that are easy to
notice.[citation needed]
In many countries, such as France, the state is legally banned from maintaining data based on race,
which often makes the police issue wanted notices to the public that include labels like "dark skin
complexion", etc.[citation needed].
In the United States, the practice of racial profiling has been ruled to be both unconstitutional and a
violation of civil rights. There is active debate regarding the cause of a marked correlation between the
recorded crimes, punishments meted out, and the country's populations. Many consider de facto racial
profiling an example of institutional racism in law enforcement. The history of misuse of racial categories to
impact adversely one or more groups and/or to offer protection and advantage to another has a clear impact
on debate of the legitimate use of known phenotypical or genotypical characteristics tied to the presumed
race of both victims and perpetrators by the government.
More recent work in racial taxonomy based on DNA cluster analysis (see Lewontin's Fallacy) has led
law enforcement to narrow their search for individuals based on a range of phenotypic characteristics found
consistent with DNA evidence.[112]
While controversial, DNA analysis has been successful in helping police identify both victims and
perpetrators by indicating what phenotypical characteristics to look for and what community the individual
may have lived in. For example, in one case phenotypic characteristics suggested that the friends and family
of an unidentified victim would be found among the Asian community, but the DNA evidence directed official
attention to missing Native Americans, where her true identity was eventually confirmed.[113] In an attempt
to avoid potentially misleading associations suggested by the word "race," this classification is called
"biogeographical ancestry" (BGA),[114] but the terms for the BGA categories are similar to those used as for
race.
The difference is that ancestry-informative DNA markers identify continent-of-ancestry admixture, not
ethnic self-identity, and provide a wide range of phenotypical characteristics such that some people in a
biogeographical category will not match the stereotypical image of an individual belonging to the
corresponding race. To facilitate the work of officials trying to find individuals based on the evidence of their
DNA traces, firms providing the genetic analyses also provide photographs showing a full range of
phenotypical characteristics of people in each biogeographical group. Of special interest to officials trying to
find individuals on the basis of DNA samples that indicate a diverse genetic background is what range of
phenotypical characteristics people with that general mixture of genotypical characteristics may display.
Forensic anthropology
Main article: Forensic anthropology
Similarly, forensic anthropologists draw on highly heritable morphological features of human remains
(e.g. cranial measurements) to aid in the identification of the body, including in terms of race. In a recent
article anthropologist Norman Sauer asked, "if races don't exist, why are forensic anthropologists so good at
identifying them?"[115] Sauer observed that the use of 19th century racial categories is widespread among
forensic anthropologists:
• "In many cases there is little doubt that an individual belonged to the Negro, Caucasian, or
Mongoloid racial stock."[116]
• "Thus the forensic anthropologist uses the term race in the very broad sense to differentiate
what are commonly known as white, black and yellow racial stocks."[117]
• "In estimating race forensically, we prefer to determine if the skeleton is Negroid, or Non-
Negroid. If findings favor Non-Negroid, then further study is necessary to rule out Mongoloid."[118]
According to Sauer, "The assessment of these categories is based upon copious amounts of
research on the relationship between biological characteristics of the living and their skeletons."
Nevertheless, he says he agrees with other anthropologists that race is not a valid biological taxonomic
category, and that races are socially constructed. He argued there is nevertheless a strong relationship
between the phenotypic features forensic anthropologists base their identifications on, and popular racial
categories. Thus, he argued, forensic anthropologists apply a racial label to human remains because their
analysis of physical morphology enables them to predict that when the person was alive, a particular racial
label would have been applied to them.[115]
See also
• Race and • Racial
• Breed health superiority
• Social
• Clan • Race • Racism
interpretations of race
• Cultural baiting • The
• Nationalism
difference • Race Race of the
• Ethnic
• List of (fantasy) Future
nationalism
ethnic groups • Race • The
• White
• Multiraci (U.S. census) Race Question
Supremacism
al • Racial • White
• White
• Pre- discrimination Nationalism
Separatism
Adamite • Racial • Whitenes
stereotypes s studies
Footnotes
1. ^ "race". Encyclopædia Britannica Online. 2010.
http://www.britannica.com/EBchecked/topic/488030/race. Retrieved 2010-08-03.
2. ^ See:
• Lie 2004
• Thompson, William; Joseph Hickey (2005). Society in Focus. Boston, MA: Pearson.
ISBN 0-205-41365-X.
• Gordon, Milton Myron (1964). Assimilation in American life: the role of race, religion,
and national origins. Oxford: Oxford University Press. ISBN 978-0-19-500896-
8. [page needed]
• "American Anthropological Association Statement on "Race"". Aaanet.org. 1998-05-
17. http://www.aaanet.org/stmts/racepp.htm. Retrieved 2009-04-18.
• Palmié, Stephan (May 2007). "Genomics, divination, 'racecraft'". American
Ethnologist 34: 205–22. doi:10.1525/ae.2007.34.2.205.
• Mevorach, Katya Gibel (2007). "Race, racism, and academic complicity". American
Ethnologist 34: 238. doi:10.1525/ae.2007.34.2.238.
• Segal, Daniel A (1991). "'The European'_ Allegories of Racial Purity". Anthropology
Today (Royal Anthropological Institute of Great Britain and Ireland) 7 (5): 7–9.
• Bindon, Jim. University of Alabama. "Post World War II". 2005. August 28, 2006.
3. ^ See:
• Gill G. "Does Race Exist? A proponent's perspective". Pbs.org.
http://www.pbs.org/wgbh/nova/first/gill.html. Retrieved 2009-04-18.
• Armelagos, George; Smay, Diana (2000). "Galileo wept: A critical assessment of the
use of race in forensic anthropolopy". Transforming Anthropology 9: 19–29.
doi:10.1525/tran.2000.9.2.19. http://www.anthropology.emory.edu/FACULTY/ANTGA/Web
%20Site/PDFs/Galileo%20Wept-%20A%20Critical%20Assessment%20of%20the%20Use
%20of%20Race%20in%20Forensic%20Anthropology.pdf
• Risch et al. 2002
• Bloche, Gregg M. (2004). "Race-Based Therapeutics". New England Journal of
Medicine 351 (20): 2035–2037. doi:10.1056/NEJMp048271. PMID 15533852.
http://content.nejm.org/cgi/content/full/351/20/2035.
4. ^ King 2007: For example, "the association of blacks with poverty and welfare ... is due, not
to race per se, but to the link that race has with poverty and its associated disadvantages" –p.75).
5. ^ a b Graves 2001
6. ^ a b Lee et al. 2008: We caution against making the naive leap to a genetic explanation for
group differences in complex traits, especially for human behavioral traits such as IQ scores
7. ^ a b c d e f Keita et al. 2004
8. ^ AAPA 1996 Pure races, in the sense of genetically homogeneous populations, do not exist
in the human species today, nor is there any evidence that they have ever existed in the past. -p.714
9. ^ a b Brace 2000
10.^ Montagu, Ashley (2008 [1962]). "The Concept of Race". American Ethnography
Quasimonthly. http://www.americanethnography.com/article.php?id=36. Retrieved 26 January 2009.
11.^ For example, a person who in the United States would be called "Hispanic" or "African
American" might be called "Branca" (white) in the racial categorization system commonly used in
Brazil.
12.^ Bamshad & Olson 2003
13.^ Sober E (2000). Philosophy of biology (2nd ed.). Boulder, CO: Westview Press.
14.^ For example, the following statement expresses the official viewpoint of the American
Anthropological Association at their web page: "Evidence from the analysis of genetics (e.g., DNA)
indicates that most physical variation, about 94%, lies within so-called racial groups. Conventional
geographic "racial" groupings differ from one another only in about 6% of their genes. This means
that there is greater variation within "racial" groups than between them."
15.^ a b c Lee 1997
16.^ See, for example, National Research Council (2004). Measuring racial discrimination (Ch.
2). Washington: The National Academies Press.
17.^ cf. Smaje C (1997). "Not just a social construct: Theorising race and ethnicity". Sociology
31 (2): 307–327. doi:10.1177/0038038597031002007.
18.^ a b Harris CI (1995). "Whiteness as property". In K Crenshaw; N Gotanda; G Peller; K
Thomas (Eds.) Critical Race Theory: The Key Writings That Formed the Movement (pp. 276 –291), p.
287.
19.^ a b c Morgan ES, cited in 1997 (), p. 407.
20.^ a b Nobles 2000
21.^ Smedley 2007; presented at the conference “Race, Human Variation and Disease:
Consensus and Frontiers”, sponsored by the American Anthropological Association (AAA). The
views expressed are the author's.
22.^ Sivanandan A, cited in Miles R (2000). "Apropos the idea of 'race' ... again". In L Black; J
Solomos (Eds.), Theories of Race and Racism (pp. 125–143). London: Routledge.
23.^ Crenshaw KW (1988). "Race, reform, and retrenchment: Transformation and legitimation in
antidiscrimination law". Harvard Law Review 101 (7): 1331–1337. doi:10.2307/1341398.
http://www.jstor.org/pss/1341398.
24.^ Conley D (2007). "Being black, living in the red". In PS Rothenberg (Ed.), Race, Class, and
Gender in the United States (7th ed.), pp. 350–358. New York: Worth Publishers.
25.^ The notion of racial hierarchy has ancient origins: "It was Aristotle who first arranged all
animals into a single, graded scale that placed humans at the top as the most perfect iteration. By the
late 19th century, the idea that inequality was the basis of natural order, known as the great chain of
being, was part of the common lexicon." Winfield AG (2007). Eugenics and education in America:
Institutionalized racism and the implications of history, ideology, and memory (pp. 45–46, emphasis in
original). New York: Peter Lang Publishing, Inc.
26.^ a b Gill GW (2000). "Does race exist? A proponent's perspective". NOVA Online. Pbs.org.
Retrieved 14 October 2010.
27.^ "The very naturalness of 'reality' is itself the effect of a particular set of discursive
constructions. In this way, discourse does not simply reflect reality, but actually participates in its
construction" Lee 1997, p. 396). Therefore, as people define race in different ways, they help to
create multiple realities of race (Lee 1997)
28.^ Attributions of "race" to razza without the link to the earlier French as here, miss the actual
origin. Viz. The Oxford Etymologist Looks at Race, Class and Sex (but not Gender), or, Beating a
Willing Horse, retrieved 09-Aug-2010, by Anatoly Liberman, citing an article published in 1959 by
Gianfranco Contini; weekly column on word etymology. Liberman is author of multiple works on
etymology.
29.^ Marco Polo, in the 13th century, writes of the North Persians: "The people are of the
Mahometan religion. They are in general a handsome race, especially the women, who, in my
opinion, are the most beautiful in the world." Travels of Marco Polo, Chapter 21.
30.^ Smedley 2007
31.^ a b Smedley 1999
32.^ Meltzer 1993
33.^ Takaki 1993
34.^ Banton 1977
35.^ For examples see:
• Lewis 1990
• Dikötter 1992
36.^ a b c d Race, Ethnicity, and Genetics Working Group (October 2005). "The use of racial,
ethnic, and ancestral categories in human genetics research". American Journal of Human Genetics
77 (4): 519–32. doi:10.1086/491747. PMID 16175499.
37.^ Todorov 1993
38.^ a b c d e Lieberman & Jackson 1995
39.^ a b Pleijel & Rouse 2000
40.^ Haig et al. 2006
41.^ Keita et al. 2004 , Templeton 1998 , Long & Kittles 2003
42.^ a b c d e f g Templeton 1998
43.^ O'Brien & Mayr 1991
44.^ Amadon 1949 , Mayr 1969 , Patten & Unitt 2002
45.^ a b Wright 1978
46.^ Human Genome Project Information: Minorities, Race, and Genomics
47.^ a b c Graves 2006
48.^ Keita et al. 2004 , Bamshad et al. 2004 , Tishkoff & Kidd 2004 , Jorde Wooding2004
49.^ a b Long & Kittles 2003
50.^ "Understanding Race and Human Variation: A Public Education Program". Anthropology
News 47 (2): 7. 2006. doi:10.1525/an.2006.47.2.7.
51.^ Currell & Cogdell 2006
52.^ Cravens 2010
53.^ Cravens 2010 , Baum 2006 , Angier 2000 , Amundson 2005 , Reardon 2005
54.^ Smedley 2002; Boas 1912
55.^ Marks 2002 , Montagu 1941 and Montagu 1942
56.^ Wilson & Brown 1953
57.^ Brace 1964
58.^ a b Livingstone & Dobzhansky 1962
59.^ Ehrlich & Holm 1964
60.^ Weiss 2005
61.^ Marks 2002
62.^ Krulwich 2009
63.^ a b Waples & Gaggiotti 2006
64.^ Lewontin 1972
65.^ Koertvelyessy & Nettleship 1996 , Koertvelyessy 1995 , Pettener 1990 , Biondi et al. 1990
66.^ Mayr 2002
67.^ Boyd 1950
68.^ Molnar 1992
69.^ AAPA 1996
70.^ Keita & Kittles 1997
71.^ Relethford 2002
72.^ a b Witherspoon et al. 2007
73.^ Lieberman, Leonard; Kirk, Rodney C.; Littlefield, Alice (2003). "Perishing Paradigm:
Race1931-99". American Anthropologist 105: 110. doi:10.1525/aa.2003.105.1.110.
A following article in the same issue questions the precise rate of decline, but from their opposing
perspective agrees that the Negroid/Caucasoid/Mongoloid paradigm has fallen into near-total
disfavor: Cartmill, Matt; Brown, Kaye (2003). "Surveying the Race Concept: A Reply to Lieberman,
Kirk, and Littlefield". American Anthropologist 105: 114. doi:10.1525/aa.2003.105.1.114.
74.^ "American Anthropological Association Statement on "Race"". Aaanet.org. 1998-05-17.
http://www.aaanet.org/stmts/racepp.htm. Retrieved 2009-04-18.
75.^ Wilson et al. 2001, Cooper, Kaufman & Ward 2003 (given in summary by Bamshad et al.
2004, p. 599)
76.^ (Schwartz 2001), (Stephens 2003) (given in summary by Bamshad et al. 2004, p. 599)
77.^ Smedley & Smedley 2005, (Helms et al. 2005), [1]. Lewontin, for example argues that there
is no biological basis for race on the basis of research indicating that more genetic variation exists
within such races than among them (Lewontin 1972).
78.^ (Bamshad 2005), Risch et al. 2002. Neil Risch argues: "One could make the same
arguments about sex and age! ... you can undermine any definitional system... In a recent study... we
actually had a higher discordance rate between self-reported sex and markers on the X chromosome
[than] between genetic structure [based on microsatellite markers] versus [racial] self-description,
[which had a] 99.9% concordance... So you could argue that sex is also a problematic category. And
there are differences between sex and gender; self-identification may not be correlated with biology
perfectly. And there is sexism. And you can talk about age the same way. A person's chronological
age does not perfectly correspond to his biological age for a variety of reasons, both inherited and
non-inherited. Perhaps just using someone's actual birth year is not a very good way of measuring
age. Does that mean we should throw it out? ... Any category you come up with is going to be
imperfect, but that doesn't preclude you from using it or the fact that it has utility"(Gitschier 2005).
79.^ Harpending 2003, Bamshad & Olson 2003, Edwards 2003, Bamshad et al. 2004, p. 599,
Tang et al. 2004, Rosenberg et al. 2005: "If enough markers are used... individuals can be partitioned
into genetic clusters that match major geographic subdivisions of the globe".
80.^ (Mountain and Risch 2004)
81.^ Rivara, Frederick P.; Finberg, Laurence (2001). "Use of the Terms Race and Ethnicity".
Archives of Pediatrics & Adolescent Medicine 155 (2): 119.
For similar author's guidelines, see Schwartz, RS (2001). "Racial profiling in medical research.". The
New England journal of medicine 344 (18): 1392–3. doi:10.1056/NEJM200105033441810.
PMID 11333999. ; Fullilove, MT (1998). "Comment: abandoning "race" as a variable in public health
research--an idea whose time has come.". American journal of public health 88 (9): 1297–8.
doi:10.2105/AJPH.88.9.1297. PMID 9736864. ; and Bhopal, R; Donaldson, L (1998). "White,
European, Western, Caucasian, or what? Inappropriate labeling in research on race, ethnicity, and
health.". American journal of public health 88 (9): 1303–7. doi:10.2105/AJPH.88.9.1303.
PMID 9736867.
82.^ See program announcement and requests for grant applications at the NIH website, at
nih.gov.
83.^ Bindon, Jim. University of Alabama. "Post World War II". 2005. August 28, 2006.
84.^ Lieberman, L (February 2001). "How "Caucasoids" got such big crania and why they
shrank. From Morton to Rushton." (PDF). Current anthropology 42 (1): 69–95. doi:10.1086/318434.
PMID 14992214. http://www.ssc.uwo.ca/psychology/faculty/rushtonpdfs/Lieberman2001CA.pdf.
85.^ American Anthropological Association (May 17, 1998). Statement on 'race'.
86.^ Kaszycka, Katarzyna A.; Strziko, Jan (2003). "'Race' Still an Issue for Physical
Anthropology? Results of Polish Studies Seen in the Light of the U.S. Findings". American
Anthropologist 105: 116–24. doi:10.1525/aa.2003.105.1.116.
87.^ a b Marks 1995
88.^ Gordon, Milton Myron (1964). Assimilation in American life: the role of race, religion, and
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89.^ "New Ideas, New Fuels: Craig Venter at the Oxonian". FORA.tv. 2008-11-03.
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90.^ Palmié, Stephan (May 2007). "Genomics, divination, 'racecraft'". American Ethnologist 34:
205–22. doi:10.1525/ae.2007.34.2.205.
91.^ Mevorach, Katya Gibel (2007). "Race, racism, and academic complicity". American
Ethnologist 34: 238. doi:10.1525/ae.2007.34.2.238.
92.^ Parra et al. 1998
93.^ a b Shriver et al. 2003
94.^ Spickard 1992
95.^ Mörner 1967
96.^ "Revisions to the Standards for the Classification of Federal Data on Race and Ethnicity".
Office of Management and Budget. 1997-10-30.
http://www.whitehouse.gov/omb/fedreg/1997standards.html. Retrieved 2009-03-19. Also: U.S.
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97.^ Harris 1980
98.^ a b Shriver & Kittles 2004
99.^ Hammer MF, Redd AJ, Wood ET, et al. (June 2000). "Jewish and Middle Eastern non-
Jewish populations share a common pool of Y-chromosome biallelic haplotypes". Proceedings of the
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100.^ Thomas MG, Skorecki K, Ben-Ami H, Parfitt T, Bradman N, Goldstein DB (July 1998).
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101.^ El-Haj, Nadia ABU (2007). "Rethinking genetic genealogy: A response to Stephan
Palmié". American Ethnologist 34: 223. doi:10.1525/ae.2007.34.2.223.
102.^ Frank, Reanne. Back with a Vengeance: the Reemergence of a Biological
Conceptualization of Race in Research on Race/Ethnic Disparities in Health .
http://paa2006.princeton.edu/download.aspx?submissionId=61713. Retrieved 2009-04-18.
103.^ Rotimi CN (December 2003). "Genetic ancestry tracing and the African identity: a double-
edged sword?". Developing World Bioethics 3 (2): 151–8. doi:10.1046/j.1471-8731.2003.00071.x.
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104.^ Palmié, Stephan (2007). "Rejoinder: Genomic moonlighting, Jewish cyborgs, and Peircian
abduction". American Ethnologist 34: 245. doi:10.1525/ae.2007.34.2.245.
105.^ Office of Minority Health
106.^ a b c Risch et al. 2002
107.^ a b Condit et al. 2003
108.^ Lee et al. 2008
109.^ Kahn, J. (2009). "Beyond BiDil: the Expanding Embrace of Race in Biomedical Research
and Product Development" (PDF). St. Louis University Journal of Health Law & Policy 3: 61–92.
http://law.slu.edu/healthlaw/journal/archives/Kahn_Article.pdf. Retrieved 30 December 2010. ; In
2005, the Food and Drug Administration licensed a drug, BiDil, targeted specifically for the treatment
of heart disease in African Americans. The recommendation of the drug for "blacks" is criticized
because clinical trials were limited only to self-identified African Americans. It has been conceded by
the trial investigators that there is no basis to claim the drug works differently in any other population.
However, being approved and marketed to African Americans only, that specificity alone has been
used in turn to claim genetic differences.
110.^ In summary, Condit et al. (2003) argues that, in order to predict the clinical success of
pharmacogenomic research, scholars must conduct subsidiary research on two fronts: Science,
wherein the degree of correspondence between popular and professional racial categories can be
assessed; and society at large, through which attitudinal factors moderate the relationship between
scientific soundness and societal acceptance. To accept race-as-proxy, then, may be necessary but
insufficient to solidify the future of race-based pharmacogenomics.
111.^ "FBI - Most Wanted - The FBI's Ten Most Wanted Fugitives".
http://www.fbi.gov/wanted/topten/fugitives/fugitives.htm.
112.^ Molecular eyewitness: DNA gets a human face Controversial crime-scene test smacks of
racial profiling, critics say[dead link] CAROLYN ABRAHAM June 25, 2005
113.^ Willing, Richard (16 August 2005). "DNA tests offer clues to suspect's race". USA Today.
http://www.usatoday.com/news/nation/2005-08-16-dna_x.htm.
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External links
Wikiquote has a collection of quotations related to: Race (classification of humans)
Official statements and standards

• "The Race Question", UNESCO, 1950
• US Census Bureau: Definition of Race
• American Association of Physical Anthropologists' Statement on Biological Aspects of Race
• "Standards for Maintaining, Collecting, and Presenting Federal Data on Race and Ethnicity" ,
Federal Register 1997
• American Anthropological Association's Statement on Race and RACE: Are we so different?
a public education program developed by the American Anthropological Association.
Popular press
• The Myth of Race On the lack of scientific basis for the concept of human races (Medicine
Magazine, 2007).
• Race - The power of an illusion Online companion to California Newsreel's documentary
about race in society, science, and history
• Steven and Hilary Rose, The Guardian, "Why we should give up on race", 9 April 2005
• Times Online, "Gene tests prove that we are all the same under the skin", 27 October 2004.
• Michael J. Bamshad, Steve E. Olson "Does Race Exist?", Scientific American, December
2003
• "Gene Study Identifies 5 Main Human Populations, Linking Them to Geography" , Nicholas
Wade, NYTimes, December 2002. Covering
• Scientific American Magazine (December 2003 Issue) Does race exists ?.
• DNA Study published by United Press International showing how 30% of White Americans
have at least one Black ancestor
• Yehudi O. Webster Twenty-one Arguments for Abolishing Racial Classification, The
Abolitionist Examiner, June 2000
• The Tex(t)-Mex Galleryblog, An updated, online supplement to the University of Texas Press
book (2007), Tex(t)-Mex
• Times of India - Article about Asian racism
• South China Morning Post - Going beyond ‘sorry’
• Is Race "Real"? forum organized by the Social Science Research Council, includes 2005 op-
ed article by A.M. Leroi from the New York Times advocating biological conceptions of race and
responses from scholars in various fields More from Leori with responses
• Richard Dawkins: Race and creation (extract from The Ancestor's Tale: A Pilgrimage to the
Dawn of Life) - On race, its usage and a theory of how it evolved. (Prospect Magazine October 2004)
Others
• Race: the Power of an Illusion a three part documentary from California Newsreel.
• James, Michael (2008) Race, in the Stanford Encyclopedia of Philosophy.
• Ten Things Everyone Should Know About Race by California Newsreel.
• American Anthropological Association's educational website on race with links for primary
school educators and researchers
• Boas's remarks on race to a general audience
• Catchpenny mysteries of ancient Egypt, "What race were the ancient Egyptians?", Larry
Orcutt.
• Judy Skatssoon, "New twist on out-of-Africa theory", ABC Science Online, Wednesday, 14
July 2004.
• Racial & Ethnic Distribution of ABO Blood Types - bloodbook.com
• Are White Athletes an Endangered Species? And Why is it Taboo to Talk About It?
Discussion of racial differences in athletics
• "Does Race Exist? A proponent's perspective" - Author argues that the evidence from
forensic anthropology supports the idea of race.
• "Does Race Exist? An antagonist's perspective" - The author argues that clinal variation
undermines the idea of race.
• American Ethnography - The concept of race Ashley Montagu's 1962 article in American
Anthropology
• American Ethnography - The genetical theory of race, and anthropological method Ashley
Montagu's 1942 American Anthropology article
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W000
Meme

For other uses, see Meme (disambiguation).
challenged and removed. (November 2009)
A meme ( /ˈmiːm/, rhyming with "cream"[1]), a relatively newly coined term, identifies ideas or
beliefs that are transmitted from one person or group of people to another. The concept comes from an
analogy: as genes transmit biological information, memes can be said to transmit idea and belief information.
A meme acts as a unit for carrying cultural ideas symbols or practices, which can be transmitted from
one mind to another through writing, speech, gestures, rituals or other imitable phenomena. Supporters of
the concept regard memes as cultural analogues to genes, in that they self-replicate, mutate and respond to
selective pressures.[2]
The word meme is a shortening (modeled on gene) of mimeme (from Ancient Greek μίμημα Greek
pronunciation: [míːmɛːma] mimēma, "something imitated", from μιμεῖσθαι mimeisthai, "to imitate", from μῖμος
mimos "mime")[3] and it was coined by the British scientist Richard Dawkins in The Selfish Gene (1976)[1][4]
as a concept for discussion of evolutionary principles in explaining the spread of ideas and cultural
phenomena. Examples of memes given in the book included melodies, catch-phrases, fashion, and the
technology of building arches.[5]
Advocates of the meme idea say that memes may evolve by natural selection, in a manner
analogous to that of biological evolution. Memes do this through the processes of variation, mutation,
competition, and inheritance, each of which influencing a meme's reproductive success.
Memes spread through the behaviors that they generate in their hosts. Memes that propagate less
prolifically may become extinct, while others may survive, spread, and (for better or for worse) mutate.
Memes which replicate the most effectively spread best. Some memes may replicate effectively even when
they prove to be detrimental to the welfare of their hosts.[6]
A field of study called memetics[7] arose in the 1990s to explore the concepts and transmission of
memes in terms of an evolutionary model. Criticism from a variety of fronts has challenged the notion that
scholarship can examine memes empirically. Some commentators[ who?] question the idea that one can
meaningfully categorize culture in terms of discrete units.
Contents
[hide]
• 1 History
• 1.1 Origins
• 2 Concept
• 3 Transmission
• 4 Memes as discrete units
• 5 Evolutionary influences on memes
• 6 Memetics
• 7 Criticism of meme theory
• 7.1 Lack of philosophical foundation
• 7.2 Applications
• 8 Religion
• 9 Memetic explanations of racism
• 10 Internet culture
• 11 Meme maps
• 12 See also
• 13 Notes
• 14 References
[edit] History
[edit] Origins
Historically, the notion of a unit of social evolution, and a similar term (from Greek mneme,
“memory”), first appeared in 1904 in a work by the German Lamarckist biologist Richard Semon titled Die
Mnemischen Empfindungen in ihren Beziehungen zu den Originalempfindungen (loosely translatable as
“Memory-feelings in relation to original feelings”). According to the OED, the word mneme appears in English
in 1921 in L. Simon's translation of Semon's book: The Mneme.[8]
Laurent noted the use of the term mneme in Maurice Maeterlinck's The Life of the White Ant (1926),
and has highlighted similarities to Dawkins' concept.[9]
The word meme originated with Dawkins' 1976 book The Selfish Gene. To emphasize commonality
with genes, Dawkins coined the term "meme" by shortening "mimeme", which derives from the Greek word
mimema ("something imitated").[1]
Dawkins states that he did not know of the "mneme",[ citation needed] and said that he wanted "a
monosyllable that sounds a bit like 'gene'".[1] Dawkins wrote that evolution depended not on the particular
chemical basis of genetics, but only on the existence of a self-replicating unit of transmission – in the case of
biological evolution, the gene. For Dawkins, the meme exemplified another self-replicating unit with potential
significance in explaining human behavior and cultural evolution.
[edit] Concept
Dawkins used the term to refer to any cultural entity that an observer might consider a replicator. He
hypothesised that one could view many cultural entities as replicators, and pointed to melodies, fashions and
learned skills as examples. Memes generally replicate through exposure to humans, who have evolved as
efficient copiers of information and behaviour. Because humans do not always copy memes perfectly, and
because they may refine, combine or otherwise modify them with other memes to create new memes, they
can change over time. Dawkins likened the process by which memes survive and change through the
evolution of culture to the natural selection of genes in biological evolution.[5]
Dawkins defined the meme as a unit of cultural transmission, or a unit of imitation and replication, but later
definitions would vary. The meme, as analogous of gene, can be selected as "good" or "bad" and then
reinforced or eliminated. The lack of a consistent, rigorous, and precise understanding of what typically
makes up one unit of cultural transmission remains a problem in debates about memetics.[10] In contrast, the
concept of genetics gained concrete evidence with the discovery of the biological functions of DNA. In the
context of the natural or life sciences, memetics suffers in comparison because, unlike the idea of genes,
memes do not necessarily have or need a concrete medium in order to transfer.
[edit] Transmission
Life-forms can transmit information both vertically (from parent to child, via replication of genes) and
horizontally (through viruses and other means). Malcolm Gladwell wrote, "A meme is an idea that behaves
like a virus--that moves through a population, taking hold in each person it infects." Memes can replicate
vertically or horizontally within a single biological generation. They may also lie dormant for long periods of
time. Memes spread by the behaviors that they generate in their hosts. Imitation counts as an important
characteristic in the propagation of memes. Imitation often involves the copying of an observed behaviour of
another individual, but memes may transmit from one individual to another through a copy recorded in an
inanimate source, such as a book or a musical score. Researchers have observed memetic copying in just a
few species on Earth, including hominids, dolphins and birds (which learn how to sing by imitating their
parents or neighbors).[11]
Some commentators have likened the transmission of memes to the spread of contagions.[12] Social
contagions such as fads, hysteria, copycat crime, and copycat suicide exemplify memes seen as the
contagious imitation of ideas. Observers distinguish the contagious imitation of memes from instinctively
contagious phenomena such as yawning and laughing, which they consider innate (rather than socially
learned) behaviors.[11]
Aaron Lynch described seven general patterns of meme transmission, or "thought contagion":[13]
1. Quantity of parenthood: an idea which influences the number of children one has. Children
respond particularly receptively to the ideas of their parents, and thus ideas which directly or
indirectly encourage a higher birthrate will replicate themselves at a higher rate than those that
discourage higher birthrates.
2. Efficiency of parenthood: an idea which increases the proportion of children who will adopt
ideas of their parents. Cultural separatism exemplifies one practice in which one can expect a higher
rate of meme-replication — because the meme for separation creates a barrier from exposure to
competing ideas.
3. Proselytic: ideas generally passed to others beyond one's own children. Ideas that
encourage the proselytism of a meme, as seen in many religious or political movements, can
replicate memes horizontally through a given generation, spreading more rapidly than parent-to-child
meme-transmissions do.
4. Preservational: ideas which influence those that hold them to continue to hold them for a long
time. Ideas which encourage longevity in their hosts, or leave their hosts particularly resistant to
abandoning or replacing these ideas, enhance the preservability of memes and afford protection from
the competition or proselytism of other memes.
5. Adversative: ideas which influence those that hold them to attack or sabotage competing
ideas and/or those that hold them. Adversative replication can give an advantage in meme
transmission when the meme itself encourages aggression against other memes.
6. Cognitive: ideas perceived as cogent by most in the population who encounter them.
Cognitively transmitted memes depend heavily on a cluster of other ideas and cognitive traits already
widely held in the population, and thus usually spread more passively than other forms of meme
transmission. Memes spread in cognitive transmission do not count as self-replicating.
7. Motivational: ideas that people adopt because they perceive some self-interest in adopting
them. Strictly speaking, motivationally transmitted memes do not self-propagate, but this mode of
transmission often occurs in association with memes self-replicated in the efficiency parental,
proselytic and preservational modes.
[edit] Memes as discrete units

Richard Dawkins initially defined meme as a noun which "conveys the idea of a unit of cultural
transmission, or a unit of imitation".[5] John S. Wilkins retained the notion of meme as a kernel of cultural
imitation while emphasizing the meme's evolutionary aspect, defining the meme as "the least unit of
sociocultural information relative to a selection process that has favourable or unfavourable selection bias
that exceeds its endogenous tendency to change."[14] The meme as a unit provides a convenient means of
discussing "a piece of thought copied from person to person", regardless if that thought contains others
inside it, or forms part of a larger meme. A meme could consist of a single word, or a meme could consist of
the entire speech in which that word first occurred. This forms an analogy to the idea of a gene as a single
unit of self-replicating information found on the self-replicating chromosome.
While the identification of memes as "units" conveys their nature to replicate as discrete, indivisible
entities, it does not imply that thoughts somehow become quantized or that "atomic" ideas exist which cannot
be dissected into smaller pieces. A meme has no given size. Susan Blackmore writes that melodies from
Beethoven's symphonies are commonly used to illustrate the difficulty involved in delimiting memes as
discrete units. She notes that while the first four notes of Beethoven's Fifth Symphony ( listen (help·info))
form a meme widely replicated as an independent unit, one can regard the entire symphony as a single
meme as well.[10]
Some critics[who?] have seen the inability to pin an idea or cultural feature to its key units as an
insurmountable problem for memetics. Blackmore meets such criticism by stating that memes compare with
genes in this respect: that while a gene has no particular size, nor can we ascribe every phenotypic feature
directly to a particular gene, it has value because it encapsulates that key unit of inherited expression subject
to evolutionary pressures. To illustrate, she notes evolution selects for the gene for features such as eye
color; it does not select for the individual nucleotide in a strand of DNA. Memes play a comparable role in
understanding the evolution of imitated behaviors.[10]
The 1981 book Genes, Mind, and Culture: The Coevolutionary Process by Charles J. Lumsden and
E. O. Wilson proposed the theory that genes and culture co-evolve, and that the fundamental biological units
of culture must correspond to neuronal networks that function as nodes of semantic memory. They coined
their own term, "culturgen", which did not catch on. Coauthor Wilson later acknowledged the term meme as
the best label for the fundamental unit of cultural inheritance in his 1998 book Consilience: The Unity of
Knowledge, which elaborates upon the fundamental role of memes in unifying the natural and social
sciences.[15]
[edit] Evolutionary influences on memes
Richard Dawkins noted the three conditions which must exist for evolution to occur:[16]
1. variation, or the introduction of new change to existing elements
2. heredity or replication, or the capacity to create copies of elements
3. differential "fitness", or the opportunity for one element to be more or less suited to the
environment than another
Dawkins emphasizes that the process of evolution naturally occurs whenever these conditions co-
exist, and that evolution does not apply only to organic elements such as genes. He also regards memes as
having the properties necessary for evolution, and thus sees meme evolution as not simply analogous to
genetic evolution, but as a real phenomenon subject to the laws of natural selection. Dawkins noted that as
various ideas pass from one generation to the next, they may either enhance or detract from the survival of
the people who obtain those ideas, or influence the survival of the ideas themselves. For example, a certain
culture may develop unique designs and methods of tool-making that give it a competitive advantage over
another culture. Each tool-design thus acts somewhat similarly to a biological gene in that some populations
have it and others do not, and the meme's function directly affects the presence of the design in future
generations. In keeping with the thesis that in evolution one can regard organisms simply as suitable "hosts"
for reproducing genes, Dawkins argues that one can view people as "hosts" for replicating memes.
Consequently, a successful meme may or may not need to provide any benefit to its host.[16]
Unlike genetic evolution, memetic evolution can show both Darwinian and Lamarckian traits. Cultural
memes will have the characteristic of Lamarckian inheritance when a host aspires to replicate the given
meme through inference rather than by exactly copying it. Take for example the case of the transmission of a
simple skill such as hammering a nail, a skill which a learner imitates from watching a demonstration without
necessarily imitating every discrete movement modeled by the teacher in the demonstration, stroke for
stroke.[17] Susan Blackmore distinguishes the difference between the two modes of inheritance in the
evolution of memes, characterizing the Darwinian mode as "copying the instructions" and the Lamarckian as
"copying the product."[10]
Clusters of memes, or memeplexes (also known as meme complexes or as memecomplexes), such
as cultural or political doctrines and systems, may also play a part in the acceptance of new memes.
Memeplexes comprise groups of memes that replicate together and coadapt.[10] Memes that fit within a
successful memeplex may gain acceptance by "piggybacking" on the success of the memeplex. As an
example, John D. Gottsch discusses the transmission, mutation and selection of religious memeplexes and
the theistic memes contained.[18] Theistic memes discussed include the "prohibiton of aberrant sexual
practices such as incest, adultery, homosexuality, bestiality, castration, and religious prostitution", which may
have increased vertical transmission of the parent religious memeplex. Similar memes are thereby included
in the majority of religious memeplexes, and harden over time; they become an "inviolable canon" or set of
dogmas, eventually finding their way into secular law. This could also be referred to as the propagation of a
taboo.
[edit] Memetics
Main article: Memetics
The discipline of memetics, which dates from the mid 1980s, provides an approach to evolutionary
models of cultural information transfer based on the concept of the meme. Memeticists have proposed that
just as memes function analogously to genes, memetics functions analogously to genetics. Memetics
attempts to apply conventional scientific methods (such as those used in population genetics and
epidemiology) to explain existing patterns and transmission of cultural ideas.
Principal criticisms of memetics include the claim that memetics ignores established advances in
other fields of cultural study, such as sociology, cultural anthropology, cognitive psychology, and social
psychology. Questions remain whether or not the meme concept counts as a validly disprovable scientific
theory. This view regards memetics as a theory in its infancy: a protoscience to proponents, or a
pseudoscience to some detractors.
[edit] Criticism of meme theory

An objection to the study of the evolution of memes in genetic terms (although not to the existence of
memes) involves a perceived gap in the gene/meme analogy: the cumulative evolution of genes depends on
biological selection-pressures neither too great nor too small in relation to mutation-rates. There seems no
reason to think that the same balance will exist in the selection pressures on memes.[19]
Luis Benitez-Bribiesca M.D., a critic of memetics, calls the theory a "pseudoscientific dogma" and "a
dangerous idea that poses a threat to the serious study of consciousness and cultural evolution". As a factual
criticism, Benitez-Bribiesca points to the lack of a "code script" for memes (analogous to the DNA of genes),
and to the excessive instability of the meme mutation mechanism (that of an idea going from one brain to
another), which would lead to a low replication accuracy and a high mutation rate, rendering the evolutionary
process chaotic.[20]
Another critique comes from semiotic theorists such as Deacon[21] and Kull[22] This view regards
the concept of "meme" as a primitivized concept of "sign". The meme is thus described[by whom?] in
memetics as a sign lacking a triadic nature. Semioticians can regard a meme as a "degenerate" sign, which
includes only its ability of being copied. Accordingly, in the broadest sense, the objects of copying are
memes, whereas the objects of translation and interpretation are signs.[ clarification needed]
Fracchia and Lewontin regard memetics as reductionist and inadequate.[23]
[edit] Lack of philosophical foundation
In his chapter titled "Truth" published in the Encyclopedia of Phenomenology, Dieter Lohmar
questions the memeticists' reduction of the highly complex body of ideas (such as religion, politics, war,
justice, and science itself) to a putatively one-dimensional series of memes. He sees memes as an
abstraction and such a reduction as failing to produce greater understanding of those ideas. The highly
interconnected, multi-layering of ideas resists memetic simplification to an atomic or molecular form; as does
the fact that each of our lives remains fully enmeshed and involved in such "memes". Lohmar argues that
one cannot view memes through a microscope in the way one can detect genes. The leveling-off of all such
interesting "memes" down to some neutralized molecular "substance" such as "meme-substance" introduces
a bias toward scientism and abandons the very essence of what makes ideas interesting, richly available,
and worth studying.[24]
[edit] Applications
Opinions differ as to how best to apply the concept of memes within a "proper" disciplinary
framework. One view sees memes as providing a useful philosophical perspective with which to examine
cultural evolution. Proponents of this view (such as Susan Blackmore and Daniel Dennett) argue that
considering cultural developments from a meme's-eye view— as if memes themselves respond to pressure to
maximise their own replication and survival—can lead to useful insights and yield valuable predictions into
how culture develops over time. Others such as Bruce Edmonds and Robert Aunger have focused on the
need to provide an empirical grounding for memetics to become a useful and respected scientific discipline.
[25][26] A third approach, described[by whom?] as "radical memetics", seeks to place memes at the centre of
a materialistic theory of mind and of personal identity.[27]
Prominent researchers in evolutionary psychology and anthropology, including Scott Atran, Dan
Sperber, Pascal Boyer, John Tooby and others, argue the possibility of incompatibility between modularity of
mind and memetics.[citation needed] In their view, minds structure certain communicable aspects of the
ideas produced, and these communicable aspects generally trigger or elicit ideas in other minds through
inference (to relatively rich structures generated from often low-fidelity input) and not high-fidelity replication
or imitation. Atran discusses communication involving religious beliefs as a case in point. In one set of
experiments he asked religious people to write down on a piece of paper the meanings of the Ten
Commandments. Despite the subjects' own expectations of consensus, interpretations of the
commandments showed wide ranges of variation, with little evidence of consensus. In another experiment,
normal subjects and autistic subjects interpreted ideological and religious sayings (for example, "Let a
thousand flowers bloom" or "To everything there is a season"). Autistics showed a significant tendency to
closely paraphrase and repeat content from the original statement (for example: "Don't cut flowers before
they bloom"). Controls tended to infer a wider range of cultural meanings with little replicated content (for
example: "Go with the flow" or "Everyone should have equal opportunity"). Only the autistic subjects—who
lack the degree of inferential capacity normally associated with aspects of theory of mind—came close to
functioning as "meme machines".[28]
In his book The Robot's Rebellion, Stanovich uses the memes and memeplex concepts to describe a
program of cognitive reform which he refers to as a "rebellion". Specifically, Stanovich argues that the use of
memes as a descriptor for cultural units is beneficial because it serves to emphasize transmission and
acquisition properties that parallel the study of epidemiology. These properties make salient the sometimes
parasitic nature of acquired memes, and as a result individuals should be motivated to reflectively acquire
memes using what he calls a "Neurathian bootstrap" process.[29]
[edit] Religion
See also: Evolutionary psychology of religion
Although social scientists such as Max Weber sought to understand and explain religion in terms of a
cultural attribute, Richard Dawkins called for a re-analysis of religion in terms of the evolution of self-
replicating ideas apart from any resulting biological advantages they might bestow.
As an enthusiastic Darwinian, I have been dissatisfied with explanations that my fellow-
enthusiasts have offered for human behaviour. They have tried to look for 'biological
advantages' in various attributes of human civilization. For instance, tribal religion has been
seen as a mechanism for solidifying group identity, valuable for a pack-hunting species whose
individuals rely on cooperation to catch large and fast prey. Frequently the evolutionary
preconception in terms of which such theories are framed is implicitly group-selectionist, but it is
possible to rephrase the theories in terms of orthodox gene selection.
—Richard Dawkins, The Selfish Gene
Consider the idea of God. We do not know how it arose in the meme pool.
—Richard Dawkins, The Selfish Gene
He argued that the role of key replicator in cultural evolution belongs not to genes, but to memes
replicating thought from person to person by means of imitation. These replicators respond to selective
pressures that may or may not affect biological reproduction or survival.[5]
In her book The Meme Machine, Susan Blackmore regards religions as particularly tenacious
memes. Many of the features common to the most widely practiced religions provide built-in advantages in
an evolutionary context, she writes. For example, religions that preach of the value of faith over evidence
from everyday experience or reason inoculate societies against many of the most basic tools people
commonly use to evaluate their ideas. By linking altruism with religious affiliation, religious memes can
proliferate more quickly because people perceive that they can reap societal as well as personal rewards.
The longevity of religious memes improves with their documentation in revered religious texts.[10]
Aaron Lynch attributed the robustness of religious memes in human culture to the fact that such
memes incorporate multiple modes of meme transmission. Religious memes pass down the generations
from parent to child and across a single generation through the meme-exchange of proselytism. Most people
will hold the religion taught them by their parents throughout their life. Many religions feature adversarial
elements, punishing apostasy, for instance, or demonizing infidels. In Thought Contagion Lynch identifies the
memes of transmission in Christianity as especially powerful in scope. Believers view the conversion of non-
believers both as a religious duty and as an act of altruism. The promise of heaven to believers and threat of
hell to non-believers provide a strong incentive for members to retain their belief. Lynch asserts that belief in
the Crucifixion of Jesus in Christianity amplifies each of its other replication advantages through the
indebtedness believers have to their Savior for sacrifice on the cross. The image of the crucifixion recurs in
religious sacraments, and the proliferation of symbols of the cross in homes and churches potently reinforces
the wide array of Christian memes.[13]
[edit] Memetic explanations of racism

In Cultural Software: A Theory of Ideology, Jack Balkin argued that memetic processes can explain
many of the most familiar features of ideological thought. His theory of "cultural software" maintained that
memes form narratives, networks of cultural associations, metaphoric and metonymic models, and a variety
of different mental structures. Balkin maintains that the same structures used to generate ideas about free
speech or free markets also serve to generate racist beliefs. To Balkin, whether memes become harmful or
maladaptive depends on the environmental context in which they exist rather than in any special source or
manner to their origination. Balkin describes racist beliefs as "fantasy" memes which become harmful or
unjust "ideologies" when diverse peoples come together, as through trade or competition.[30]
[edit] Internet culture

Main article: Internet meme
The term "Internet meme" refers to a catchphrase or concept that spreads rapidly from person to
person via the Internet, largely through Internet-based email, blogs, forums, Imageboards, social networking
sites and instant messaging.
[edit] Meme maps

One technique of meme mapping represents the evolution and transmission of a meme across time
and space.[31] Such a meme map uses a figure-8 diagram (an analemma) to map the gestation (in the lower
loop), birth (at the choke point), and development (in the upper loop) of the selected meme. Such meme
maps are non-scalar, with time mapped onto the y-axis and space onto the x-axis transect. One can read the
temporal progress of the mapped meme from south to north on such a meme map. Paull has published a
worked example using the "organics meme" (as in organic agriculture).[31]
Robertson (2010) [32] used a second technique of meme mapping to create two-dimensional
representations of the selves of eleven participants drawn from both individualist and collectivist cultures.
Participant narratives were transcribed, segmented and coded using a method similar to grounded theory.
Coded segments exhibiting referent, connotative, affective and behavioral dimensions were declared to be
memes. Memes that shared connotative, affective or behavioral qualities were linked. All of the maps in
Robertson's sample evidenced volition, constancy, uniqueness, production, intimacy, and social interest.
[edit] See also
• Dual • Survivals
inheritance theory • Spiral
• Electronic Dynamics
Revolution • Viral marketing
• Know Your • Viral
Meme phenomenon
• Memetic • Viral video
engineering
• Psycholinguistic
s
• Sociocultural
evolution
[edit] Notes
1. ^ a b c d Dawkins, Richard (1989), The Selfish Gene (2 ed.), Oxford University Press, p. 192,
ISBN 0-19-286092-5, http://books.google.com/?id=WkHO9HI7koEC&pg=PA192, "We need a name
for the new replicator, a noun that conveys the idea of a unit of cultural transmission, or a unit of
imitation. 'Mimeme' comes from a suitable Greek root, but I want a monosyllable that sounds a bit like
'gene'. I hope my classicist friends will forgive me if I abbreviate mimeme to meme. If it is any
consolation, it could alternatively be thought of as being related to 'memory', or to the French word
même. It should be pronounced to rhyme with 'cream'."
2. ^ Graham 2002
3. ^ The American Heritage Dictionary of the English Language: Fourth Edition, 2000
4. ^ Millikan 2004, p. 16; Varieties of meaning "Richard Dawkins invented the term 'memes' to
stand for items that are reproduced by imitation rather than reproduced genetically."
5. ^ a b c d Dawkins 1989, p. 352
6. ^ Kelly & 1994 p.360:"But if we consider culture as its own self organizing system,— a system
with its own agenda and pressure to survive— then the history of humanity gets even more
interesting. As Richard Dawkins has shown, systems of self-replicating ideas or memes can quickly
accumulate their own agenda and behaviours. I assign no higher motive to a cultural entity than the
primitive drive to reproduce itself and modify its environment to aid its spread. One way the self
organizing system can do this is by consuming human biological resources."
7. ^ Heylighen & Chielens 2009
8. ^ Semon, Richard Wolfgang (1921), The Mneme, London: George Allen & Unwin
9. ^ Laurent, John (1999), "A Note on the Origin of 'Memes'/'Mnemes'", Journal of Memetics 3
(1): 14–19, http://cfpm.org/jom-emit/1999/vol3/laurent_j.html, retrieved 2008-03-17
10.^ a b c d e f Blackmore 1999
11.^ a b Blackmore 1998
12.^ Blackmore 1998; "The term 'contagion' is often associated with memetics. We may say that
certain memes are contagious, or more contagious than others."
13.^ a b Lynch 1996
14.^ Wilkins, John S. (1998), "What's in a Meme? Reflections from the perspective of the history
and philosophy of evolutionary biology", Journal of Memetics 2, http://jom-emit.cfpm.org/
15.^ Wilson 1998
16.^ a b Dennett 1991
17.^ Dawkins 2004
18.^ "Mutation, Selection, And Vertical Transmission Of Theistic Memes In Religious Canons" in
Journal of Memetics - Evolutionary Models of Information Transmission, Volume 5, Issue 1, 2001.
Online version retrieved 2008-01-27.
19.^ Sterelny & Griffiths 1999; p.333
20.^ Benitez Bribiesca, Luis (January 2001), "Memetics: A dangerous idea" (PDF), Interciencia:
Revista de Ciencia y Technologia de América (Venezuela: Asociación Interciencia) 26 (1): 29–31,
ISSN 0378-1844, http://redalyc.uaemex.mx/redalyc/pdf/339/33905206.pdf, retrieved 2010-02-11, "If
the mutation rate is high and takes place over short periods, as memetics predict, instead of
selection, adaptation and survival a chaotic disintegration occurs due to the accumulation of errors."
21.^ Terrence Deacon, "The trouble with memes (and what to do about it)". The Semiotic
Review of Books 10(3).
22.^ Kalevi Kull (2000), "Copy versus translate, meme versus sign: development of biological
textuality". European Journal for Semiotic Studies 12(1), 101–120.
23.^ Fracchia, Joseph; R C Lewontin (February 2005), "The price of metaphor" (PDF), History
and theory (Weleyan University) 44 (44): 14–29, doi:10.1111/j.1468-2303.2005.00305.x, ISSN 0018-
2656, http://www.jstor.org/pss/3590779, retrieved 2010-03-28, "The selectionist paradigm requires
the reduction of society and culture to inheritance systems that consist of randomly varying,
individual units, some of which are selected, and some not; and with society and culture thus
reduced to inheritance systems, history can be reduced to "evolution." [...] [W]e conclude that while
historical phenomena can always be modeled selectionistically, selectionist explanations do no work,
nor do they contribute anything new except a misleading vocabulary that anesthetizes history."
24.^ Dieter Lohmar - "Truth", in Lester Embree, Encyclopedia of phenomenology, Dordrecht,
Kluwer Academic Publishers, 1997
25.^ See Edmonds, Bruce (2002-09), "Three Challenges for the Survival of Memetics", Journal
of Memetics - Evolutionary Models of Information Transmission 6 (2), http://cfpm.org/jom-
emit/2002/vol6/edmonds_b_letter.html, retrieved 2009-02-03
26.^ Aunger 2000
27.^ Poulshock 2002
28.^ Atran 2002
29.^ Stanovich, Keith E. (2004-05-15). The Robot's Rebellion: Finding Meaning in the Age of
Darwin (1 ed.). University Of Chicago Press. ISBN 0226770893.
30.^ Balkin 1998
31.^ a b Paull, John (2009), "Meme Maps: A Tool for Configuring Memes in Time and Space",
European Journal of Scientific Research 31 (1): 11–18, http://orgprints.org/15752/1/15752.pdf.
32.^ Robertson, Lloyd Hawkeye (2010), "Mapping the self with units of culture", Psychology 1
(3): 185-193, http://www.scirp.org/journal/psych/
[edit] References
• Atran, Scott (2002), In gods we trust: the evolutionary landscape of religion , Oxford
[Oxfordshire]: Oxford University Press, ISBN 0-19-514930-0
• Atran, Scott (2001), "The Trouble with Memes", Human Nature 4 (12),
http://sitemaker.umich.edu/satran/files/human_nature_01.pdf
• Aunger, Robert (2000), Darwinizing culture: the status of memetics as a science , Oxford
[Oxfordshire]: Oxford University Press, ISBN 0-19-263244-2
• Aunger, Robert (2002), The electric meme: a new theory of how we think, New York: Free
Press, ISBN 0-7432-0150-7
• Balkin, J. M. (1998), Cultural software: a theory of ideology , New Haven, Conn: Yale
University Press, ISBN 0-300-07288-0
• Bloom, Howard S. (1997), The Lucifer Principle: A Scientific Expedition into the Forces of
History, Boston: Atlantic Monthly Press (published 1997-02), pp. 480, ISBN 0-87113-664-3
• Blackmore, Susan (1998), "Imitation and the definition of a meme" (PDF), Journal of
Memetics - Evolutionary Models of Information Transmission, http://www.baillement.com/texte-
blakemore.pdf
• Blackmore, Susan J. (1999), The meme machine, Oxford [Oxfordshire]: Oxford University
Press (published 1999-04-08), pp. 288, ISBN 0-19-850365-2 [trade paperback ISBN 0-9658817-8-4
(1999), ISBN 0-19-286212-X (2000)]
• Brodie, Richard (1996), Virus of the mind: the new science of the meme, Seattle, Wash:
Integral Press, pp. 251, ISBN 0-9636001-1-7
• Dawkins, Richard (2004), A Devil's Chaplain : Reflections on Hope, Lies, Science, and Love ,
Boston: Mariner Books, pp. 263, ISBN 0-618-48539-2
• Dawkins, Richard (1989), "11. Memes:the new replicators", The Selfish Gene (2nd ed., new
ed.), Oxford: Oxford University Press, pp. 368, ISBN 0192177737
• Dennett, Daniel C. (2006), Breaking the Spell, Viking (Penguin), ISBN 0-670-03472-X
• Dennett, Daniel (1991), Consciousness Explained, Boston: Little, Brown and Co.,
ISBN 0316180653
• Distin, Kate (2005), The selfish meme: a critical reassessment , Cambridge, UK: Cambridge
University Press, pp. 238, ISBN 0-521-60627-6
• Farnish, Keith (2009), Time's Up! An Uncivilized Solution To A Global Crisis , Totnes: Green
Books, pp. 256, ISBN 190032248X
• Graham, Gordon (2002), Genes: a philosophical inquiry, New York: Routledge, pp. 196,
ISBN 0-415-25257-1
• Henson, H. Keith: "Evolutionary Psychology, Memes and the Origin of War."
• Henson, H. Keith: "Sex, Drugs, and Cults. An evolutionary psychology perspective on why
and how cult memes get a drug-like hold on people, and what might be done to mitigate the effects",
The Human Nature Review 2002 Volume 2: 343-355
• Heylighen, Francis; Chielens, K. (2009), "Evolution of Culture, Memetics", in Meyers, B.,
Encyclopedia of Complexity and Systems Science, Springer,
http://pespmc1.vub.ac.be/Papers/Memetics-Springer.pdf
• Ingold, T (2000), "The poverty of selectionism", Anthropology Today 16 (3).
• Heylighen, Francis, (1992) : "Selfish Memes and the Evolution of Cooperation", Journal of
Ideas vol. 2, no. 4, pp, 77–84.
• Jan, Steven: The Memetics of Music: A Neo-Darwinian View of Musical Structure and
Culture (Aldershot: Ashgate, 2007)
• Kelly, Kevin (1994), Out of control: the new biology of machines, social systems and the
economic world, Boston: Addison-Wesley, pp. 360, ISBN 0-201-48340-8
• Lynch, Aaron (1996), Thought contagion: how belief spreads through society, New York:
BasicBooks, pp. 208, ISBN 0-465-08467-2
• Millikan, Ruth G. (2004), Varieties of meaning: the 2002 Jean Nicod lectures, Cambridge,
Massachusetts: MIT Press, pp. 242, ISBN 0-262-13444-6
• Post, Stephen Garrard; Underwood, Lynn G; Schloss, Jeffrey P Garrard (2002), Altruism &
Altruistic Love: Science, Philosophy, & Religion in Dialogue , Oxford University Press US, pp. 500,
ISBN 0195143582
• Moritz, Elan. (1995): "Metasystems, Memes and Cybernetic Immortality," in: Heylighen F.,
Joslyn C. & Turchin V. (eds.), The Quantum of Evolution. Toward a theory of metasystem transitions ,
(Gordon and Breach Science Publishers, New York) (special issue of World Futures: the journal of
general evolution, vol. 45, p. 155-171).
• Poulshock, Joseph (2002), "The Problem and Potential of Memetics", Journal of Psychology
and Theology (Rosemead School of Psychology, Gale Group (2004)): 68+
• Sterelny, Kim; Griffiths, Paul E. (1999), Sex and death: an introduction to philosophy of
biology, Chicago: University of Chicago Press, pp. 456, ISBN 0-226-77304-3
• Wilson, Edward O. (1998), Consilience: the unity of knowledge, New York: Knopf, pp. 352,
ISBN 0-679-45077-7

Look up meme in Wiktionary, the free dictionary.
• Dawkins' speech on the 30th anniversary of the publication of The Selfish Gene, Dawkins
2006
• "Evolution and Memes: The human brain as a selective imitation device" : article by Susan
Blackmore.
• Godwin, Mike. "Meme, Counter-meme". Wired.
http://www.wired.com/wired/archive/2.10/godwin.if_pr.html. Retrieved 2009-11-05.
• Journal of Memetics, a peer-refereed journal of memetics published from 1997 until 2005
• Susan Blackmore: Memes and "temes" , TED Talks February 2008
[hide]v · d · eRichard Dawkins
The Selfish Gene (1976) · The Extended Phenotype (1982) · The Blind
Watchmaker (1986) · River Out of Eden (1995) · Climbing Mount Improbable
Books (1996) · Unweaving the Rainbow (1998) · A Devil's Chaplain (2003) · The
Ancestor's Tale (2004) · The God Delusion (2006) · The Greatest Show on Earth:
The Evidence for Evolution (2009) · List of publications
Growing Up in the Universe (1991) · Dawkins vs. Gould (2001) · Beyond

Related works Belief (2006) · Richard Dawkins: How a Scientist Changed the Way We Think
(2006) · The Oxford Book of Modern Science Writing (2008)
Nice Guys Finish First (1987) · Break the Science Barrier (1996) · The
Documentaries Atheism Tapes (2004) · The Root of All Evil? (2006) · The Enemies of Reason
(2007) · The Genius of Charles Darwin (2008) · Faith School Menace (2010)
Meme · Out Campaign · Gerin oil · Foundation for Reason and Science ·
See also Ultimate Boeing 747 gambit · Lalla Ward · Frameshift · Weasel program · Marian
Stamp Dawkins · Middle World · Go God Go · The Courtier's Reply
Book:Richard Dawkins · Category:Richard Dawkins · Portal:Biography

Retrieved from "http://en.wikipedia.org/wiki/Meme"
Categories: Memes | Collective intelligence | Cultural anthropology | Evolutionary psychology |

Futurology | Philosophy of mind | Units of morphological analysis | Units of information (cognitive processes) |
Words coined in the 1970s
W000
Evolutionary developmental biology


Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
Evolutionary developmental biology (evolution of development or informally, evo-devo) is a field of
biology that compares the developmental processes of different organisms to determine the ancestral
relationship between them, and to discover how developmental processes evolved. It addresses the origin
and evolution of embryonic development; how modifications of development and developmental processes
lead to the production of novel features, such as the evolution of feathers;[1] the role of developmental
plasticity in evolution; how ecology impacts in development and evolutionary change; and the developmental
basis of homoplasy and homology.[2]
Although interest in the relationship between ontogeny and phylogeny extends back to the nineteenth
century, the contemporary field of evo-devo has gained impetus from the discovery of genes regulating
embryonic development in model organisms. General hypotheses remain hard to test because organisms
differ so much in shape and form.[3]
Nevertheless, it now appears that just as evolution tends to create new genes from parts of old genes
(molecular economy), evo-devo demonstrates that evolution alters developmental processes (genes and
gene networks) to create new and novel structures from the old gene networks (such as bone structures of
the jaw deviating to the ossicles of the middle ear) or will conserve (molecular economy) a similar program in
a host of organisms such as eye development genes in molluscs, insects, and vertebrates.[4] [5] Initially the
major interest has been in the evidence of homology in the cellular and molecular mechanisms that regulate
body plan and organ development. However more modern approaches include developmental changes
associated with speciation.[6]
Contents
[hide]
• 1 Basic principles
• 2 History
• 3 The developmental-genetic toolkit
• 4 Development and the origin of novelty
• 5 See also
• 6 References
• 6.1 Sources
[edit] Basic principles

Charles Darwin's theory of evolution is based on three principles: natural selection, heredity, and
variation. At the time that Darwin wrote, the principles underlying heredity and variation were poorly
understood. In the 1940s, however, biologists incorporated Gregor Mendel's principles of genetics to explain
both, resulting in the modern synthesis. It was not until the 1980s and 1990s, however, when more
comparative molecular sequence data between different kinds of organisms was amassed and detailed, that
an understanding of the molecular basis of the developmental mechanisms has arisen.
Currently, it is well understood how genetic mutation occurs. However, developmental mechanisms
are not understood sufficiently to explain which kinds of phenotypic variation can arise in each generation
from variation at the genetic level. Evolutionary developmental biology studies how the dynamics of
development determine the phenotypic variation arising from genetic variation and how that affects
phenotypic evolution (especially its direction). At the same time evolutionary developmental biology also
studies how development itself evolves.
Thus, the origins of evolutionary developmental biology come from both an improvement in
molecular biology techniques as applied to development, and the full appreciation of the limitations of classic
neo-Darwinism as applied to phenotypic evolution. Some evo-devo researchers see themselves as
extending and enhancing the modern synthesis by incorporating into it findings of molecular genetics and
developmental biology. Others, drawing on findings of discordances between genotype and phenotype and
epigenetic mechanisms of development, are mounting an explicit challenge to neo-Darwinism.
Evolutionary developmental biology is not yet a unified discipline, but can be distinguished from
earlier approaches to evolutionary theory by its focus on a few crucial ideas. One of these is modularity: as
has been long recognized, plants and animal bodies are modular: they are organized into developmentally
and anatomically distinct parts. Often these parts are repeated, such as fingers, ribs, and body segments.
Evo-devo seeks the genetic and evolutionary basis for the division of the embryo into distinct modules, and
for the partly independent development of such modules.
Another central idea is that some gene products function as switches whereas others act as diffusible
signals. Genes specify proteins, some of which act as structural components of cells and others as enzymes
that regulate various biochemical pathways within an organism. Most biologists working within the modern
synthesis assumed that an organism is a straightforward reflection of its component genes. The modification
of existing, or evolution of new, biochemical pathways (and, ultimately, the evolution of new species of
organisms) depended on specific genetic mutations. In 1961, however, Jacques Monod, Jean-Pierre
Changeux and François Jacob discovered within the bacterium Escherichia coli a gene that functioned only
when "switched on" by an environmental stimulus.[7] Later, scientists discovered specific genes in animals,
including a subgroup of the genes which contain the homeobox DNA motif, called Hox genes, that act as
switches for other genes, and could be induced by other gene products, morphogens, that act analogously to
the external stimuli in bacteria. These discoveries drew biologists' attention to the fact that genes can be
selectively turned on and off, rather than being always active, and that highly disparate organisms (for
example, fruit flies and human beings) may use the same genes for embryogenesis (e.g., the genes of the
"developmental-genetic toolkit", see below), just regulating them differently.
Similarly, organismal form can be influenced by mutations in promoter regions of genes, those DNA
sequences at which the products of some genes bind to and control the activity of the same or other genes,
not only protein-specifying sequences. In addition to providing new support for Darwin's assertion that all
organisms are descended from a common ancestor, this finding suggested that the crucial distinction
between different species (even different orders or phyla) may be due less to differences in their content of
gene products than to differences in spatial and temporal expression of conserved genes. The implication
that large evolutionary changes in body morphology are associated with changes in gene regulation, rather
than the evolution of new genes, suggested that the action of natural selection on promoters responsive to
Hox and other "switch" genes may play a major role in evolution.
Another focus of evo-devo is developmental plasticity, the basis of the recognition that organismal
phenotypes are not uniquely determined by their genotypes. If generation of phenotypes is conditional, and
dependent on external or environmental inputs, evolution can proceed by a "phenotype-first" route,[3][8] with
genetic change following, rather than initiating, the formation of morphological and other phenotypic
novelties. The case for this was argued for by Mary Jane West-Eberhard in her 2003 book Developmental
plasticity and evolution.[8]
[edit] History
An early version of recapitulation theory, also called the biogenetic law or embryological parallelism,
was put forward by Étienne Serres in 1824–26 as what became known as the "Meckel-Serres Law" which
attempted to provide a link between comparative embryology and a "pattern of unification" in the organic
world. It was supported by Étienne Geoffroy Saint-Hilaire as part of his ideas of idealism, and became a
prominent part of his version of Lamarckism leading to disagreements with Georges Cuvier. It was widely
supported in the Edinburgh and London schools of higher anatomy around 1830, notably by Robert Edmond
Grant, but was opposed by Karl Ernst von Baer's embryology of divergence in which embryonic parallels only
applied to early stages where the embryo took a general form, after which more specialised forms diverged
from this shared unity in a branching pattern. The anatomist Richard Owen used this to support his idealist
concept of species as showing the unrolling of a divine plan from an archetype, and in the 1830s attacked the
transmutation of species proposed by Lamarck, Geoffroy and Grant.[9] In the 1850s Owen began to support
an evolutionary view that the history of life was the gradual unfolding of a teleological divine plan,[10] in a
continuous "ordained becoming", with new species appearing by natural birth.[11]
In On the Origin of Species (1859), Charles Darwin proposed evolution through natural selection, a
theory central to modern biology. Darwin recognised the importance of embryonic development in the
understanding of evolution, and the way in which von Baer's branching pattern matched his own idea of
descent with modification[12]:
“ We can see why characters derived from the embryo should be of equal
importance with those derived from the adult, for a natural classification of course
includes all ages.[13] ”
Ernst Haeckel (1866), in his endeavour to produce a synthesis of Darwin's theory with Lamarckism
and Naturphilosophie, proposed that "ontogeny recapitulates phylogeny," that is, the development of the
embryo of every species (ontogeny) fully repeats the evolutionary development of that species (phylogeny),
in Geoffroy's linear model rather than Darwin's idea of branching evolution.[12] Haeckel's concept explained,
for example, why humans, and indeed all vertebrates, have gill slits and tails early in embryonic
development. His theory has since been discredited. However, it served as a backdrop for a renewed interest
in the evolution of development after the modern evolutionary synthesis was established (roughly 1936 to
1947).
Stephen Jay Gould called this approach to explaining evolution as terminal addition; as if every
evolutionary advance was added as new stage by reducing the duration of the older stages. The idea was
based on observations of neoteny.[14] This was extended by the more general idea of heterochrony
(changes in timing of development) as a mechanism for evolutionary change.[15]
D'Arcy Thompson postulated that differential growth rates could produce variations in form in his
1917 book On Growth and Form. He showed the underlying similarities in body plans and how geometric
transformations could be used to explain the variations.
Edward B. Lewis discovered homeotic genes, rooting the emerging discipline of evo-devo in
molecular genetics. In 2000, a special section of the Proceedings of the National Academy of Sciences
(PNAS) was devoted to "evo-devo",[16] and an entire 2005 issue of the Journal of Experimental Zoology Part
B: Molecular and Developmental Evolution was devoted to the key evo-devo topics of evolutionary innovation
and morphological novelty.[17]
[edit] The developmental-genetic toolkit

The developmental-genetic toolkit consists of a small fraction of the genes in an organism's genome
whose products control its development. These genes are highly conserved among Phyla. Differences in
deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. The
majority of toolkit genes are components of signaling pathways, and encode for the production of
transcription factors, cell adhesion proteins, cell surface receptor proteins, and secreted morphogens, all of
these participate in defining the fate of undifferentiated cells, generating spatial and temporal patterns, which
in turn form the body plan of the organism. Among the most important of the toolkit genes are those of the
Hox gene cluster, or complex. Hox genes, transcription factors containing the more broadly distributed
homeobox protein-binding DNA motif, function in patterning the body axis. Thus, by combinatorial specifying
the identity of particular body regions, Hox genes determine where limbs and other body segments will grow
in a developing embryo or larva. A paragon of a toolbox gene is Pax6/eyeless, which controls eye formation
in all animals. It has been found to produce eyes in mice and Drosophila, even if mouse Pax6/eyeless was
expressed in Drosophila.[18]
This means that a big part of the morphological evolution undergone by organisms is a product of
variation in the genetic toolkit, either by the genes changing their expression pattern or acquiring new
functions. A good example of the first is the enlargement of the beak in Darwin's Large Ground-finch
(Geospiza magnirostris), in which the gene BMP is responsible for the larger beak of this bird, relative to the
other finches.[19]
The loss of legs in snakes and other squamates is another good example of genes changing their
expression pattern. In this case the gene Distal-less is very under-expressed, or not expressed at all, in the
regions where limbs would form in other tetrapods.[20] This same gene determines the spot pattern in
butterfly wings,[21] which shows that the toolbox genes can change their function.
Toolbox genes, as well as being highly conserved, also tend to evolve the same function
convergently or in parallel. Classic examples of this are the already mentioned Distal-less gene, which is
responsible for appendage formation in both tetrapods and insects, or, at a finer scale, the generation of wing
patterns in the butterflies Heliconius erato and Heliconius melpomene. These butterflies are Müllerian mimics
whose coloration pattern arose in different evolutionary events, but is controlled by the same genes.[22] The
previous supports Kirschner and Gerhardt's theory of Facilitated Variation, which states that morphological
evolutionary novelty is generated by regulatory changes in various members of a large set of conserved
mechanisms of development and physiology.[23]
[edit] Development and the origin of novelty

Among the more surprising and, perhaps, counterintuitive (from a neo-Darwinian viewpoint) results of
recent research in evolutionary developmental biology is that the diversity of body plans and morphology in
organisms across many phyla are not necessarily reflected in diversity at the level of the sequences of
genes, including those of the developmental genetic toolkit and other genes involved in development.
Indeed, as Gerhart and Kirschner have noted, there is an apparent paradox: "where we most expect to find
variation, we find conservation, a lack of change".[24]
Even within a species, the occurrence of novel forms within a population does not generally correlate
with levels of genetic variation sufficient to account for all morphological diversity. For example, there is
significant variation in limb morphologies amongst salamanders and in differences in segment number in
centipedes, even when the respective genetic variation is low.
A major question then, for evo-devo studies, is: If the morphological novelty we observe at the level
of different clades is not always reflected in the genome, where does it come from? Apart from neo-
Darwinian mechanisms such as mutation, translocation and duplication of genes, novelty may also arise by
mutation-driven changes in gene regulation. The finding that much biodiversity is not due to differences in
genes, but rather to alterations in gene regulation, has introduced an important new element into evolutionary
theory.[25] Diverse organisms may have highly conserved developmental genes, but highly divergent
regulatory mechanisms for these genes. Changes in gene regulation are "second-order" effects of genes,
resulting from the interaction and timing of activity of gene networks, as distinct from the functioning of the
individual genes in the network.
The discovery of the homeotic Hox gene family in vertebrates in the 1980s allowed researchers in
developmental biology to empirically assess the relative roles of gene duplication and gene regulation with
respect to their importance in the evolution of morphological diversity. Several biologists, including Sean B.
Carroll of the University of Wisconsin–Madison suggest that "changes in the cis-regulatory systems of genes"
are more significant than "changes in gene number or protein function".[26] These researchers argue that the
combinatorial nature of transcriptional regulation allows a rich substrate for morphological diversity, since
variations in the level, pattern, or timing of gene expression may provide more variation for natural selection
to act upon than changes in the gene product alone.
Epigenetic alterations of gene regulation or phenotype generation that are subsequently consolidated
by changes at the gene level constitute another class of mechanisms for evolutionary innovation. Epigenetic
changes include modification of the genetic material due to methylation and other reversible chemical
alteration,[27] as well as nonprogrammed remolding of the organism by physical and other environmental
effects due to the inherent plasticity of developmental mechanisms.[8] The biologists Stuart A. Newman and
Gerd B. Müller have suggested that organisms early in the history of multicellular life were more susceptible
to this second category of epigenetic determination than are modern organisms, providing a basis for early
macroevolutionary changes.[28]
[edit] See also

• Animal evolution
• Plant Evolutionary Developmental Biology
• Baldwin effect
• Developmental systems theory
• Evolution of multicellularity
• Genetic assimilation
• Ontogeny
• Ontogeny recapitulates phylogeny
• List of gene families
• Important publications in evolutionary developmental biology
• Evolution and Development Leading journal
• Body plan
• Cell signaling
• Signal transduction
• Cell signaling networks
• Transcription factor
• Enhancer
• Enhanceosome
• promoter (biology)
• Gene regulatory network
[edit] References
1. ^ Prum, R.O., Brush, A.H. (March 2003). "Which Came First, the Feather or the Bird?".
Scientific American 288 (3): 84–93. doi:10.1038/scientificamerican0303-84. PMID 12616863.
2. ^ Hall, Brian K. (2000). "Evo-devo or devo-evo—does it matter". Evolution & Development 2:
177–178. doi:10.1046/j.1525-142x.2000.00003e.x. PMID 11252559.
3. ^ a b Palmer, RA (2004). "Symmetry breaking and the evolution of development". Science
306 (5697): 828–833. doi:10.1126/science.1103707. PMID 15514148.
4. ^ Tomarev, Stanislav I.; Callaerts, Patrick; Kos, Lidia; Zinovieva, Rina; Halder, Georg;
Gehring, Walter; Piatigorsky, Joram (1997). "Squid Pax-6 and eye development". Proceedings of the
National Academy of Sciences 94 (6): 2421–2426. doi:10.1073/pnas.94.6.2421.
http://www.pnas.org/content/94/6/2421.full.
5. ^ Pichaud, Franck; Desplan, Claude (August 2002). "Pax genes and eye organogenesis".
Current opinion in genetics and development 12 (4): 430–434. doi:10.1016/S0959-437X(02)00321-0.
PMID 12100888.
6. ^ Pennisi, E (2002). "EVOLUTIONARY BIOLOGY:Evo-Devo Enthusiasts Get Down to
Details". Science 298 (5595): 953–955.. doi:10.1126/science.298.5595.953. PMID 12411686.
7. ^ Monod, J; Changeux, JP; Jacob, F (1963). "Allosteric proteins and cellular control
systems". Journal of Molecular Biology 6: 306–329. doi:10.1016/S0022-2836(63)80091-1.
PMID 13936070.
8. ^ a b c West-Eberhard, M-J. (2003). Developmental plasticity and evolution. New York:
Oxford University Press. ISBN 978-0-19-512235-0.
9. ^ Desmond 1989, pp. 53–53, 86–88, 337–340
Secord 2003, pp. 252–253
10.^ Bowler 2003, pp. 120–128, 208
Secord 2003, pp. 424, 512
11.^ Desmond & Moore 1991, pp. 490–491
12.^ a b Bowler 2003, pp. 170, 190–191
13.^ Darwin, Charles (1859). On the Origin of Species. London: John Murray. pp. 439–430.
ISBN 0801413192.
14.^ Ridley, Mark (2003). Evolution. Wiley-Blackwell. ISBN 978-1-4051-0345-9.
http://www.blackwellpublishing.com/ridley/.
15.^ Gould, Stephen Jay (1977). Ontogeny and Phylogeny. Cambridge, Massachusetts:
Harvard University Press. ISBN 0-674-63940-5.
16.^ Goodman CS and Coughlin BS (Eds). (2000). "Special feature: The evolution of evo-devo
biology". Proceedings of the National Academy of Sciences 97 (9): 4424–4456.
doi:10.1073/pnas.97.9.4424. PMID 10781035. PMC 18255.
http://www.pnas.org/cgi/content/full/97/9/4424.
17.^ Müller GB and Newman SA (Eds.) (2005). "Special issue: Evolutionary Innovation and
Morphological Novelty". Journal of Exp. Zool. Part B: Molecular and Developmental Evolution 304B:
485–631. http://www3.interscience.wiley.com/cgi-bin/jissue/112149101.
18.^ Xu, P.X., Woo, I., Her, H., Beier, D.R., Maas, R.L. (1997). "Mouse Eya homologues of the
Drosophila eyes absent gene require Pax6 for expression in lens and nasal placode". Development
124 (1): 219–231. PMID 9006082.
19.^ Abzhanov, A.; Protas, M.; Grant, B.R.; Grant, P.R.; Tabin, C.J. (2004). "Bmp4 and
Morphological Variation of Beaks in Darwin's Finches". Science 305 (5689): 1462–1465.
doi:10.1126/science.1098095. PMID 15353802.
20.^ Cohn, M.J.; Tickle, C. (1999). "Developmental basis of limblessness and axial patterning in
snakes.". Nature 399 (6735): 474–479. doi:10.1038/20944. PMID 10365960.
21.^ Beldade, P.; Brakefield, P.M.; Long, A.D. (2002). "Contribution of Distal-less to quantitative
variation in butterfly eyespots". Nature 415 (6869): 315–318. doi:10.1038/415315a. PMID 11797007.
22.^ Baxter, S.W.; Papa, R.; Chamberlain, N.; Humphray, S.J.; Joron, M.; Morrison, C.; ffrench-
Constant, R.H.; McMillan, W.O.; Jiggins, C.D. (2008). "Convergent Evolution in the Genetic Basis of
Mullerian Mimicry in Heliconius Butterflies". Genetics 180 (3): 1567–1577.
doi:10.1534/genetics.107.082982. PMID 18791259.
23.^ Gerhart, John; Kirschner, Marc (2007). "The theory of facilitated variation". Proceedings of
the National Academy of Sciences 104 (suppl1): 8582–8589. doi:10.1073/pnas.0701035104.
PMID 17494755.
24.^ Gerhart, John; Kirschner, Marc (1997). Cells, Embryos and Evolution. Blackwell Science.
ISBN 978-0865425743.
25.^ Carroll, Sean B.; Grenier, Jennifer K.; Weatherbee, Scott D. (2005). From DNA to Diversity:
Molecular Genetics and the Evolution of Animal Design — Second Edition. Blackwell Publishing.
ISBN 1405119500.
26.^ Carroll, Sean B. (2000). "Endless forms: the evolution of gene regulation and morphological
diversity". Cell 101: 577–80. doi:10.1016/S0092-8674(00)80868-5.
27.^ Jablonka, Eva; Lamb, Marion (1995). Epigenetic Inheritance and Evolution: The
Lamarckian Dimension. Oxford, New York: Oxford University Press. ISBN 978-0198540632.
28.^ Müller, Gerd B. and Newman, Stuart A., ed (2003). Origination of Organismal Form:
Beyond the Gene in Developmental and Evolutionary Biology . MIT Press.
[edit] Sources
• Bowler, Peter J. (2003). Evolution: the history of an idea. Berkeley: University of California
Press. ISBN 0-520-23693-9.
• Desmond, Adrian J. (1989). The politics of evolution: morphology, medicine, and reform in
radical London. Chicago: University of Chicago Press. ISBN 0-226-14374-0.
• Desmond, Adrian J.; Moore, James William (1991). Darwin. London: Michael Joseph.
ISBN 0-7181-3430-3.
• Secord, James A. (2003). Victorian sensation: the extraordinary publication, reception, and
secret authorship of Vestiges of the natural history of creation. Chicago: University of Chicago Press.
ISBN 0-226-74411-6.

• Buss, Leo W. (1987). The Evolution of Individuality. Princeton University Press. ISBN 978-
0691084688.
• Carroll, Sean B. (2005). Endless Forms Most Beautiful: The New Science of Evo Devo and
the Making of the Animal Kingdom. Norton. ISBN 9780393060164.
• Goodwin, Brian (1994). How the Leopard Changed its Spots. Phoenix Giants.
ISBN 9780691088099.
• Hall, Brian K. & Olsen, Wendy M., ed (2007). Keywords and Concepts in Evolutionary
Developmental Biology. New Delhi, India: Discovery Publishing House. ISBN 978-81-8356-256-0.
• Kirschner, Marc; Gerhart, John (2005). The Plausibility of Life: Resolving Darwin's Dilemma .
Yale University Press. ISBN 9780300108651.
• Laubichler, Manfred D. and Maienschein, Jane, ed (2007). From Embryology to Evo-Devo: A
History of Developmental Evolution. The MIT Press. ISBN 978-0-262-12283-2.
• Minelli, Alessandro (2003). The Development of Animal Form: Ontogeny, Morphology, and
Evolution. Cambridge University Press. ISBN 978-0521808514.
• Orr, H. Allen (2005-10-24). "Turned on: A revolution in the field of evolution?". The New
Yorker. http://www.newyorker.com/critics/books/articles/051024crbo_books1. Discussion of Carroll,
Endless Forms Most Beautiful
• Raff, Rudolf A. (1996). The Shape of Life: Genes, Development, and the Evolution of Animal
Form. The University of Chicago Press. ISBN 978-0226702667.
• Sommer, Ralf J. (2009). "The future of evo–devo: model systems and evolutionary theory".
Nature Reviews Genetics 10 (6): 416–422. doi:10.1038/nrg2567. PMID 19369972.

• Scott F. Gilbert, The morphogenesis of evolutionary developmental biology
• Tardigrades (water bears) as evo-devo models, a short video from NPR's Science Friday
Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of


Retrieved from "http://en.wikipedia.org/wiki/Evolutionary_developmental_biology"
Categories: Evolutionary biology | Developmental biology

W000

"History of evolution" redirects here. It is not to be confused with History of evolutionary thought.
"History of life" redirects here. For other uses, see Life history.
Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
The evolutionary history of life on Earth traces the processes by which living and fossil organisms
evolved. It stretches from the origin of life on Earth, thought to be over 3,500 million years ago, to the present
day. The similarities between all present day organisms indicate the presence of a common ancestor from
which all known species have diverged through the process of evolution.[1]
Microbial mats of coexisting bacteria and archaea were the dominant form of life in the early Archean
and many of the major steps in early evolution are thought to have taken place within them.[2] The evolution
of oxygenic photosynthesis, around 3,500 million years ago, eventually led to the oxygenation of the
atmosphere, beginning around 2,400 million years ago.[3] The earliest evidence of eukaryotes (complex cells
with organelles), dates from 1,850 million years ago,[4][5] and while they may have been present earlier, their
diversification accelerated when they started using oxygen in their metabolism. Later, around 1,700 million
years ago, multicellular organisms began to appear, with differentiated cells performing specialised functions.
[6]
The earliest land plants date back to around 450 million years ago,[7] though evidence suggests that
algal scum formed on the land as early as 1,200 million years ago. Land plants were so successful that they
are thought to have contributed to the late Devonian extinction event.[8] Invertebrate animals appear during
the Vendian period,[9] while vertebrates originated about 525 million years ago during the Cambrian
explosion.[10]
During the Permian period, synapsids, including the ancestors of mammals, dominated the land,[11]
but the Permian–Triassic extinction event 251 million years ago came close to wiping out all complex life.[12]
During the recovery from this catastrophe, archosaurs became the most abundant land vertebrates,
displacing therapsids in the mid-Triassic.[13] One archosaur group, the dinosaurs, dominated the Jurassic
and Cretaceous periods,[14] with the ancestors of mammals surviving only as small insectivores.[15] After
the Cretaceous–Tertiary extinction event 65 million years ago killed off the non-avian dinosaurs[16] mammals
increased rapidly in size and diversity.[17] Such mass extinctions may have accelerated evolution by
providing opportunities for new groups of organisms to diversify.[18]
Fossil evidence indicates that flowering plants appeared and rapidly diversified in the Early
Cretaceous, between 130 million years ago and 90 million years ago, probably helped by coevolution with
pollinating insects. Flowering plants and marine phytoplankton are still the dominant producers of organic
matter. Social insects appeared around the same time as flowering plants. Although they occupy only small
parts of the insect "family tree", they now form over half the total mass of insects. Humans evolved from a
lineage of upright-walking apes whose earliest fossils date from over 6 million years ago. Although early
members of this lineage had chimpanzee-sized brains, there are signs of a steady increase in brain size after
about 3 million years ago.
Contents
[hide]
• 1 Earliest history of Earth
• 2 Earliest evidence for life on Earth
• 3 Origins of life on Earth
• 3.1 Life "seeded" from elsewhere
• 3.2 Independent emergence on Earth
• 3.2.1 Replication first: RNA world
• 3.2.2 Metabolism first: Iron-sulfur world
• 3.2.3 Membranes first: Lipid world
• 3.2.4 The clay theory
• 4 Environmental and evolutionary impact of microbial mats
• 5 Diversification of eukaryotes
• 6 Multicellular organisms and sexual reproduction
• 6.1 Multicellularity
• 6.2 Evolution of sexual reproduction
• 6.3 Fossil evidence for multicellularity and sexual
reproduction
• 7 Emergence of animals
• 8 Colonization of land
• 8.1 Evolution of soil
• 8.2 Plants and the Late Devonian wood crisis
[edit] Earliest history of Earth
History of Earth and its life
-4500 —
–
-4000 —
–
-3500 —
–
-3000 —
–
-2500 —
–
-2000 —
–
-1500 —
–
-1000 —
–
-500 —
–
0—
Hadean
Archean
Protero
-zoic
Phanero
-zoic
Eo
Paleo
Meso
Neo
Paleo
Meso
Neo
Paleo
Meso
Ceno
←
Solar system formed
←
Impact formed Moon
←
? Cool surface, oceans, atmosphere
←
Late Heavy Bombardment
←
? Earliest evidence of life
←
Oxygenation of atmosphere
←
Earliest multicellular organism[19]
←
Earliest known fungi
←
Earliest known cnidarians
←
? Cambrian explosion
←
Earliest land invertebrates and plants
←
Earliest land vertebrates
←
Earliest known dinosaur
←
Extinction of non-avian dinosaurs
Scale:
Millions of years
Main article: History of the Earth
The oldest meteorite fragments found on Earth are about 4,540 million years old, this, coupled
primarily with the dating of ancient lead deposits, has put the estimated age of Earth at around that time.[20]
The Moon has the same composition as Earth's crust but does not contain an iron-rich core like the Earth's.
Many scientists think that about 40 million years later a planetoid struck the Earth, throwing into orbit crust
material that formed the Moon. Another hypothesis is that the Earth and Moon started to coalesce at the
same time but the Earth, having much stronger gravity, attracted almost all the iron particles in the area.[21]
Until recently the oldest rocks found on Earth were about 3,800 million years old,[20] leading
scientists to believe for decades that Earth's surface had been molten until then. Accordingly, they named
this part of Earth's history the Hadean eon, whose name means "hellish".[22] However analysis of zircons
formed 4,400 to 4,000 million years ago indicates that Earth's crust solidified about 100 million years after the
planet's formation and that the planet quickly acquired oceans and an atmosphere, which may have been
capable of supporting life.[23]
Evidence from the Moon indicates that from 4,000 to 3,800 million years ago it suffered a Late Heavy
Bombardment by debris that was left over from the formation of the Solar system, and the Earth should have
experienced an even heavier bombardment due to its stronger gravity.[22][24] While there is no direct
evidence of conditions on Earth 4,000 to 3,800 million years ago, there is no reason to think that the Earth
was not also affected by this late heavy bombardment.[25] This event may well have stripped away any
previous atmosphere and oceans; in this case gases and water from comet impacts may have contributed to
their replacement, although volcanic outgassing on Earth would have contributed at least half.[26]
[edit] Earliest evidence for life on Earth

The earliest identified organisms were minute and relatively featureless, and their fossils look like
small rods, which are very difficult to tell apart from structures that arise through abiotic physical processes.
The oldest undisputed evidence of life on Earth, interpreted as fossilized bacteria, dates to 3,000 million
years ago.[27] Other finds in rocks dated to about 3,500 million years ago have been interpreted as bacteria,
[28] with geochemical evidence also seeming to show the presence of life 3,800 million years ago.[29]
However these analyses were closely scrutinized, and non-biological processes were found which could
produce all of the "signatures of life" that had been reported.[30][31] While this does not prove that the
structures found had a non-biological origin, they cannot be taken as clear evidence for the presence of life.
Geochemical signatures from rocks deposited 3,400 million years ago have been interpreted as evidence for
life,[27][32] although these statements have not been thoroughly examined by critics.
[edit] Origins of life on Earth

Evolutionary tree showing the divergence of modern species from their common ancestor in the
center.[33] The three domains are colored, with bacteria blue, archaea green, and eukaryotes red.
Further information: Evidence of common descent, Common descent, and Homology (biology)
Biologists reason that all living organisms on Earth must share a single last universal ancestor,
because it would be virtually impossible that two or more separate lineages could have independently
developed the many complex biochemical mechanisms common to all living organisms.[34][35] As previously
mentioned the earliest organisms for which fossil evidence is available are bacteria, cells far too complex to
have arisen directly from non-living materials.[36] The lack of fossil or geochemical evidence for earlier
organisms has left plenty of scope for hypotheses, which fall into two main groups: 1) that life arose
spontaneously on Earth or 2) that it was "seeded" from elsewhere in the universe.
[edit] Life "seeded" from elsewhere

Main articles: Panspermia, Life on Mars, Fermi paradox, and Rare Earth hypothesis
The idea that life on Earth was "seeded" from elsewhere in the universe dates back at least to the
fifth century BCE.[37] In the twentieth century it was proposed by the physical chemist Svante Arrhenius,[38]
by the astronomers Fred Hoyle and Chandra Wickramasinghe,[39] and by molecular biologist Francis Crick
and chemist Leslie Orgel.[40] There are three main versions of the "seeded from elsewhere" hypothesis:
from elsewhere in our Solar system via fragments knocked into space by a large meteor impact, in which
case the only credible source is Mars;[41] by alien visitors, possibly as a result of accidental contamination by
micro-organisms that they brought with them;[40] and from outside the Solar system but by natural means.
[38][41] Experiments suggest that some micro-organisms can survive the shock of being catapulted into
space and some can survive exposure to radiation for several days, but there is no proof that they can
survive in space for much longer periods.[41] Scientists are divided over the likelihood of life arising
independently on Mars,[42] or on other planets in our galaxy.[41]
[edit] Independent emergence on Earth

Main article: Abiogenesis
Life on Earth is based on carbon and water. Carbon provides stable frameworks for complex
chemicals and can be easily extracted from the environment, especially from carbon dioxide. The only other
element with similar chemical properties, silicon, forms much less stable structures and, because most of its
compounds are solids, would be more difficult for organisms to extract. Water is an excellent solvent and has
two other useful properties: the fact that ice floats enables aquatic organisms to survive beneath it in winter;
and its molecules have electrically negative and positive ends, which enables it to form a wider range of
compounds than other solvents can. Other good solvents, such as ammonia, are liquid only at such low
temperatures that chemical reactions may be too slow to sustain life, and lack water's other advantages.[43]
Organisms based on alternative biochemistry may however be possible on other planets.[44]
Research on how life might have emerged unaided from non-living chemicals focuses on three
possible starting points: self-replication, an organism's ability to produce offspring that are very similar to
itself; metabolism, its ability to feed and repair itself; and external cell membranes, which allow food to enter
and waste products to leave, but exclude unwanted substances.[45] Research on abiogenesis still has a long
way to go, since theoretical and empirical approaches are only beginning to make contact with each other.
[46][47]
[edit] Replication first: RNA world

Main articles: Last universal ancestor and RNA world
Even the simplest members of the three modern domains of life use DNA
to record their "recipes" and a complex array of RNA and protein molecules to
"read" these instructions and use them for growth, maintenance and self-
replication. This system is far too complex to have emerged directly from non-
living materials.[36] The discovery that some RNA molecules can catalyze both
their own replication and the construction of proteins led to the hypothesis of
earlier life-forms based entirely on RNA.[48] These ribozymes could have formed
an RNA world in which there were individuals but no species, as mutations and
horizontal gene transfers would have meant that the offspring in each generation
were quite likely to have different genomes from those that their parents started
with.[49] RNA would later have been replaced by DNA, which is more stable and
therefore can build longer genomes, expanding the range of capabilities a single
organism can have.[49][50][51] Ribozymes remain as the main components of
ribosomes, modern cells' "protein factories".[52]
Although short self-replicating RNA molecules have been artificially
produced in laboratories,[53] doubts have been raised about where natural non-
biological synthesis of RNA is possible.[54] The earliest "ribozymes" may have
been formed of simpler nucleic acids such as PNA, TNA or GNA, which would
have been replaced later by RNA.[55][56]
In 2003 it was proposed that porous metal sulfide precipitates would
assist RNA synthesis at about 100 °C (212 °F) and ocean-bottom pressures near
hydrothermal vents. In this hypothesis lipid membranes would be the last major The replicator in
cell components to appear and until then the proto-cells would be confined to the virtually all known life is
pores.[57] deoxyribonucleic acid.
DNA's structure and
replication systems are
far more complex than
those of the original
replicator.[36]
[edit] Metabolism first: Iron-sulfur world
Main article: Iron-sulfur world theory
A series of experiments starting in 1997 showed that early stages in the formation of proteins from
inorganic materials including carbon monoxide and hydrogen sulfide could be achieved by using iron sulfide
and nickel sulfide as catalysts. Most of the steps required temperatures of about 100 °C (212 °F) and
moderate pressures, although one stage required 250 °C (482 °F) and a pressure equivalent to that found
under 7 kilometres (4.3 mi) of rock. Hence it was suggested that self-sustaining synthesis of proteins could
have occurred near hydrothermal vents.[58]
[edit] Membranes first: Lipid world

It has been suggested that double-walled "bubbles" of
lipids like those that form the external membranes of cells may
have been an essential first step.[59] Experiments that = water-attracting heads of lipid
simulated the conditions of the early Earth have reported the
formation of lipids, and these can spontaneously form
liposomes, double-walled "bubbles", and then reproduce = water-repellent tails
themselves. Although they are not intrinsically information-
carriers as nucleic acids are, they would be subject to natural
selection for longevity and reproduction. Nucleic acids such as
RNA might then have formed more easily within the liposomes
than they would have outside.[60]
Cross-section through a liposome.

[edit] The clay theory
Main articles: Graham Cairns-Smith#Clay Theory and RNA world
RNA is complex and there are doubts about whether it can be produced non-biologically in the wild.
[54] Some clays, notably montmorillonite, have properties that make them plausible accelerators for the
emergence of an RNA world: they grow by self-replication of their crystalline pattern; they are subject to an
analog of natural selection, as the clay "species" that grows fastest in a particular environment rapidly
becomes dominant; and they can catalyze the formation of RNA molecules.[61] Although this idea has not
become the scientific consensus, it still has active supporters.[62]
Research in 2003 reported that montmorillonite could also accelerate the conversion of fatty acids
into "bubbles", and that the "bubbles" could encapsulate RNA attached to the clay. These "bubbles" can then
grow by absorbing additional lipids and then divide. The formation of the earliest cells may have been aided
by similar processes.[63]
A similar hypothesis presents self-replicating iron-rich clays as the progenitors of nucleotides, lipids
and amino acids.[64]
[edit] Environmental and evolutionary impact of microbial mats

Main articles: Microbial mat and Oxygen catastrophe
Modern stromatolites in Shark Bay, Western Australia.
Microbial mats are multi-layered, multi-species colonies of bacteria and other organisms that are
generally only a few millimeters thick, but still contain a wide range of chemical environments, each of which
favors a different set of micro-organisms.[65] To some extent each mat forms its own food chain, as the by-
products of each group of micro-organisms generally serve as "food" for adjacent groups.[66]
Stromatolites are stubby pillars built as microbes in mats slowly migrate upwards to avoid being
smothered by sediment deposited on them by water.[65] There has been vigorous debate about the validity
of alleged fossils from before 3,000 million years ago,[67] with critics arguing that so-called stromatolites
could have been formed by non-biological processes.[30] In 2006 another find of stromatolites was reported
from the same part of Australia as previous ones, in rocks dated to 3,500 million years ago.[68]
In modern underwater mats the top layer often consists of photosynthesizing cyanobacteria which
create an oxygen-rich environment, while the bottom layer is oxygen-free and often dominated by hydrogen
sulfide emitted by the organisms living there.[66] It is estimated that the appearance of oxygenic
photosynthesis by bacteria in mats increased biological productivity by a factor of between 100 and 1,000.
The reducing agent used by oxygenic photosynthesis is water, which is much more plentiful than the
geologically-produced reducing agents required by the earlier non-oxygenic photosynthesis.[69] From this
point onwards life itself produced significantly more of the resources it needed than did geochemical
processes.[70] Oxygen is toxic to organisms that are not adapted to it, but greatly increases the metabolic
efficiency of oxygen-adapted organisms.[71][72] Oxygen became a significant component of Earth's
atmosphere about 2,400 million years ago.[73] Although eukaryotes may have been present much earlier,
[74][75] the oxygenation of the atmosphere was a prerequisite for the evolution of the most complex
eukaryotic cells, from which all multicellular organisms are built.[76] The boundary between oxygen-rich and
oxygen-free layers in microbial mats would have moved upwards when photosynthesis shut down overnight,
and then downwards as it resumed on the next day. This would have created selection pressure for
organisms in this intermediate zone to acquire the ability to tolerate and then to use oxygen, possibly via
endosymbiosis, where one organism lives inside another and both of them benefit from their association.[2]
Cyanobacteria have the most complete biochemical "toolkits" of all the mat-forming organisms.
Hence they are the most self-sufficient of the mat organisms and were well-adapted to strike out on their own
both as floating mats and as the first of the phytoplankton, providing the basis of most marine food chains.[2]
Eukaryotes
Bikonta
Apusozoa
[edit] Diversification of eukaryotes Archaeplastida (Land plants

Main article: Eukaryote green algae, red algae, and
glaucophytes)
Eukaryotes may have been present long before the
oxygenation of the atmosphere,[74] but most modern eukaryotes
require oxygen, which their mitochondria use to fuel the Chromalveolata
production of ATP, the internal energy supply of all known cells.
[76] In the 1970s it was proposed and, after much debate, widely
accepted that eukaryotes emerged as a result of a sequence of Rhizaria
endosymbioses between "procaryotes". For example: a
predatory micro-organism invaded a large procaryote, probably
an archaean, but the attack was neutralized, and the attacker Excavata
took up residence and evolved into the first of the mitochondria;
one of these chimeras later tried to swallow a photosynthesizing
cyanobacterium, but the victim survived inside the attacker and
the new combination became the ancestor of plants; and so on.
After each endosymbiosis began, the partners would have Unikonta
eliminated unproductive duplication of genetic functions by re-
arranging their genomes, a process which sometimes involved Amoebozoa
transfer of genes between them.[79][80][81] Another hypothesis
proposes that mitochondria were originally sulfur- or hydrogen- Opisthokonta
metabolising endosymbionts, and became oxygen-consumers
later.[82] On the other hand mitochondria might have been part Metazoa
of eukaryotes' original equipment.[83] (Animals)
Choanozoa
Eumycota
(Fungi)
There is a debate about when eukaryotes first appeared: the presence of steranes in Australian
shales may indicate that eukaryotes were present 2,700 million years ago;[75] however an analysis in 2008
concluded that these chemicals infiltrated the rocks less than 2,200 million years ago and prove nothing
about the origins of eukaryotes.[84] Fossils of the alga Grypania have been reported in 1,850 million-year-old
rocks (originally dated to 2,100 million years ago but later revised[5]), and indicates that eukaryotes with
organelles had already evolved.[85] A diverse collection of fossil algae were found in rocks dated between
1,500 million years ago and 1,400 million years ago.[86] The earliest known fossils of fungi date from 1,430
million years ago.[87]
[edit] Multicellular organisms and sexual reproduction

[edit] Multicellularity
Main articles: Multicellular organism , Evolution of multicellularity , and Sexual reproduction
The simplest definitions of "multicellular", for example "having multiple cells", could include colonial
cyanobacteria like Nostoc. Even a professional biologist's definition such as "having the same genome but
different types of cell" would still include some genera of the green alga Volvox, which have cells that
specialize in reproduction.[88] Multicellularity evolved independently in organisms as diverse as sponges and
other animals, fungi, plants, brown algae, cyanobacteria, slime moulds and myxobacteria.[5][89] For the sake
of brevity this article focuses on the organisms that show the greatest specialization of cells and variety of
cell types, although this approach to the evolution of complexity could be regarded as "rather
anthropocentric".[90]
A slime mold solves a maze. The mold (yellow) explored and filled the maze (left). When the
researchers placed sugar (red) at two separate points, the mold concentrated most of its mass there and left
only the most efficient connection between the two points (right).[91]
The initial advantages of multicellularity may have included: increased resistance to predators, many
of which attacked by engulfing; the ability to resist currents by attaching to a firm surface; the ability to reach
upwards to filter-feed or to obtain sunlight for photosynthesis;[92] the ability to create an internal environment
that gives protection against the external one;[90] and even the opportunity for a group of cells to behave
"intelligently" by sharing information.[91] These features would also have provided opportunities for other
organisms to diversify, by creating more varied environments than flat microbial mats could.[92]
Multicellularity with differentiated cells is beneficial to the organism as a whole but disadvantageous
from the point of view of individual cells, most of which lose the opportunity to reproduce themselves. In an
asexual multicellular organism, rogue cells which retain the ability to reproduce may take over and reduce the
organism to a mass of undifferentiated cells. Sexual reproduction eliminates such rogue cells from the next
generation and therefore appears to be a prerequisite for complex multicellularity.[92]
The available evidence indicates that eukaryotes evolved much earlier but remained inconspicuous
until a rapid diversification around 1,000 million years ago. The only respect in which eukaryotes clearly
surpass bacteria and archaea is their capacity for variety of forms, and sexual reproduction enabled
eukaryotes to exploit that advantage by producing organisms with multiple cells that differed in form and
function.[92]
[edit] Evolution of sexual reproduction

Main article: Evolution of sexual reproduction
The defining characteristic of sexual reproduction is recombination, in which each of the offspring
receives 50% of its genetic inheritance from each of the parents.[93] Bacteria also exchange DNA by
bacterial conjugation, the benefits of which include resistance to antibiotics and other toxins, and the ability to
utilize new metabolites.[94] However conjugation is not a means of reproduction, and is not limited to
members of the same species – there are cases where bacteria transfer DNA to plants and animals.[95]
The disadvantages of sexual reproduction are well-known: the genetic reshuffle of recombination
may break up favorable combinations of genes; and since males do not directly increase the number of
offspring in the next generation, an asexual population can out-breed and displace in as little as 50
generations a sexual population that is equal in every other respect.[93] Nevertheless the great majority of
animals, plants, fungi and protists reproduce sexually. There is strong evidence that sexual reproduction
arose early in the history of eukaryotes and that the genes controlling it have changed very little since then.
[96] How sexual reproduction evolved and survived is an unsolved puzzle.[97]
The Red Queen Hypothesis suggests that sexual reproduction provides protection against parasites,
because it is easier for parasites to evolve means of overcoming the defenses of genetically identical clones
than those of sexual species that present moving targets, and there is some experimental evidence for this.
However there is still doubt about whether it would explain the survival of sexual species if multiple similar
clone species were present, as one of the clones may survive the attacks of parasites for long enough to out-
breed the sexual species.[93]
The Mutation Deterministic Hypothesis assumes that each organism has more than one harmful
mutation and the combined effects of these mutations are more harmful than the sum of the harm done by
each individual mutation. If so, sexual recombination of genes will reduce the harm that bad mutations do to
offspring and at the same time eliminate some bad mutations from the gene pool by isolating them in
individuals that perish quickly because they have an above-average number of bad mutations. However the
evidence suggests that the MDH's assumptions are shaky, because many species have on average less
than one harmful mutation per individual and no species that has been investigated shows evidence of
synergy between harmful mutations.[93]
Horodyskia apparently re-arranged itself into fewer but larger main masses as the sediment grew
deeper round its base.[5]
The random nature of recombination causes the relative abundance of alternative traits to vary from
one generation to another. This genetic drift is insufficient on its own to make sexual reproduction
advantageous, but a combination of genetic drift and natural selection may be sufficient. When chance
produces combinations of good traits, natural selection gives a large advantage to lineages in which these
traits become genetically linked. On the other hand the benefits of good traits are neutralized if they appear
along with bad traits. Sexual recombination gives good traits the opportunities to become linked with other
good traits, and mathematical models suggest this may be more than enough to offset the disadvantages of
sexual reproduction.[97] Other combinations of hypotheses that are inadequate on their own are also being
examined.[93]
[edit] Fossil evidence for multicellularity and sexual reproduction

The Francevillian Group Fossil, dated to 2,100 million years ago, is the
earliest known fossil organism that is clearly multicellular.[19] This may have
had differentiated cells.[99] Another early multicellular fossil, Qingshania,[note
1] dated to 1,700 million years ago, appears to consist of virtually identical
cells. The red alga called Bangiomorpha, dated at 1,200 million years ago, is
the earliest known organism which certainly has differentiated, specialized
cells, and is also the oldest known sexually-reproducing organism.[92] The
1,430 million-year-old fossils interpreted as fungi appear to have been
multicellular with differentiated cells.[87] The "string of beads" organism
Horodyskia, found in rocks dated from 1,500 million years ago to 900 million
years ago, may have been an early metazoan;[5] however it has also been
interpreted as a colonial foraminiferan.[98]
Horodyskia may
have been an early
metazoan,[5] or a colonial
foraminiferan[98]
[edit] Emergence of animals Bilaterians
Main articles: Animal, Ediacara biota, Cambrian
Explosion, Burgess shale type fauna, and Stem group Deuterostomes
Animals are multicellular eukaryotes,[note 2] and are (chordates
distinguished from plants, algae, and fungi by lacking cell walls. hemichordates
[101] All animals are motile,[102] if only at certain life stages. All echinoderms
animals except sponges have bodies differentiated into separate Protostomes
tissues, including muscles, which move parts of the animal by
Ecdysozoa
contracting, and nerve tissue, which transmits and processes
(arthropods,
signals.[103]
nematodes, tardigrades,
The earliest widely-accepted animal fossils are rather etc.)
modern-looking cnidarians (the group that includes jellyfish, sea
anemones and hydras), possibly from around 580 million years Lophotrochozoa
ago, although fossils from the Doushantuo Formation can only (molluscs, annelids,
be dated approximately. Their presence implies that the brachiopods, etc.)
cnidarian and bilaterian lineages had already diverged.[104]
The Ediacara biota, which flourished for the last
40 million years before the start of the Cambrian,[105] were the
first animals more than a very few centimeters long. Many were
flat and had a "quilted" appearance, and seemed so strange that
there was a proposal to classify them as a separate kingdom,
Vendozoa.[106] Others, however, been interpreted as early
molluscs (Kimberella[107][108]), echinoderms (Arkarua[109]),
and arthropods (Spriggina,[110] Parvancorina[111]). There is still debate about the classification of these
specimens, mainly because the diagnostic features which allow taxonomists to classify more recent
organisms, such as similarities to living organisms, are generally absent in the Ediacarans. However there
seems little doubt that Kimberella was at least a triploblastic bilaterian animal, in other words significantly
more complex than cnidarians.[112]
The small shelly fauna are a very mixed collection of fossils found between the Late Ediacaran and
Mid Cambrian periods. The earliest, Cloudina, shows signs of successful defense against predation and may
indicate the start of an evolutionary arms race. Some tiny Early Cambrian shells almost certainly belonged to
molluscs, while the owners of some "armor plates", Halkieria and Microdictyon, were eventually identified
when more complete specimens were found in Cambrian lagerstätten that preserved soft-bodied animals.
[113]
Opabinia made the largest single contribution to modern interest in the Cambrian explosion.[114]
In the 1970s there was already a debate about whether the emergence of the modern phyla was
"explosive" or gradual but hidden by the shortage of Pre-Cambrian animal fossils.[113] A re-analysis of
fossils from the Burgess Shale lagerstätte increased interest in the issue when it revealed animals, such as
Opabinia, which did not fit into any known phylum. At the time these were interpreted as evidence that the
modern phyla had evolved very rapidly in the "Cambrian explosion" and that the Burgess Shale's "weird
wonders" showed that the Early Cambrian was a uniquely experimental period of animal evolution.[115] Later
discoveries of similar animals and the development of new theoretical approaches led to the conclusion that
many of the "weird wonders" were evolutionary "aunts" or "cousins" of modern groups[116] – for example that
Opabinia was a member of the lobopods, a group which includes the ancestors of the arthropods, and that it
may have been closely related to the modern tardigrades.[117] Nevertheless there is still much debate about
whether the Cambrian explosion was really explosive and, if so, how and why it happened and why it
appears unique in the history of animals.[118]
Acanthodians were among the earliest vertebrates with jaws.[119]

Most of the animals at the heart of the Cambrian explosion debate are protostomes, one of the two
main groups of complex animals. One deuterostome group, the echinoderms, many of which have hard
calcite "shells", are fairly common from the Early Cambrian small shelly fauna onwards.[113] Other
deuterostome groups are soft-bodied, and most of the significant Cambrian deuterostome fossils come from
the Chengjiang fauna, a lagerstätte in China.[120] The Chengjiang fossils Haikouichthys and Myllokunmingia
appear to be true vertebrates,[121] and Haikouichthys had distinct vertebrae, which may have been slightly
mineralized.[122] Vertebrates with jaws, such as the Acanthodians, first appeared in the Late Ordovician.
[123]
[edit] Colonization of land
Adaptation to life on land is a major challenge: all land organisms need to avoid drying-out and all
those above microscopic size have to resist gravity; respiration and gas exchange systems have to change;
reproductive systems cannot depend on water to carry eggs and sperm towards each other.[124][125]
Although the earliest good evidence of land plants and animals dates back to the Ordovician period
(488 to 444 million years ago), modern land ecosystems only appeared in the late Devonian, about
385 to 359 million years ago.[126]
[edit] Evolution of soil

Before the colonization of land, soil, a combination of mineral particles and decomposed organic
matter, did not exist. Land surfaces would have been either bare rock or unstable sand produced by
weathering. Water and any nutrients in it would have drained away very quickly.[126]
Lichens growing on concrete

Films of cyanobacteria, which are not plants but use the same photosynthesis mechanisms, have
been found in modern deserts, and only in areas that are unsuitable for vascular plants. This suggests that
microbial mats may have been the first organisms to colonize dry land, possibly in the Precambrian. Mat-
forming cyanobacteria could have gradually evolved resistance to desiccation as they spread from the seas
to tidal zones and then to land.[126] Lichens, which are symbiotic combinations of a fungus (almost always
an ascomycete) and one or more photosynthesizers (green algae or cyanobacteria),[127] are also important
colonizers of lifeless environments,[126] and their ability to break down rocks contributes to soil formation in
situations where plants cannot survive.[127] The earliest known ascomycete fossils date from 423 to 419
million years ago in the Silurian.[126]
Soil formation would have been very slow until the appearance of burrowing animals, which mix the
mineral and organic components of soil and whose feces are a major source of the organic components.
[126] Burrows have been found in Ordovician sediments, and are attributed to annelids ("worms") or
arthropods.[126][128]
[edit] Plants and the Late Devonian wood crisis

Main article: Evolutionary history of plants
Reconstruction of Cooksonia, a vascular plant from the Silurian
Fossilized trees from the Mid-Devonian Gilboa fossil forest
In aquatic algae, almost all cells are capable of photosynthesies and are nearly independent. Life on
land required plants to become internally more complex and specialized: photosynthesis was most efficient
at the top; roots were required in order to extract water from the ground; the parts in between became
supports and transport systems for water and nutrients.[124][129]
Spores of land plants, possibly rather like liverworts, have been found in Mid Ordovician rocks dated
to about 476 million years ago. In Mid Silurian rocks 430 million years ago there are fossils of actual plants
including clubmosses such as Baragwanathia; most were under 10 centimetres (3.9 in) high, and some
appear closely related to vascular plants, the group that includes trees.[129]
By the Late Devonian 370 million years ago, trees such as Archaeopteris were so abundant that they
changed river systems from mostly braided to mostly meandering, because their roots bound the soil firmly.
[130] In fact they caused a "Late Devonian wood crisis",[131] because:
• They removed more carbon dioxide from the atmosphere, reducing the greenhouse effect
and thus causing an ice age in the Carboniferous period.[132] In later ecosystems the carbon dioxide
"locked up" in wood is returned to the atmosphere by decomposition of dead wood. However the
earliest fossil evidence of fungi that can decompose wood also comes from the Late Devonian.[133]
• The increasing depth of plants' roots led to more washing of nutrients into rivers and seas by
rain. This caused algal blooms whose high consumption of oxygen caused anoxic events in deeper
waters, increasing the extinction rate among deep-water animals.[132]
[edit] Land invertebrates
Animals had to change their feeding and excretory systems, and most land animals developed
internal fertilization of their eggs. The difference in refractive index between water and air required changes
in their eyes. On the other hand in some ways movement and breathing became easier, and the better
transmission of high-frequency sounds in air encouraged the development of hearing.[125]
Some trace fossils from the Cambrian-Ordovician boundary about 490 million years ago are
interpreted as the tracks of large amphibious arthropods on coastal sand dunes, and may have been made
by euthycarcinoids,[134] which are thought to be evolutionary "aunts" of myriapods.[135] Other trace fossils
from the Late Ordovician a little over 445 million years ago probably represent land invertebrates, and there
is clear evidence of numerous arthropods on coasts and alluvial plains shortly before the Silurian-Devonian
boundary, about 415 million years ago, including signs that some arthropods ate plants.[136] Arthropods
were well pre-adapted to colonise land, because their existing jointed exoskeletons provided protection
against desiccation, support against gravity and a means of locomotion that was not dependent on water.
[137]
The fossil record of other major invertebrate groups on land is poor: none at all for non-parasitic
flatworms, nematodes or nemerteans; some parasitic nematodes have been fossilized in amber; annelid
worm fossils are known from the Carboniferous, but they may still have been aquatic animals; the earliest
fossils of gastropods on land date from the Late Carboniferous, and this group may have had to wait until leaf
litter became abundant enough to provide the moist conditions they need.[125]
The earliest confirmed fossils of flying insects date from the Late Carboniferous, but it is thought that
insects developed the ability to fly in the Early Carboniferous or even Late Devonian. This gave them a wider
range of ecological niches for feeding and breeding, and a means of escape from predators and from
unfavorable changes in the environment.[138] About 99% of modern insect species fly or are descendants of
flying species.[139]
[edit] Land vertebrates

Main article: Tetrapod
Acanthostega changed views about the early evolution of tetrapods.[140]

"Fish"
Acanthostega
Ichthyostega
Tulerpeton
Early
amphibians
Anthracosauria
Amniotes
Family tree of tetrapods[141]
Tetrapods, vertebrates with four limbs, evolved from other rhipidistian fish over a relatively short
timespan during the Late Devonian, between 370 million years ago and 360 million years ago.[142] From the
1950s to the early 1980s it was thought that tetrapods evolved from fish that had already acquired the ability
to crawl on land, possibly in order to go from a pool that was drying out to one that was deeper. However in
1987 nearly-complete fossils of Acanthostega from about 363 million years ago showed that this Late
Devonian transitional animal had legs and both lungs and gills, but could never have survived on land: its
limbs and its wrist and ankle joints were too weak to bear its weight; its ribs were too short to prevent its
lungs from being squeezed flat by its weight; its fish-like tail fin would have been damaged by dragging on
the ground. The current hypothesis is that Acanthostega, which was about 1 metre (3.3 ft) long, was a wholly
aquatic predator that hunted in shallow water. Its skeleton differed from that of most fish, in ways that
enabled it to raise its head to breathe air while its body remained submerged, including: its jaws show
modifications that would have enabled it to gulp air; the bones at the back of its skull are locked together,
providing strong attachment points for muscles that raised its head; the head is not joined to the shoulder
girdle and it has a distinct neck.[140]
The Devonian proliferation of land plants may help to explain why air-breathing would have been an
advantage: leaves falling into streams and rivers would have encouraged the growth of aquatic vegetation;
this would have attracted grazing invertebrates and small fish that preyed on them; they would have been
attractive prey but the environment was unsuitable for the big marine predatory fish; air-breathing would have
been necessary because these waters would have been short of oxygen, since warm water holds less
dissolved oxygen than cooler marine water and since the decomposition of vegetation would have used
some of the oxygen.[140]
Later discoveries revealed earlier transitional forms between Acanthostega and completely fish-like
animals.[143] Unfortunately there is then a gap of about 30 million years between the fossils of ancestral
tetrapods and Mid Carboniferous fossils of vertebrates that look well-adapted for life on land. Some of these
look like early relatives of modern amphibians, most of which need to keep their skins moist and to lay their
eggs in water, while others are accepted as early relatives of the amniotes, whose water-proof skins and
eggs enable them to live and breed far from water.[141]
[edit] Dinosaurs, birds and mammals

Main articles: Dinosaur evolution, Origin of Birds, and Evolution of mammals
Amniotes
Synapsids
Early synapsids
(extinct)
Pelycosaurs
Extinct pelycosaurs
Therapsids
Extinct therapsids
Mammaliformes
Extinct mammaliformes
Mammals
Sauropsids
Diapsids
Squ
(lizards and
snakes)
Archosaurs
Extinct
archosaurs
Crocodilians
Pterosaurs
(extinct)
Dinosaurs
Theropods
Extinct
theropods
Birds
Sauropods
(extinct)
Ornithischians
(extinct)
Possible family tree of dinosaurs, birds and mammals[145][146]
Amniotes, whose eggs can survive in dry environments, probably evolved in the Late Carboniferous
period, between 330 million years ago and 314 million years ago. The earliest fossils of the two surviving
amniote groups, synapsids and sauropsids, date from around 313 million years ago.[145][146] The synapsid
pelycosaurs and their descendants the therapsids are the most common land vertebrates in the best-known
Permian fossil beds, between 229 million years ago and 251 million years ago. However at the time these
were all in temperate zones at middle latitudes, and there is evidence that hotter, drier environments nearer
the Equator were dominated by sauropsids and amphibians.[147]
The Permian-Triassic extinction wiped out almost all land vertebrates,[148] as well as the great
majority of other life.[149] During the slow recovery from this catastrophe, estimated to be 30M years,[150] a
previously obscure sauropsid group became the most abundant and diverse terrestrial vertebrates: a few
fossils of archosauriformes ("shaped like archosaurs") have been found in Late Permian rocks,[151] but by
the Mid Triassic archosaurs were the dominant land vertebrates. Dinosaurs distinguished themselves from
other archosaurs in the Late Triassic, and became the dominant land vertebrates of the Jurassic and
Cretaceous periods, between 199 million years ago and 65 million years ago.[152]
During the Late Jurassic, birds evolved from small, predatory theropod dinosaurs.[153] The first birds
inherited teeth and long, bony tails from their dinosaur ancestors,[153] but some developed horny, toothless
beaks by the very Late Jurassic[154] and short pygostyle tails by the Early Cretaceous.[155]
While the archosaurs and dinosaurs were becoming more dominant in the Triassic, the mammaliform
successors of the therapsids could only survive as small, mainly nocturnal insectivores. This apparent set-
back may actually have promoted the evolution of mammals, for example nocturnal life may have
accelerated the development of endothermy ("warm-bloodedness") and hair or fur.[156] By 195 million years
ago in the Early Jurassic there were animals that were very nearly mammals.[157] Unfortunately there is a
gap in the fossil record throughout the Mid Jurassic.[158] However fossil teeth discovered in Madagascar
indicate that true mammals existed at least 167 million years ago.[159] After dominating land vertebrate
niches for about 150 million years, the dinosaurs perished 65 million years ago in the Cretaceous–Tertiary
extinction along with many other groups of organisms.[160] Mammals throughout the time of the dinosaurs
had been restricted to a narrow range of taxa, sizes and shapes, but increased rapidly in size and diversity
after the extinction,[161][162] with bats taking to the air within 13 million years,[163] and cetaceans to the sea
within 15 million years.[164]
[edit] Flowering plants
Main articles: Flowering plant and Gymnosperm
Gymnosperms Gymnosp
Gnetales
(gymnosperm)
Welwitschia Cycads
(gymnosperm) (gymnosperm)
Bennettitales
Ephedra
(gymnosperm)
Gingk
Bennettitales
Angiosperms Gnetales
(flowering plants) (gymnosperm)
Conifers
(gymnosperm)
One possible family tree of flowering plants.[165]
Another possible family tree.[166]

The 250,000 to 400,000 species of flowering plants outnumber all other ground plants combined, and
are the dominant vegetation in most terrestrial ecosystems. There is fossil evidence that flowering plants
diversified rapidly in the Early Cretaceous, between 130 million years ago and 90 million years ago,[165]
[166] and that their rise was associated with that of pollinating insects.[166] Among modern flowering plants
Magnolias are thought to be close to the common ancestor of the group.[165] However paleontologists have
not succeeded in identifying the earliest stages in the evolution of flowering plants.[165][166]
[edit] Social insects

Main article: Social insects
The social insects are remarkable because the great majority of individuals in each colony are sterile.
This appears contrary to basic concepts of evolution such as natural selection and the selfish gene. In fact
there are very few eusocial insect species: only 15 out of approximately 2,600 living families of insects
contain eusocial species, and it seems that eusociality has evolved independently only 12 times among
arthropods, although some eusocial lineages have diversified into several families. Nevertheless social
insects have been spectacularly successful; for example although ants and termites account for only about
2% of known insect species, they form over 50% of the total mass of insects. Their ability to control a territory
appears to be the foundation of their success.[167]
These termite mounds have survived a bush fire.
The sacrifice of breeding opportunities by most individuals has long been explained as a
consequence of these species' unusual haplodiploid method of sex determination, which has the paradoxical
consequence that two sterile worker daughters of the same queen share more genes with each other than
they would with their offspring if they could breed.[168] However Wilson and Hölldobler argue that this
explanation is faulty: for example, it is based on kin selection, but there is no evidence of nepotism in
colonies that have multiple queens. Instead, they write, eusociality evolves only in species that are under
strong pressure from predators and competitors, but in environments where it is possible to build "fortresses";
after colonies have established this security, they gain other advantages though co-operative foraging. In
support of this explanation they cite the appearance of eusociality in bathyergid mole rats,[167] which are not
haplodiploid.[169]
The earliest fossils of insects have been found in Early Devonian rocks from about 400 million years
ago, which preserve only a few varieties of flightless insect. The Mazon Creek lagerstätten from the Late
Carboniferous, about 300 million years ago, include about 200 species, some gigantic by modern standards,
and indicate that insects had occupied their main modern ecological niches as herbivores, detritivores and
insectivores. Social termites and ants first appear in the Early Cretaceous, and advanced social bees have
been found in Late Cretaceous rocks but did not become abundant until the Mid Cenozoic.[170]
[edit] Humans
Main article: Human evolution
Modern humans evolved from a lineage of upright-walking apes that has been traced back over 6
million years ago to Sahelanthropus.[171] The first known stone tools were made about 2.5 million years ago,
apparently by Australopithecus garhi, and were found near animal bones that bear scratches made by these
tools.[172] The earliest hominines had chimp-sized brains, but there has been a fourfold increase in the last
3 million years; a statistical analysis suggests that hominine brain sizes depend almost completely on the
date of the fossils, while the species to which they are assigned has only slight influence.[173] There is a
long-running debate about whether modern humans evolved all over the world simultaneously from existing
advanced hominines or are descendants of a single small population in Africa, which then migrated all over
the world less than 200,000 years ago and replaced previous hominine species.[174] There is also debate
about whether anatomically-modern humans had
an intellectual, cultural and technological "Great
Leap Forward" under 100,000 years ago and, if so,
whether this was due to neurological changes that
are not visible in fossils.[175]
[edit] Mass extinctions

Main article: Mass extinction
Life on Earth has suffered occasional
mass extinctions at least since 542 million years
ago. Although they are disasters at the time, mass
extinctions have sometimes accelerated the
evolution of life on Earth. When dominance of
particular ecological niches passes from one
group of organisms to another, it is rarely because
the new dominant group is "superior" to the old
and usually because an extinction event
eliminates the old dominant group and makes way
for the new one.[176][177]
The fossil record appears to show that the
gaps between mass extinctions are becoming
Apparent extinction intensity, i.e. the fraction of

genera going extinct at any given time, as reconstructed
from the fossil record. (Graph not meant to include
recent epoch of Holocene extinction event)
longer and the average and background rates of extinction are decreasing. Both of these phenomena could
be explained in one or more ways:[178]
• The oceans may have become more hospitable to life over the last 500 million years and less
vulnerable to mass extinctions: dissolved oxygen became more widespread and penetrated to
greater depths; the development of life on land reduced the run-off of nutrients and hence the risk of
eutrophication and anoxic events; and marine ecosystems became more diversified so that food
chains were less likely to be disrupted.[179][180]
• Reasonably complete fossils are very rare, most extinct organisms are represented only by
partial fossils, and complete fossils are rarest in the oldest rocks. So paleontologists have mistakenly
assigned parts of the same organism to different genera which were often defined solely to
accommodate these finds – the story of Anomalocaris is an example of this. The risk of this mistake is
higher for older fossils because these are often unlike parts of any living organism. Many of the
"superfluous" genera are represented by fragments which are not found again and the "superfluous"
genera appear to become extinct very quickly.[178]
Biodiversity in the fossil record, which is
"the number of distinct genera
alive at any given time; that is, those
whose first occurrence predates and
whose last occurrence postdates that
time"[181]
shows a different trend: a fairly swift rise from
542 to 400 million years ago; a slight decline from
400 to 200 million years ago, in which the devastating
Permian–Triassic extinction event is an important factor;
and a swift rise from 200 million years ago to the
Thousands of genera
present.[181]
[edit] The present

Oxygenic photosynthesis accounts for virtually
all of the production of organic matter from non-organic
ingredients. Production is split about evenly between
land and marine plants, and phytoplankton are the
dominant marine producers.[182]
The processes that drive evolution are still
operating. Well-known examples include the changes in
coloration of the peppered moth over the last 200 years
and the more recent appearance of pathogens that are
Phanerozoic biodiversity as shown by the
fossil record
resistant to antibiotics.[183][184] There is even evidence that humans are still evolving, and possibly at an
accelerating rate over the last 40,000 years.[185]
[edit] See also

Biology portal
Book:Evolution

• Evolution
• Evolution of mammals
• Evolutionary history of plants
• Taxonomy of commonly fossilised invertebrates
• Timeline of evolution
• Treatise on Invertebrate Paleontology
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[edit] Footnotes
1. ^ Name given as in Butterfield's paper "Bangiomorpha pubescens ..." (2000). A fossil fish,
also from China, has also been named Qingshania. The name of one of these will have to change.
2. ^ Myxozoa were thought to be an exception, but are now thought to be heavily modified
members of the Cnidaria: Jímenez-Guri, E., Philippe, H., Okamura, B. and Holland, P. W. H. (July
2007). "Buddenbrockia is a cnidarian worm". Science 317 (116): 116–118.
doi:10.1126/science.1142024. PMID 17615357.
http://www.sciencemag.org/cgi/content/abstract/317/5834/116. Retrieved 2008-09-03.
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• General information on evolution- Fossil Museum nav.
• Understanding Evolution from University of California, Berkeley
• National Academies Evolution Resources
• Evolution poster- PDF format "tree of life"
• Everything you wanted to know about evolution by New Scientist
• Howstuffworks.com — How Evolution Works
• Synthetic Theory Of Evolution: An Introduction to Modern Evolutionary Concepts and
Theories
History of evolutionary thought
• The Complete Work of Charles Darwin Online
• Understanding Evolution: History, Theory, Evidence, and Implications
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Categories: History by topic | Paleontology | Evolutionary biology

W000
Evolution of cetaceans

The approximately 80 modern species in the order Cetacea.
The cetaceans (whales, dolphins and porpoises) are marine mammal descendants of land mammals.
Their terrestrial origins are indicated by:
• Their need to breathe air from the surface;
• The bones of their fins, which resemble the limbs of land mammals
• The vertical movement of their spines, characteristic more of a running mammal than of the
horizontal movement of fish.
The question of how land animals evolved into ocean-going leviathans was a mystery until recent
discoveries in Pakistan revealed several stages in the transition of cetaceans from land to sea.
Contents
[hide]
• 1 Earliest ancestors
• 2 The earliest cetaceans: Pakicetids or Indohyus?
• 3 Ambulocetids and remingtonocetids
• 4 Protocetids
• 5 Basilosaurids and dorudontids: fully marine cetaceans
• 6 Early echolocation
• 7 Early baleen whales
• 8 Early dolphins
• 9 Skeletal evolution
• 10 See also
• 11 References
[edit] Earliest ancestors
The family tree, including Ungulates.

The traditional theory of cetacean evolution was that whales were related to the mesonychids, an
extinct order of carnivorous ungulates (hoofed animals), which looked rather like wolves with hooves and
were a sister group of artiodactyls. These animals possessed unusual triangular teeth that are similar to
those of whales. For this reason, scientists had long believed that whales evolved from a form of
mesonychid; however, more recent molecular phylogeny data suggest that whales are more closely related
to the artiodactyls, specifically the hippopotamus.[1] The strong evidence for a clade combining cetaceans
and artiodactyls is further discussed under the entry Cetartiodactyla. However, hippos' anthracothere
ancestors do not appear in the fossil record until millions of years after Pakicetus, the first known whale
ancestor.
The recent discovery of Pakicetus, the earliest proto-whale (see below) supports the molecular data.
The skeletons of Pakicetus demonstrate that whales did not derive directly from mesonychids. Instead, they
are a form of artiodactyl (another type of ungulate) that began to take to the water after the artiodactyl family
split from the mesonychids. In other words, the proto-whales were early artiodactyls that retained aspects of
their mesonychid ancestry (such as the triangular teeth) which modern artiodactyls have since lost. An
interesting implication is that the earliest ancestors of all hoofed mammals were probably at least partly
carnivorous or scavengers, today's artiodactyls and perissodactyls having switched to a plant diet later in
their evolution. Whales, due to the readier availability of animal prey and their need for higher caloric content,
in order to live as marine endotherms, naturally retained their carnivorous diet, as did mesonychids, who
were however out-competed by better-adapted animals like the Carnivora later on (mesonychids became
specialized carnivores when the overall availability of large animal prey was still low; thus their adaptation
was likely at a disadvantage when new forms had filled the gaps left by the dinosaurs).
[edit] The earliest cetaceans: Pakicetids or Indohyus?
Reconstruction of Pakicetus
The pakicetids are hoofed mammals that are sometimes classified as the earliest whales.[2][3] They
lived in the early Eocene, around 53 million years ago. They looked rather like dogs with hoofed feet and
long, thick tails. They have been linked to whales by their ears: the structure of the auditory bulla is formed
from the ectotympanic bone only. The shape of the ear region in Pakicetus is highly unusual and only
resembles the skulls of whales. The feature is diagnostic for cetaceans and is found in no other species. It
was initially thought that the ears of Pakicetus were adapted for underwater hearing, but, as would be
expected from the anatomy of the rest of this creature, the ears of Pakicetus are specialized for hearing on
land, and if Pakicetus is related to the ancestors of whales, underwater hearing must have been a later
adaptation.[4] According to Thewissen, the teeth of Pakicetus also resemble the teeth of fossil whales, being
less like a dog's incisors, with a serrated triangular shape, similar to a shark's tooth, which is another link to
more modern whales.[5]
Reconstruction of Indohyus.
Thewissen has since found the same ear structure in fossils of a small deer-like creature, Indohyus,
which lived about 48 million years ago in Kashmir.[3] About the size of a raccoon or domestic cat, this
herbivorous creature shared some of the traits of whales, and showed signs of adaptations to aquatic life,
including a thick and heavy outer coating to bones which is similar to the bones of modern creatures such as
the hippopotamus,[6][7] and reduces buoyancy so that they can stay underwater. This suggests a similar
survival strategy to the African mousedeer or water chevrotain which, when threatened by a bird of prey,
dives into water and hides beneath the surface for up to four minutes.[8][9][10]
[edit] Ambulocetids and remingtonocetids
Reconstruction of Kutchicetus, a remingtonocetid
Reconstruction of Ambulocetus natans

The most remarkable of the recent discoveries in Pakistan has been Ambulocetus, which looked like
a three-metre long mammalian crocodile. Ambulocetus was clearly amphibious, as its back legs are better
adapted for swimming than for walking on land, and it probably swam by undulating its back vertically, as
otters, seals and whales do. It has been speculated that Ambulocetids hunted like crocodiles, lurking in the
shallows to snatch unsuspecting riparian prey and fish.
A smaller cousin of Ambulocetus was the remingtonocetidae family, which had longer snouts than
Ambulocetus, and were slightly better adapted for underwater life. It has been speculated that they lived like
modern sea otters, hunting for fish in the shallows.
In both groups, the nasal openings were at the tip of the snout, like in land mammals.
[edit] Protocetids
Reconstruction of Protocetus
Reconstruction of Rodhocetus
The protocetids form a diverse and heterogeneous group known from Asia, Europe, Africa, and North
America. There were many genera, and some of these are very well known (e.g., Rodhocetus). Known
protocetids had large fore- and hindlimbs that could support the body on land, and it is likely that they lived
amphibiously: in the sea and on land. It is unclear at present whether protocetids had flukes (the horizontal
tail fin of modern cetaceans). However, what is clear is that they are adapted even further to an aquatic life-
style. In Rodhocetus, for example, the sacrum – a bone that in land-mammals is a fusion of five vertebrae that
connects the pelvis with the rest of the vertebral column – was divided into loose vertebrae. However, the
pelvis was still connected to one of the sacral vertebrae. Furthermore, the nasal openings are now halfway
up the snout; a first step towards the telescoped condition in modern whales. Their supposed amphibious
nature is supported by the discovery of a pregnant Maiacetus[11], in which the fossilised fetus was positioned
for a head-first delivery, suggesting that Maiacetus gave birth on land. The ungulate ancestry of these early
whales is still underlined by characteristics like the presence of hoofs at the ends of toes in Rodhocetus.
[edit] Basilosaurids and dorudontids: fully marine cetaceans

Reconstruction of Basilosaurus
Basilosaurus (discovered in 1840 and initially mistaken for a reptile, hence its name) and Dorudon
lived around 38 million years ago, and were fully recognizable whales which lived entirely in the ocean.
Basilosaurus was as big as the larger modern whales, up to 18 m (60 ft) long; dorudontids were smaller,
about 5 m (16 ft) long.
Reconstruction of Dorudon
Although they look very much like modern whales, basilosaurids and dorudontids lacked the 'melon
organ' that allows their descendants to use echolocation as effectively as modern whales. They had small
brains; this suggests they were solitary and did not have the complex social structure of some modern
cetaceans. Basilosaurus had two tiny but well-formed hind legs which were probably used as claspers when
mating; they are a small reminder of the lives of their ancestors. Interestingly, the pelvic bones associated
with these hind limbs was now no longer connected to the vertebral column as it was in protocetids.
Essentially, any sacral vertebrae can no longer be clearly distinguished from the other vertebrae.
[edit] Early echolocation
Reconstruction of Squalodon
Toothed whales (Odontocetes) echolocate by creating a series of clicks emitted at various
frequencies. Sound pulses are emitted through their melon-shaped foreheads, reflected off objects, and
retrieved through the lower jaw. Skulls of Squalodon show evidence for the first hypothesized appearance of
echolocation. Squalodon lived from the early to middle Oligocene to the middle Miocene, around 33-14
million years ago. Squalodon featured several commonalities with modern Odontocetes. The cranium was
well compressed, the rostrum telescoped outward (a characteristic of the modern suborder Odontoceti),
giving Squalodon an appearance similar to that of modern toothed whales. However, it is thought unlikely
that squalodontids are direct ancestors of living dolphins.
[edit] Early baleen whales
Reconstruction of Cetotherium
All modern mysticetes are large filter-feeding or baleen whales, though the exact means by which
baleen is used differs among species (gulp-feeding with balaenopterids, skim-feeding with balaenids, and
bottom ploughing with eschrichtiids). The first members of some modern groups appeared during the middle
Miocene. These changes may have been a result of worldwide environmental change and physical changes
in the oceans. A large scale change in ocean current and temperature could have initiated the radiation of
modern mysticetes, leading to the demise of the archaic forms. Generally it is speculated the four modern
mysticete families have separate origins among the cetotheres. Modern baleen whales, Balaenopteridae
(rorquals and humpback whale, Megaptera novaengliae), Balaenidae (right whales), Eschrichtiidae (gray
whale, Eschrictius robustus), and Neobalaenidae (pygmy right whale, Caperea marginata) all have derived
characteristics presently unknown in any cetothere.
[edit] Early dolphins
Skeleton of Xiphiacetus sp.

During the early Miocene (about 20 Ma), echolocation developed in its modern form. Various extinct
dolphin-like families flourished. Early dolphins include Kentriodon and Hadrodelphis. These belong to
Kentriodontidae, which were small to medium-sized toothed cetaceans with largely symmetrical skulls, and
thought likely to include ancestors of some modern species. Kentriodontids date to the late Oligocene to late
Miocene. Kentriodontines ate small fish and other nectonic organisms; they are thought to have been active
echolocators, and might have formed schools. Diversity, morphology and distribution of fossils appear
parallel to some modern species.
[edit] Skeletal evolution
Today, the whale hind parts are internal and reduced. Occasionally, the genes that code for longer
extremities cause a modern whale to develop miniature legs (known as atavism).
Whereas early cetaceans such as the Pakicetus had the nasal openings at the end of the snout, in
later species such as the Rodhocetus, the openings had begun to drift toward the top of the skull. This is
known as nasal drift.
The nostrils of modern whales have become modified into blowholes that allow them to break to the
surface, inhale, and submerge with convenience. The ears began to move inward as well, and, in the case of
Basilosaurus, the middle ears began to receive vibrations from the lower jaw. Today's modern toothed
whales use the 'melon organ', a pad of fat, for echolocation.
[edit] See also

Cetaceans portal
• Dolphin, Evolution and anatomy

• Archaeoceti
• Aquatic adaptation
• Indohyus
• Transitional form
• Evolution of sirenians
• Evolution of mammals
• List of extinct cetaceans
[edit] References
1. ^ University Of California, Berkeley (2005, February 7). "UC Berkeley, French Scientists Find
Missing Link Between The Whale And Its Closest Relative, The Hippo". ScienceDaily.
2. ^ Philip D. Gingerich, D. E. Russell (1981). "Pakicetus inachus, a new archaeocete
(Mammalia, Cetacea) from the early-middle Eocene Kuldana Formation of Kohat (Pakistan)". Univ.
Mich. Contr. Mus. Paleont 25: 235–246.
3. ^ a b Northeastern Ohio Universities Colleges of Medicine and Pharmacy (2007, December
21). "Whales Descended From Tiny Deer-like Ancestors". ScienceDaily.
4. ^ J. G. M. Thewissen, E. M. Williams, L. J. Roe and S. T. Hussain (2001). "Skeletons of
terrestrial cetaceans and the relationship of whales to artiodactyls". Nature 413 (6853): 277–281.
doi:10.1038/35095005. PMID 11565023.
5. ^ Whale Origins
6. ^ University Of Michigan (2001, September 20). "New Fossils Suggest Whales And Hippos
Are Close Kin". ScienceDaily. http://www.sciencedaily.com/releases/2001/09/010920072245.htm.
7. ^ University Of California, Berkeley (2005, February 7). "UC Berkeley, French Scientists Find
Missing Link Between The Whale And Its Closest Relative, The Hippo". ScienceDaily.
8. ^ Carl Zimmer (2007-12-19). "The Loom : Whales: From So Humble A Beginning..." .
ScienceBlogs. http://scienceblogs.com/loom/2007/12/19/whales_from_so_humble_a_beginn.php.
9. ^ Ian Sample (2007-12-19). "Whales may be descended from a small deer-like animal".
Guardian Unlimited. http://www.guardian.co.uk/science/2007/dec/19/whale.deer?
gusrc=rss&feed=networkfront. Retrieved 2007-12-21.
10.^ PZ Myers (2007-12-19). "Pharyngula: Indohyus". Pharyngula. ScienceBlogs.
http://scienceblogs.com/pharyngula/2007/12/indohyus.php. Retrieved 2007-12-21.
11.^ Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, et al.. "New
Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and
Sexual Dimorphism". PLoS one. http://www.plosone.org/article/info%3Adoi
%2F10.1371%2Fjournal.pone.0004366. Retrieved 2009-02-04.

For a review of whale evolution, see Uhen, M. D. (2010). "The Origin(s) of Whales". Annual Review
of Earth and Planetary Sciences 38: 189–219. doi:10.1146/annurev-earth-040809-152453. edit
• Timeline of Whale Evolution - Smithsonian Ocean Portal
• Cetacean Paleobiology - University of Bristol
• BBC: Whale's evolution
• BBC: Whale Evolution - The Fossil Evidence
• Hooking Leviathan by Its Past by Stephen Jay Gould
• Whale Origins, Thewissen Lab, Northeastern Ohio Universities College of Medicine
• Digital Library of Dolphin Development , Thewissen Lab
• Research on the Origin and Early Evolution of Whales (Cetacea) , Gingerich, P.D., University
of Michigan
• Evolution of Whales Adapted from National Geographic, November 2001, Revised 2006 Dr.
J.G.M. Thewissen
• Pakicetus inachus, a new archaeocete (Mammalia, Cetacea) from the early-middle Eocene
Kuldana Formation of Kohat (Pakistan). Gingerich, P.D., 1981, Museum of Paleontology, The
University of Michigan
• Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls , Nature 413,
277-281 (20 September 2001), J. G. M. Thewissen, E. M. Williams, L. J. Roe and S. T. Hussain
• Evolution of Whales segment from the Whales Tohorā Exhibition Minisite of the Museum of
New Zealand Te Papa Tongarewa
Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of


Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_cetaceans"
Categories: Cetaceans | Evolution by taxon

W000
Evolution of the eye


Major stages in the evolution of the eye.
The evolution of the eye has been a subject of significant study, as a distinctive example of a
homologous organ present in a wide variety of taxa. Certain components of the eye, such as the visual
pigments, appear to have a common ancestry – that is, they evolved once, before the animals radiated.
However, complex, image-forming eyes evolved some 50 to 100 times[1] – using many of the same proteins
and genetic toolkits in their construction.[2][3]
Complex eyes appear to have first evolved within a few million years, in the rapid burst of evolution
known as the Cambrian explosion. There is no evidence of eyes before the Cambrian, but a wide range of
diversity is evident in the Middle Cambrian Burgess shale.
Eyes show a wide range of adaptations to meet the requirements of the organisms which bear them.
Eyes may vary in their acuity, the range of wavelengths they can detect, their sensitivity in low light levels,
their ability to detect motion or resolve objects, and whether they can discriminate colours.
Contents
[hide]
• 1 History of research
• 2 Rate of evolution
• 3 One origin or many?
• 4 Stages of eye evolution
• 4.1 Early eyes
• 4.2 Lens formation and diversification
• 4.3 Other developments
• 5 Evolutionary baggage
• 6 Footnotes
• 7 References
[edit] History of research
The human eye, demonstrating the iris.

Since 1802, the evolution of a structure as complex as the projecting eye by natural selection has
been said to be difficult to explain.[4] Charles Darwin himself wrote, in his Origin of Species, that the
evolution of the eye by natural selection at first glance seemed "absurd in the highest possible degree".
However, he went on to explain that despite the difficulty in imagining it, it was perfectly feasible:
...if numerous gradations from a perfect and complex eye to one very imperfect and simple,
each grade being useful to its possessor, can be shown to exist; if further, the eye does vary
ever so slightly, and the variations be inherited, which is certainly the case; and if any variation
or modification in the organ be ever useful to an animal under changing conditions of life, then
the difficulty of believing that a perfect and complex eye could be formed by natural selection,
though insuperable by our imagination, can hardly be considered real.[5]
He suggested a gradation from "an optic nerve merely coated with pigment, and without any other
mechanism" to "a moderately high stage of perfection", giving examples of extant intermediate grades of
evolution.[5]
Darwin's suggestions were soon shown to be correct, and current research is investigating the
genetic mechanisms responsible for eye development and evolution.[6]
[edit] Rate of evolution

The first fossils of eyes appeared during the lower Cambrian period (about 540 million years ago).[7]
This period saw a burst of apparently rapid evolution, dubbed the "Cambrian explosion". One of the many
hypotheses for "causes" of this diversification, the "Light Switch" theory of Andrew Parker holds that the
evolution of eyes initiated an arms race that led to a rapid spate of evolution.[8] Earlier than this, organisms
may have had use for light sensitivity, but not for fast locomotion and navigation by vision.
Since the fossil record, particularly of the Early Cambrian, is so poor, it is difficult to estimate the rate
of eye evolution. Simple modelling, invoking small mutations exposed to natural selection, demonstrates that
a primitive optical sense organ based upon efficient photopigments could evolve into a complex human-like
eye in approximately 400,000 years.[9][note 1]
[edit] One origin or many?
Whether one considers the eye to have evolved once or multiple times depends somewhat on the
definition of an eye. Much of the genetic machinery employed in eye development is common to all eyed
organisms, which may suggest that their ancestor utilized some form of light-sensitive machinery – even if it
lacked a dedicated optical organ. However, even photoreceptor cells may have evolved more than once from
molecularly similar chemoreceptors, and photosensitive cells probably existed long before the Cambrian
explosion.[10] Higher-level similarities – such as the use of the protein crystalin in the independently derived
cephalopod and vertebrate lenses[11] – reflect the co-option of a protein from a more fundamental role to a
new function within the eye.[12]
Shared traits common to all light-sensitive organs include the family of photo-receptive proteins
called opsins. All seven sub-families of opsin were already present in the last common ancestor of animals.
In addition, the genetic toolkit for positioning eyes is common to all animals: the PAX6 gene controls where
the eye develops in organisms ranging from mice to humans to fruit flies.[13][14][15] These high-level genes
are, by implication, much older than many of the structures that they are today seen to control; they must
originally have served a different purpose, before being co-opted for a new role in eye development.[12]
Sensory organs probably evolved before the brain did—there is no need for an information-processing
organ (brain) before there is information to process.[16]
[edit] Stages of eye evolution
The stigma (2) of the euglena hides a light-sensitive spot.

The earliest predecessors of the eye were photoreceptor proteins that sense light, found even in
unicellular organisms, called "eyespots". Eyespots can only sense ambient brightness: they can distinguish
light from dark, sufficient for photoperiodism and daily synchronization of circadian rhythms. They are
insufficient for vision, as they cannot distinguish shapes or determine the direction light is coming from.
Eyespots are found in nearly all major animal groups, and are common among unicellular organisms,
including euglena. The euglena's eyespot, called a stigma, is located at its anterior end. It is a small splotch
of red pigment which shades a collection of light sensitive crystals. Together with the leading flagellum, the
eyespot allows the organism to move in response to light, often toward the light to assist in photosynthesis,
[17] and to predict day and night, the primary function of circadian rhythms. Visual pigments are located in
the brains of more complex organisms, and are thought to have a role in synchronising spawning with lunar
cycles. By detecting the subtle changes in night-time illumination, organisms could synchronise the release
of sperm and eggs to maximise the probability of fertilisation.
Vision itself relies on a basic biochemistry which is common to all eyes. However, how this
biochemical toolkit is used to interpret an organism's environment varies widely: eyes have a wide range of
structures and forms, all of which have evolved quite late relative to the underlying proteins and molecules.
[17]
At a cellular level, there appear to be two main "designs" of eyes, one possessed by the protostomes
(molluscs, annelid worms and arthropods), the other by the deuterostomes (chordates and echinoderms).[17]
The functional unit of the eye is the receptor cell, which contains the opsin proteins and responds to
light by initiating a nerve impulse. The light sensitive opsins are borne on a hairy layer, to maximise the
surface area. The nature of these "hairs" differs, with two basic forms underlying photoreceptor structure:
microvilli and cilia.[18] In the protostomes, they are microvilli: extensions or protrusions of the cellular
membrane. But in the deuterostomes, they are derived from cilia, which are separate structures.[17] This
now looks like something of a simplification, as some microvilli contain traces of cilia – but other observations
appear to support a fundamental difference between protostomes and deuterostomes.[17] These
considerations centre on the response of the cells to light – some use sodium to cause the electric signal that
will form a nerve impulse, and others use potassium; further, protostomes on the whole construct a signal by
allowing more sodium to pass through their cell walls, whereas deuterostomes allow less through.[17]
This suggests that when the two lineages diverged in the Precambrian, they had only very primitive
light receptors, which developed into more complex eyes independently.
[edit] Early eyes
The basic light-processing unit of eyes is the photoreceptor cell, a specialized cell consisting of two
molecules in a membrane: the opsin, a light-sensitive protein, surrounding the chromophore, a pigment that
distinguishes colors. Groups of such cells are termed "eyespots", and have evolved independently
somewhere between 40 and 65 times. These eyespots permit animals to gain only a very basic sense of the
direction and intensity of light – enough to know when they are safely in a cave, for example, but not enough
to discriminate an object from its surroundings.[17]
Developing an optical system that can discriminate the direction of light to within a few degrees is
apparently much more difficult, and only six of the thirty-something phyla[note 2] possess such a system.
However, these phyla account for 96% of living species.[17]
The planarian has "cup" eyespots that can slightly distinguish light direction.
These complex optical systems started out as the multicellular eyepatch gradually depressed into a
cup, which first granted the ability to discriminate brightness in directions, then in finer and finer directions as
the pit deepened. While flat eyepatches were ineffective at determining the direction of light, as a beam of
light would activate exactly the same patch of photo-sensitive cells regardless of its direction, the "cup" shape
of the pit eyes allowed limited directional differentiation by changing which cells the lights would hit
depending upon the light's angle. Pit eyes, which had arisen by the Cambrian period, were seen in ancient
snails,[clarification needed] and are found in some snails and other invertebrates living today, such as
planaria. Planaria can slightly differentiate the direction and intensity of light because of their cup-shaped,
heavily-pigmented retina cells, which shield the light-sensitive cells from exposure in all directions except for
the single opening for the light. However, this proto-eye is still much more useful for detecting the absence or
presence of light than its direction; this gradually changes as the eye's pit deepens and the number of
photoreceptive cells grows, allowing for increasingly precise visual information.[19]
When a photon is absorbed by the chromophore, a chemical reaction causes the photon's energy to
be transduced into electrical energy and relayed, in higher animals, to the nervous system. These
photoreceptor cells form part of the retina, a thin layer of cells that relays visual information,[20] as well as
the light and daylength information needed by the circadian rhythm system, to the brain. However, some
jellyfish, such as Cladonema, have elaborate eyes but no brain. Their eyes transmit a message directly to the
muscles without the intermediate processing provided by a brain.[16]
During the Cambrian explosion, the development of the eye accelerated rapidly, with radical
improvements in image-processing and detection of light direction.[21]
The primitive nautilus eye functions similarly to a pinhole camera.
The "pinhole camera" eye was developed as the pit deepened into a cup, then a chamber. By
reducing the size of the opening, the organism achieved true imaging, allowing for fine directional sensing
and even some shape-sensing. Eyes of this nature are currently found in the nautilus. Lacking a cornea or
lens, they provide poor resolution and dim imaging, but are still, for the purpose of vision, a major
improvement over the early eyepatches.[22]
Overgrowths of transparent cells prevented contamination and parasitic infestation. The chamber
contents, now segregated, could slowly specialize into a transparent humour, for optimizations such as
colour filtering, higher refractive index, blocking of ultraviolet radiation, or the ability to operate in and out of
water. The layer may, in certain classes, be related to the moulting of the organism's shell or skin.
It is likely that a key reason eyes specialize in detecting a specific, narrow range of wavelengths on
the electromagnetic spectrum—the visible spectrum—is because the earliest species to develop
photosensitivity were aquatic, and only two specific wavelength ranges of electromagnetic radiation, blue and
green visible light, can travel through water. This same light-filtering property of water also influenced the
photosensitivity of plants.[23][24][25]
[edit] Lens formation and diversification
Light from a distant object and a near object being focused by changing the curvature of the lens.
Lenses evolved independently in a number of lineages. Simple 'pit-eyes' probably developed lenses
to improve the amount of light that reached the retina; the focal length of an early lobopod with lens-
containing simple eyes focussed the image behind the retina, so while no part of the image could be brought
into focus, the intensity of light allowed the organism to inhabit deeper (and therefore darker) waters.[26] A
subsequent increase of the lens's refractive index probably resulted in an in-focus image being formed.[26]
The development of the lens in camera-type eyes probably followed a different trajectory. The
transparent cells over a pinhole eye's aperture split into two layers, with liquid in between.[ citation needed]
The liquid originally served as a circulatory fluid for oxygen, nutrients, wastes, and immune functions,
allowing greater total thickness and higher mechanical protection. In addition, multiple interfaces between
solids and liquids increase optical power, allowing wider viewing angles and greater imaging resolution.
Again, the division of layers may have originated with the shedding of skin; intracellular fluid may infill
naturally depending on layer depth.[citation needed]
Note that this optical layout has not been found, nor is it expected to be found.[ citation
needed]Fossilization rarely preserves soft tissues, and even if it did, the new humour would almost certainly
close as the remains desiccated, or as sediment overburden forced the layers together, making the fossilized
eye resemble the previous layout.[citation needed]
Compound eye of Antarctic krill.

Vertebrate lenses are composed of adapted epithelial cells which have high concentrations of the
protein crystallin. In the embryo, the lens is living tissue, but the cellular machinery is not transparent so must
be removed before the organism can see. Removing the machinery means the lens is composed of dead
cells, packed with crystalins which must last the life of the organism. The refractive index gradient which
makes the lens useful is caused by the radial shift in crystallin concentration in different parts of the lens,
rather than by the specific type of protein: it is not the presence of crystallin, but the relative distribution of it,
that renders the lens useful.[27]
It is biologically difficult to maintain a transparent layer of cells. Deposition of transparent, nonliving,
material eased the need for nutrient supply and waste removal. Trilobites used calcite, a mineral which has
not been used by any other organism; in other compound eyes[ verification needed] and camera eyes, the
material is crystallin. A gap between tissue layers naturally forms a biconvex shape, which is optically and
mechanically ideal for substances of normal refractive index. A biconvex lens confers not only optical
resolution, but aperture and low-light ability, as resolution is now decoupled from hole size—which slowly
increases again, free from the circulatory constraints.
Independently, a transparent layer and a nontransparent layer may split forward from the lens: a
separate cornea and iris. (These may happen before or after crystal deposition, or not at all.) Separation of
the forward layer again forms a humour, the aqueous humour. This increases refractive power and again
eases circulatory problems. Formation of a nontransparent ring allows more blood vessels, more circulation,
and larger eye sizes. This flap around the perimeter of the lens also masks optical imperfections, which are
more common at lens edges. The need to mask lens imperfections gradually increases with lens curvature
and power, overall lens and eye size, and the resolution and aperture needs of the organism, driven by
hunting or survival requirements. This type is now functionally identical to the eye of most vertebrates,
including humans. Indeed, "the basic pattern of all vertebrate eyes is similar."[28]
[edit] Other developments

Color vision
The ability to see colors presents distinct selective advantages for species, such as being better able
to recognize predators, food and mates. Indeed, it is thought that simple sensory-neural mechanisms may
selectively control general behaviour patterns, such as escape, foraging, and hiding. Many examples of
wavelength-specific behaviour patterns have been identified, in two primary groups: less than 450 nm,
associated with natural light sources, and greater than 450 nm, associated with reflected light sources.[29]
As opsin molecules were subtly fine-tuned to detect different wavelengths of light, at some point color vision
developed when photoreceptor cells developed multiple pigments.[20] As a chemical adaption rather than a
mechanical one, this may have occurred at any of the early stages of the eye's evolution, and the capability
may have disappeared and reappeared as organisms became predator or prey. Similarly, night and day
vision emerged when receptors differentiated into rods and cones, respectively.
Further information: Evolution of color vision
Focusing mechanism
Some species move the lens back and forth, some stretch the lens flatter. Another mechanism
regulates focusing chemically and independently of these two, by controlling growth of the eye and
maintaining focal length. Note that a focusing method is not a requirement. As photographers know, focal
errors increase as aperture increases. Thus, countless organisms with small eyes are active in direct sunlight
and survive with no focus mechanism at all. As a species grows larger, or transitions to dimmer
environments, a means of focusing need only appear gradually.
Location
Prey generally have eyes on the sides of their head so to have a larger field of view, from which to
avoid predators. Predators, however, have eyes in front of their head in order to have better depth
perception.[30][31] Flatfish are predators which lie on their side on the bottom, and have eyes placed
asymmetrically on the same side of the head. A transitional fossil from the common symmetric position is
Amphistium.
[edit] Evolutionary
baggage
Main article: Evolutionary
baggage
The eyes of many taxa record
their evolutionary history in their
imperfect design. The vertebrate eye,
for instance, is built "backwards and
upside down", requiring "photons of
light to travel through the cornea, lens,
aqueous fluid, blood vessels, ganglion
cells, amacrine cells, horizontal cells,
and bipolar cells before they reach the
light-sensitive rods and cones that
transduce the light signal into neural
impulses – which are then sent to the
visual cortex at the back of the brain
for processing into meaningful
patterns."[32] This reduction in
efficiency may be countered by the Vertebrates and octopuses developed the camera eye
independently. In the vertebrate version the nerve fibers pass in
front of the retina, and there is a blind spot where the nerves pass
through the retina. In the vertebrate example, 4 represents the blind
spot, which is notably absent from the octopus eye. In vertebrates, 1
represents the retina and 2 is the nerve fibers, including the optic
nerve (3), whereas in the octopus eye, 1 and 2 represent the nerve
fibers and retina respectively.
formation of a reflective layer, the tapetum, behind the retina. Light which is not absorbed by the retina on the
first pass may bounce back and be detected.
The camera eyes of cephalopods, in contrast, are constructed the "right way out", with the nerves
attached to the rear of the retina. This means that they do not have a blind spot. This difference may be
accounted for by the origins of eyes; in cephalopods they develop as an invagination of the head surface
whereas in vertebrates they originate as an extension of the brain.
[edit] Footnotes
1. ^ David Berlinski, an intelligent design proponent, questioned the basis of the calculations,
and the author of the original paper refuted Berlinski's criticism.
• Berlinski, David (April 2001). Commentary magazine.
• Nilsson, Dan-E.. Beware of Pseudo-science: a response to David Berlinski's attack
on my calculation of how long it takes for an eye to evolve .
http://www.talkreason.org/articles/blurred.cfm#lund.
• "Evolution of the Eye" on PBS
2. ^ The precise number varies from author to author.
[edit] References
1. ^ Haszprunar (1995). "The mollusca: Coelomate turbellarians or mesenchymate annelids?".
In Taylor. Origin and evolutionary radiation of the Mollusca : centenary symposium of the
Malacological Society of London. Oxford: Oxford Univ. Press. ISBN 0-19-854980-6.
2. ^ Kozmik, Z; Daube, Michael; Frei, Erich; Norman, Barbara; Kos, Lidia; Dishaw, Larry J.;
Noll, Markus; Piatigorsky, Joram (2003). "Role of Pax Genes in Eye Evolution A Cnidarian PaxB
Gene Uniting Pax2 and Pax6 Functions". Developmental Cell 5: 773–785. doi:10.1016/S1534-
5807(03)00325-3.
3. ^ Land, M.F. and Nilsson, D.-E., Animal Eyes, Oxford University Press, Oxford (2002).
4. ^ In 1802, William Paley claimed that the eye was a miracle of design.
5. ^ a b Darwin, Charles (1859). On the Origin of Species. London: John Murray.
6. ^ Gehring WJ (2005). "New perspectives on eye development and the evolution of eyes and
photoreceptors". J. Hered. 96 (3): 171–84. doi:10.1093/jhered/esi027. PMID 15653558.
7. ^ Parker, A. R. (2009). "On the origin of optics". Optics & Laser Technology 43: 323.
doi:10.1016/j.optlastec.2008.12.020. edit
8. ^ Parker, Andrew (2003). In the Blink of an Eye: How Vision Sparked the Big Bang of
Evolution. Cambridge, MA: Perseus Pub.. ISBN 0738206075.
9. ^ Nilsson, D-E; Pelger S (1994). "A pessimistic estimate of the time required for an eye to
evolve". Proc R Soc Lond B 256 (1345): 53–58. doi:10.1098/rspb.1994.0048. PMID 8008757.
10.^ Nilsson, DE (1996). "Eye ancestry: old genes for new eyes". Current biology : CB 6 (1): 39–
42. doi:10.1016/S0960-9822(02)00417-7. PMID 8805210. edit
11.^ Zinovieva, R. (1999). "O-Crystallin, arginine kinase and ferritin from the octopus lens".
Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1431: 512–517.
doi:10.1016/S0167-4838(99)00066-7. edit
12.^ a b Scotland, R. W. (2010). "Deep homology: A view from systematics". BioEssays : news
and reviews in molecular, cellular and developmental biology 32 (5): NA–ME.
doi:10.1002/bies.200900175. PMID 20394064. edit
13.^ Halder, G; Callaerts, P; Gehring, WJ (1995). "New perspectives on eye evolution". Current
opinion in genetics & development 5 (5): 602–9. doi:10.1016/0959-437X(95)80029-8.
PMID 8664548. edit
14.^ Halder, G.; Callaerts, P.; Gehring, W. (1995). "Induction of ectopic eyes by targeted
expression of the eyeless gene in Drosophila". Science 267 (5205): 1788.
doi:10.1126/science.7892602. PMID 7892602. edit
15.^ Tomarev, SI; Callaerts, P; Kos, L; Zinovieva, R; Halder, G; Gehring, W; Piatigorsky, J
(1997). "Squid Pax-6 and eye development". Proceedings of the National Academy of Sciences of
the United States of America 94 (6): 2421–6. doi:10.1073/pnas.94.6.2421. PMID 9122210. edit
16.^ a b Gehring, W. J. (13 January 2005). "New Perspectives on Eye Development and the
Evolution of Eyes and Photoreceptors" (Full text). Journal of Heredity (Oxford Journals) 96 (3): 171–
184. doi:10.1093/jhered/esi027. PMID 15653558.
http://jhered.oxfordjournals.org/cgi/content/full/96/3/171. Retrieved 2008-04-26.
17.^ a b c d e f g h M F Land; R D Fernald (1992). "The Evolution of Eyes". Annual Review of
Neuroscience 15: 1–29. doi:10.1146/annurev.ne.15.030192.000245. PMID 1575438.
18.^ Autrum, H (1979). "Introduction". In H. Autrum (editor). Comparative Physiology and
Evolution of Vision in Invertebrates- A: Invertebrate Photoreceptors . Handbook of Sensory
Physiology. VII/6A. New York: Springer-Verlag. pp. 6–9. ISBN 3540088377
19.^ Eye-Evolution?
20.^ a b Fernald, Russell D. (2001). The Evolution of Eyes: How Do Eyes Capture Photons?
Karger Gazette 64: "The Eye in Focus".
21.^ Conway-Morris, S. (1998). The Crucible of Creation. Oxford: Oxford University Press.
22.^ Dawkins, Richard (1986). The Blind Watchmaker.
23.^ Fernald, Russell D. (2001). The Evolution of Eyes: Why Do We See What We See? Karger
Gazette 64: "The Eye in Focus".
24.^ Fernald, Russell D. (1998). Aquatic Adaptations in Fish Eyes. New York, Springer.
25.^ Fernald RD (1997). "The evolution of eyes". Brain Behav. Evol. 50 (4): 253–9.
doi:10.1159/000113339. PMID 9310200.
26.^ a b Schoenemann, B.; Liu, J. N.; Shu, D. G.; Han, J.; Zhang, Z. F. (2008). "A miniscule
optimized visual system in the Lower Cambrian". Lethaia 42: 265. doi:10.1111/j.1502-
3931.2008.00138.x. edit
27.^ Fernald, Russell D. (2001). The Evolution of Eyes: Where Do Lenses Come From? Karger
Gazette 64: "The Eye in Focus".
28.^ Ali, Mohamed Ather; Klyne, M.A. (1985). Vision in Vertebrates. New York: Plenum Press.
p. 1. ISBN 0-306-42065-1.
29.^ Menzel, Randolf (1979). "Spectral Sensitivity and Color Vision in Invertebrates". In H.
Autrum (editor). Comparative Physiology and Evolution of Vision in Invertebrates- A: Invertebrate
Photoreceptors. Handbook of Sensory Physiology. VII/6A. New York: Springer-Verlag. pp. 504–506;
551–558. ISBN 3540088377
30.^ http://www.blm.gov/id/st/en/prog/wildlife/carnivores.html
31.^ Boroditsky, Lera (6/24/99). "Light & Eyes: Lecture Notes". Lecture Notes. Stanford.
http://www-psych.stanford.edu/~lera/psych115s/notes/lecture2/. Retrieved 11 May 2010.
32.^ Dr. Michael Shermer, as quoted by Christopher Hitchens in his book "God is Not Great"
(pg.82)

• "Evolution of the Eye". WGBH Educational Foundation and Clear Blue Sky Productions .
PBS. 2001. http://www.pbs.org/wgbh/evolution/library/01/1/l_011_01.html.
• Creationism Disproved? Video from the National Center for Science Education on the
evolution of the eye
• Evolution: Education and Outreach Special Issue: Evolution and Eyes volume 1, number 4,
October 2008, pages 351-559. ISSN 1936-6426 (Print) 1936-6434 (Online)
• Myers, PZ (2007-12-21). "Evolution of vertebrate eyes". Pharyngula. ScienceBlogs.
http://scienceblogs.com/pharyngula/2007/12/evolution_of_vertebrate_eyes.php. Retrieved 2007-12-
23. "a review of Lamb TD, Collin SP, Pugh EN Jr. (2007) Evolution of the vertebrate eye: opsins,
photoreceptors, retina and eye cup. Nat Rev Neurosci 8(12):960-76."

• Lamb TD, Collin SP, Pugh EN (December 2007). "Evolution of the vertebrate eye: opsins,
photoreceptors, retina and eye cup". Nat. Rev. Neurosci. 8 (12): 960–76. doi:10.1038/nrn2283.
PMID 18026166. illustration
• Land, M. F., & Nilsson, D-E, Animal Eyes, Oxford: Oxford University Press, 2002 ISBN 0-19-
8509685 "The origin of vision", Chapter 1, pages 1–15
• Journal Evolution: Education and Outreach Volume 1, Number 4 / October 2008. Special
Issue: The Evolution of Eyes. 26 articles, free access.
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Evolution of human intelligence

Human intelligence
Measuring and varieties

Intelligence quotient
General intelligence factor
Fluid and crystallized intelligence
Cattell-Horn-Carroll theory
Triarchic theory of intelligence
Theory of multiple intelligences
Emotional intelligence
Factors associated with intelligence
Environment and intelligence
Evolution of human intelligence
Fertility and intelligence
Flynn effect
Health and intelligence
Height and intelligence
Heritability of IQ
Longevity and intelligence
Nations and intelligence
Neuroscience and intelligence
Religiosity and intelligence
Sex and intelligence
Related
Creativity · High IQ society
Genius · Giftedness · Dysrationalia
v·d·e
The evolution of human intelligence refers to a set of theories that attempt to explain how human
intelligence has evolved. The question is closely tied to the evolution of the human brain, and to the
emergence of human language.
The timeline of human evolution spans some 7 million years, from the separation of the Pan genus
until the emergence of behavioral modernity by 50,000 years ago. Of this timeline, the first 3 million years
concern Sahelanthropus, the following 2 million concern Australopithecus, while the final 2 million span the
history of actual human species (the Paleolithic).
Many traits of human intelligence, such as empathy, theory of mind, mourning, ritual, and the use of
symbols and tools, are already apparent in great apes although in lesser sophistication than in humans.
Contents
[hide]
• 1 History
• 1.1 Hominidae
• 1.2 Hominina
• 1.3 Homo
• 1.4 Homo sapiens
• 2 Models
• 2.1 Social brain hypothesis
• 2.2 Sexual selection
• 2.3 Ecological dominance-social competition model
• 2.4 Intelligence as a resistance signal
• 2.5 Group Selection and Evolvability
• 2.6 Nutritional Status
• 2.7 Flexible problem solving
• 3 See also
• 4 Notes
[edit] History
[edit] Hominidae
Chimpanzee mother and baby
Further information: Primate empathy, Great ape language, and Chimpanzee intelligence
The great apes show considerable abilities for cognition and empathy.
Chimpanzees make tools and use them to acquire foods and for social displays; they have
sophisticated hunting strategies requiring cooperation, influence and rank; they are status conscious,
manipulative and capable of deception; they can learn to use symbols and understand aspects of human
language including some relational syntax, concepts of number and numerical sequence.[1]
In one study, young chimpanzees outperformed human college students in tasks requiring
remembering numbers.[2] Chimpanzees are capable of empathy, having been observed to feed turtles in the
wild, and show curiosity in wildlife (such as pythons).
[edit] Hominina
Around 10 million years ago, the Earth's climate entered a cooler and drier phase, which led
eventually to the ice ages beginning some 2.6 million years ago. One consequence of this was that the north
African tropical forest began to retreat, being replaced first by open grasslands and eventually by desert (the
modern Sahara). This forced tree-dwelling animals to adapt to their new environment or die out. As their
environment changed from continuous forest to patches of forest separated by expanses of grassland, some
primates adapted to a partly or fully ground-dwelling life. Here they were exposed to predators, such as the
big cats, from whom they had previously been safe.
Some Hominina (Australopithecines) adapted to this challenge by adopting bipedalism: walking on
their hind legs. This gave their eyes greater elevation and the ability to see approaching danger further
off[citation needed]. It also freed the forelimbs (arms) from the task of walking and made the hands available
for tasks such as gathering food. At some point the bipedal primates developed handedness, giving them the
ability to pick up sticks, bones and stones and use them as weapons, or as tools for tasks such as killing
smaller animals, cracking nuts, or cutting up carcasses. In other words, these primates developed the use of
technology. Bipedal tool-using primates form the Hominina subtribe, of which the earliest species, such as
Sahelanthropus tchadensis, date to about 7 to 5 million years ago.
From about 5 million years ago, the Hominin brain began to develop rapidly in both size and
differentiation of function.
[edit] Homo
Further information: Homo (genus)
By 2.4 million years ago Homo habilis had appeared in East Africa: the first known human species,
and the first known to make stone tools.
The use of tools conferred a crucial evolutionary advantage, and required a larger and more
sophisticated brain to co-ordinate the fine hand movements required for this task. The evolution of a larger
brain created a problem for early humans, however. A larger brain requires a larger skull, and thus requires
the female to have a wider birth canal for the newborn's larger skull to pass through. But if the female's birth
canal grew too wide, her pelvis would be so wide that she would lose the ability to run: still a necessary skill
in the dangerous world of 2 million years ago.
The solution to this was to give birth at an early stage of fetal development, before the skull grew too
large to pass through the birth canal. This adaptation enabled the human brain to continue to grow, but it
imposed a new discipline. The need to care for helpless infants for long periods of time forced humans to
become less mobile. Human bands increasingly stayed in one place for long periods, so that females could
care for infants, while males hunted food and fought with other bands that competed for food sources. As a
result, humans became even more dependent on tool-making to compete with other animals and each other,
and relied less on size and strength.
About 200,000 years ago Europe and the Near East were colonized by Neanderthal man, extinct by
20,000 following the appearance of modern humans in the region from 40,000 years ago.
[edit] Homo sapiens

Further information: Intelligence and Archaic Homo sapiens
Further information: Behavioral modernity and Race and intelligence
Middle Stone Age bifacial points, engraved ochre and bone tools from the c. 75,000 year old M1 &
M2 phases at Blombos cave.
"The Lion Man," found in the Hohlenstein-Stadel cave of Germany's Swabian Alb and dated to
32,000 years ago, is associated with the Aurignacian culture and is the oldest known anthropomorphic
animal figurine in the world.
Between 170,000 to 120,000 years ago Homo sapiens first appears in East Africa. It is unclear to
what extent these early modern humans had developed language, music, religion etc.
They spread throughout Africa over the following 50,000 years or so: around 100-80,000 years ago,
three main lines of Homo sapiens diverged, bearers of mitochondrial haplogroup L1 (mtDNA) / A (Y-DNA)
colonizing Southern Africa (the ancestors of the Khoisan/Capoid peoples), bearers of haplogroup L2
(mtDNA) / B (Y-DNA) settling Central and West Africa (the ancestors of Niger-Congo and Nilo-Saharan
speaking peoples), while the bearers of haplogroup L3 remained in East Africa.
The "Great Leap Forward" leading to full behavioral modernity sets in only after this separation.
Rapidly increasing sophistication in tool-making and behaviour is apparent from about 80,000 years ago, and
the migration out of Africa follows towards the very end of the Middle Paleolithic, some 60,000 years ago.
Fully modern behaviour, including figurative art, music, self-ornamentation, trade, burial rites etc. is evident
by 30,000 years ago. The oldest unequivocal examples of prehistoric art date to this period, the Aurignacian
and the Gravettian periods of prehistoric Europe, such the Venus figurines and cave painting (Chauvet Cave)
and the earliest musical instruments (the bone pipe of Geissenklösterle, Germany, dated to about 36,000
years ago).[3]
[edit] Models
[edit] Social brain hypothesis
The model was proposed by Robin Dunbar, who argues that human intelligence did not evolve
primarily as a means to solve ecological problems, but rather intelligence evolved as a means of surviving in
large and complex social groups. Some of the behaviors associated with living in large groups include
reciprocal altruism, deception and coalition formation. These group dynamics relate to Theory of Mind or the
ability to understand the thoughts and emotions of others, though Dunbar himself admits in the same book
that it is not the flocking itself that causes intelligence to evolve (as shown by ruminants).[4]
Dunbar argues that when the size of a social group increases, the number of different relationships in
the group may increase by orders of magnitude. Chimpanzees live in groups of about 50 individuals whereas
humans typically have a social circle of about 150 people, which is now referred to as Dunbar's number.
According to the social brain hypothesis, when hominids started living in large groups, selection favored
greater intelligence. As evidence, Dunbar cites a relationship between neocortex size and group size of
various mammals.[4] Howewer, meerkats have far more social relationships than their small brain capacity
would suggest.[5] Another hypothesis is that it is actually intelligence that causes social relationships to
become more complex, because intelligent individuals are more difficult to learn to know.[6]
[edit] Sexual selection

See also: sexual selection in human evolution
This model is proposed by Geoffrey Miller who argues that human intelligence is unnecessarily
sophisticated for the needs of hunter gatherers to survive. He argues that the manifestations of intelligence
such as language, music and art are of no utilitarian value to the survival of ancient hominids. Rather,
intelligence may have been a fitness indicator. Hominids would have selected for intelligence as a proxy for
healthy genes and a positive feedback loop leading runaway sexual selection would have led to the evolution
of human intelligence in a relatively short period.[7]
[edit] Ecological dominance-social competition model

A predominant model describing human intelligence's evolution is ecological dominance-social
competition (EDSC) [8] explained by Mark V. Flinn, David C. Geary and Carol V. Ward based mainly on work
by Richard D. Alexander. According to the model, human intelligence was able to evolve to significant levels
due to human domination over its habitat. As a result its primary competition shifted from nature to members
or groups of its own species.
Only then humans were "free" to develop more advanced social skills such as communication of
concepts through complex language patterns. Since competition had shifted from 'nature' to their own
species, it became of relevance to outmaneuver other members of the group seeking leadership or
acceptance, by means of more advanced social skills. A more social and communicative person would be
more easily naturally selected.
Howewer, modern archaeological research shows that transitional early humans with gradually
evolving brains (such as Homo erectus) were not ecologically dominant (indeed, big cats ate them), and they
were cooperative rather than competetive, as shown by their care for their sick and disabled, eg. the Dmanisi
jaw from Georgia.[9]
[edit] Intelligence as a resistance signal
Human intelligence developed to an extreme level that is not necessarily adaptive in an evolutionary
sense. Firstly, larger-headed babies are more difficult to give birth and large brains are costly in terms of
nutrient and oxygen requirements.[10] Thus the direct adaptive benefit of human intelligence is questionable
at least in modern societies, while it is difficult to study in prehistoric societies. However, alleles coding for
even larger human brains are spreading continuously even in modern societies [11][12] This suggests that
cleverer humans may gain indirect selective benefits.
A recent study [13] argues that human cleverness is simply selected within the context of sexual
selection as an honest signal of genetic resistance against parasites and pathogens. The number of people
living with cognitive abilities seriously damaged by childhood infections is high; estimated in hundreds of
millions. Even more people live with moderate mental damages, that are not classified as ‘diseases’ by
medical standards, who may still be considered as inferior mates by potential sexual partners. Pathogens
currently playing a major role in this global challenge against human cognitive capabilities include viral
infections like meningitis, protists like Toxoplasma and Plasmodium, and animal parasites like intestinal
worms and Schistosomes.[14]
Thus, widespread, virulent, and archaic infections are greatly involved. Given this situation, our
sexual preferences for clever partners increase the chance that our descendants will inherit the best
resistance alleles. Like some people search for mates based on their (perceived) bodily beauty, height, or
social position (e.g. wealth or fame), or psychological traits such as benevolence or confidence; people are
just searching for signals of good resistance genes. Intelligence appears to be one of these signals.
[edit] Group Selection and Evolvability
Group selection theory contends that organism characteristics that provide benefits to a group (clan,
tribe, or larger population) can evolve despite individual disadvantages such as those cited above. The group
benefits of intelligence (including language, the ability to communicate between individuals, the ability to
teach others, and other cooperative aspects) have apparent utility in increasing the survival potential of a
group.
Intelligence is one of a class of inherited characteristics that depend for their utility on the acquisition
of something (in this case, experience or information concerning the outside world) that can be retained
indefinitely by an individual but not genetically transmitted to descendents. The ability of an organism to
acquire such information and then non-genetically transmit it to descendents that could then benefit from the
experience of their parent without having to acquire the experience themselves appears to be a major group
advantage and essentially multiplies the intelligence of an individual by allowing progressive group
accumulation of experience.
Evolvability, another proposed modification to classical evolution theory suggests a connection
between a purposely limited organism life span and the evolution of intelligence. The suggestion is[15] that
without a limited life span, the acquired characteristic (experience) would tend to override the inherited
characteristic (intelligence). An older and more experienced animal would tend to have an advantage over a
younger more intelligent but less experienced animal thus interfering with the evolution of intelligence. This
factor is ameliorated by an organism design that limits life span. See Evolution of ageing.
[edit] Nutritional Status

Higher cognitive functioning develops better in an environment with adequate nutrition,[16] and diets
deficient in iron, zinc, protein, iodine, B vitamins, omega 3 fatty acids, magnesium and other nutrients can
result in lower intelligence[17][18] either in the mother during pregnancy or in the child during development.
While these inputs did not have an effect on the evolution of intelligence they do govern its expression. A
higher IQ could be a signal that an individual comes from and lives in a physical and social environment
where nutrition levels are high, whereas a lower IQ could imply a child (and/or the child's mother) comes from
a physical and social environment where nutritional levels are low.
[edit] Flexible problem solving

The statement that such high intelligence "lack survival value", which is used by believers in social
intelligence and sexual selection, invariably assumes a stable environment. If climate change is factored in,
howewer, the evolution of human intelligence can be perfectly explained by flexible problem solving during
those climate changes.[19]
[edit] See also

• Behavioral modernity
• Heritability of IQ
• Human evolution
• Fisherian runaway
• Primate cognition
[edit] Notes
1. ^ "Chimpanzee intelligence". Indiana University. 2000-02-23.
http://www.indiana.edu/~origins/teach/A105/lectures/A105L12.html. Retrieved 2008-03-24.
2. ^ Rowan Hooper (2007-12-03). "Chimps outperform humans at memory task". New Scientist.
http://www.newscientist.com/article/dn12993-chimps-outperform-humans-at-memory-task.html.
3. ^ "Musical behaviours and the archaeological record: a preliminary study".
http://www.mus.cam.ac.uk/~ic108/lithoacoustics/BAR2002/BARpreprint.pdf.
4. ^ a b The Social Brain Hypothesis
5. ^ Cite error: Invalid <ref> tag; no text was provided for refs named
Vetenskapsradion.2C_Sweden; see Help:Cite errors/Cite error references no text
Inside_The_Minds_of_Animals.2C_TIME_August_16_2010; see Help:Cite errors/Cite error
references no text
7. ^ Miller. The Mating Mind. ISBN 0805857494.
8. ^ "Flinn, M. V., Geary, D. C., & Ward, C. V. (2005). Ecological dominance, social competition,
and coalitionary arms races: Why humans evolved extraordinary intelligence".
http://web.missouri.edu/~gearyd/Flinnetal2005.pdf. Retrieved 2007-05-05.
En_.C3.B6verl.C3.A4gsen_art; see Help:Cite errors/Cite error references no text
10.^ Isler K, van Schaik CP 2006. Metabolic costs of brain size evolution. Biology Letters, 2,
557–60.
11.^ Evans PD, Gilbert SL, Mekel-Bobrov N, et al. 2005. Microcephalin, a gene regulating brain
size, continues to evolve adaptively in humans. Science, 309, 1717-1720.
12.^ Mekel-Bobrov N, Gilbert SL, Evans PD, et al. 2005. Ongoing adaptive evolution of ASPM, a
brain size determinant in Homo sapiens. Science 2005;309:1720–1722.
13.^ "Rozsa L 2008. The rise of non-adaptive intelligence in humans under pathogen pressure.
Medical Hypotheses, 70, 685-690.". http://www.zoologia.hu/list/clever.pdf. Retrieved 2008-05-26.
14.^ Olness K 2003. Effects on brain development leading to cognitive impairment: a worldwide
epidemic. J Dev Behav Pediatr, 24, 120–130
15.^ Goldsmith, T. (2008). "Aging, Evolvability, and the Individual Benefit Requirement". Journal
of Theoretical Biology 262: 764–768. http://www.azinet.com/aging/aging_evolvabilityJTB2.pdf.
16.^ "'Enhanced nutrition of offspring as a crucial factor for the evolution of intelligence on land'".
http://linkinghub.elsevier.com/retrieve/pii/S0306987704000416.
17.^ "'Poor Nutrition Leads to Low IQ'".
http://www.scienceagogo.com/news/20041021205759data_trunc_sys.shtml.
18.^ "'Vitamin and Mineral Supplements Increase Intelligence'". Nutrition Health Review. 1989.
http://findarticles.com/p/articles/mi_m0876/is_n52/ai_8542509/.
19.^ William Calvin:The Ascent of Mind

• Byrne, Richard W. (1995) The Thinking Ape: Evolutionary origins of intelligence Oxford
University Press, Oxford, England, ISBN 0-19-852188-X
• Greenspan, Stanley I. and Shanker, Stuart (2004) The First Idea: How symbols, language,
and intelligence evolved from our early primate ancestors to modern humans Da Capo Press,
Cambridge, Mass., ISBN 0-7382-0680-6
• Itzkoff, Seymour W. (1983) The Form of Man: The evolutionary origins of human intelligence
Paideia Publishers, Ashfield, Mass., ISBN 0-913993-00-X
• Lynch, Gary and Granger, Richard (2008) Big Brain: The Origins and Future of Human
Intelligence Palgrave Macmillan, New York, ISBN 1-4039-7978-2
• Skoyles, John R. and Sagan, Dorion (2002) Up from Dragons: The evolution of human
intelligence McGraw-Hill, New York, ISBN 0-07-137825-1
• Tobias, Phillip V. (1971) The Brain in Hominid Evolution Columbia University Press, New
York, ISBN 0-231-03518-7
• Roth and Dicke (2005). Evolution of the brain and intelligence.
http://www.subjectpool.com/ed_teach/y3project/Roth2005_TICS_brain_size_and_intelligence.pdf.
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Evolution of biological complexity


Evolution
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The evolution of biological complexity is an important outcome of the process of evolution. Evolution
has produced some remarkably complex organisms - although the actual level of complexity is very hard to
define or measure accurately in biology, with properties such as gene content, the number of cell types or
morphology all being used to assess an organism's complexity.[1][2] This observation that complex
organisms can be produced from simpler ones has led to the common misperception of evolution being
progressive and having a direction that leads towards what are viewed as "higher organisms".[3]
Nowadays, this idea of "progression" in evolution is regarded as misleading, with natural selection
having no intrinsic direction and organisms selected for either increased or decreased complexity in
response to local environmental conditions.[4] Although there has been an increase in the maximum level of
complexity over the history of life, there has always been a large majority of small and simple organisms and
the most common level of complexity (the mode) has remained constant.
Contents
[hide]
• 1 Selection for simplicity and complexity
• 2 Types of trends in complexity
• 3 History
• 4 See also
• 5 References
[edit] Selection for simplicity and complexity

Organisms that reproduce more quickly and plentifully than their competitors have an evolutionary
advantage. Consequently, organisms can evolve to become simpler and thus multiply faster and produce
more offspring, as they require fewer resources to reproduce. A good example are parasites such as malaria
and mycoplasma; these organisms often dispense with traits that are made unnecessary through parasitism
on a host.[5]
A lineage can also dispense with complexity when a particular complex trait merely provides no
selective advantage in a particular environment. Loss of this trait need not necessarily confer a selective
advantage, but may be lost by genetic drift if its loss does not confer an immediate selective disadvantage.
For example, a parasitic organism may dispense with the synthetic pathway of a metabolite where it can
readily scavenge that metabolite from its host. Discarding this synthesis may not necessarily allow the
parasite to conserve significant energy or resources and grow faster, but may be fixed in the population
through genetic drift if no disadvantage is incurred by loss of that pathway.
However, evolution can also produce more complex organisms. Complexity often arises in the co-
evolution of hosts and pathogens,[6] with each side developing ever more sophisticated adaptations, such as
the immune system and the many techniques pathogens have developed to evade it. For example, the
parasite Trypanosoma brucei, which causes sleeping sickness, has evolved so many copies of its major
surface antigen that about 10% of its genome is devoted to different versions of this one gene. This
tremendous complexity allows the parasite to constantly change its surface and thus evade the immune
system through antigenic variation.[7]
More generally, the growth of complexity may be driven by the co-evolution between an organism
and the ecosystem of predators, prey and parasites to which it tries to stay adapted: as any of these become
more complex in order to cope better with the diversity of threats offered by the ecosystem formed by the
others, the others too will have to adapt by becoming more complex, thus triggering an on-going evolutionary
arms race[6] towards more complexity.[8] This trend may be reinforced by the fact that ecosystems
themselves tend to become more complex over time, as species diversity increases, together with the
linkages or dependencies between species.
[edit] Types of trends in complexity
Passive versus active trends in the evolution of complexity. Organisms at the beginning of the
processes are colored red. Numbers of organisms are shown by the height of the bars, with the graphs
moving up in a time series.
If evolution possessed an active trend toward complexity, then we would expect to see an increase
over time in the most common value (the mode) of complexity among organisms, as shown to the right.[9]
Indeed, some computer models have suggested that the generation of complex organisms is an inescapable
feature of evolution.[10][11] This is sometimes referred to as evolutionary self-organization. Self-organization
is the spontaneous internal organization of a system. This process is accompanied by an increase in
systemic complexity, resulting in an emergent property that is distinctly different from any of the constituent
parts.
However, the idea of increasing production of complexity in evolution can also be explained through
a passive process.[9] As shown on the left, this involves an increase in variance but the mode does not
change. Thus, the maximum level of complexity increases over time, but only as an indirect product of there
being more organisms in total.
In this hypothesis, any appearance of evolution acting with an intrinsic direction towards increasingly-
complex organisms is a result of people concentrating on the small number of large, complex organisms that
inhabit the right-hand tail of the complexity distribution and ignoring simpler and much more common
organisms. This passive model predicts that the majority of species are microscopic prokaryotes, which is
supported by estimates of 106 to 109 extant prokaryotes[12] compared to diversity estimates of 106 to 3·106
for eukaryotes.[13][14] Consequently, in this view, microscopic life dominates Earth, and large organisms
only appear more diverse due to sampling bias.
[edit] History
In the 19th century, some scientists such as Jean-Baptiste Lamarck and Ray Lankester believed that
all Nature had an innate striving to become more complex with evolution. This belief may reflect then-current
ideas of Hegel and Herbert Spencer that all creation was gradually evolving to a higher, more perfect state.
According to this view, the evolution of parasites from an independent organism to parasite was seen
as "devolution" or "degeneration", and contrary to Nature. This view has sometimes been used
metaphorically by social theorists and propagandists to decry a class of people as "degenerate parasites".
Today, "devolution" is regarded as nonsense; rather, lineages will become simpler or more complicated
according to whatever forms have a selective advantage.[15]
[edit] See also

• Biocomplexity
• Biodiversity
• Biosphere
• Complex adaptive system
• Complexity
• Ecosystem
• Orthogenesis
[edit] References
1. ^ Adami C (2002). "What is complexity?". Bioessays 24 (12): 1085–94.
doi:10.1002/bies.10192. PMID 12447974.
2. ^ Waldrop M. et al. (2008). "Language: Disputed definitions". Nature 455 (7216): 1023–1028.
doi:10.1038/4551023a. PMID 18948925.
3. ^ McShea D (1991). "Complexity and evolution: What everybody knows". Biology and
Philosophy 6 (3): 303–324. doi:10.1007/BF00132234.
4. ^ Ayala FJ (2007). "Darwin's greatest discovery: design without designer". Proc. Natl. Acad.
Sci. U.S.A. 104 Suppl 1: 8567–73. doi:10.1073/pnas.0701072104. PMID 17494753. PMC 1876431.
http://www.pnas.org/cgi/content/full/104/suppl_1/8567.
5. ^ Sirand-Pugnet P, Lartigue C, Marenda M, et al. (2007). "Being Pathogenic, Plastic, and
Sexual while Living with a Nearly Minimal Bacterial Genome". PLoS Genet. 3 (5): e75.
doi:10.1371/journal.pgen.0030075. PMID 17511520.
6. ^ a b R. Dawkins and J. R. Krebs (1979). "Arms Races between and within Species". Proc. R.
Soc. Lond.B 205 (1161): 489–511. doi:10.1098/rspb.1979.0081. PMID 42057.
7. ^ Pays E (2005). "Regulation of antigen gene expression in Trypanosoma brucei". Trends
Parasitol. 21 (11): 517–20. doi:10.1016/j.pt.2005.08.016. PMID 16126458.
8. ^ Heylighen, F. (1999a) "The Growth of Structural and Functional Complexity during
Evolution", in F. Heylighen, J. Bollen & A. Riegler (eds.) The Evolution of Complexity Kluwer
Academic, Dordrecht, 17-44.
9. ^ a b Carroll SB (2001). "Chance and necessity: the evolution of morphological complexity
and diversity". Nature 409 (6823): 1102–9. doi:10.1038/35059227. PMID 11234024.
10.^ Furusawa C, Kaneko K (2000). "Origin of complexity in multicellular organisms". Phys.
Rev. Lett. 84 (26 Pt 1): 6130–3. doi:10.1103/PhysRevLett.84.6130. PMID 10991141.
11.^ Adami C, Ofria C, Collier TC (2000). "Evolution of biological complexity". Proc. Natl. Acad.
Sci. U.S.A. 97 (9): 4463–8. doi:10.1073/pnas.97.9.4463. PMID 10781045. PMC 18257.
12.^ Oren A (2004). "Prokaryote diversity and taxonomy: current status and future challenges".
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 359 (1444): 623–38. doi:10.1098/rstb.2003.1458.
PMID 15253349. PMC 1693353. http://www.pubmedcentral.nih.gov/picrender.fcgi?
artid=1693353&blobtype=pdf.
13.^ May, R. M.; Beverton, R. J. H. (1990). "How Many Species?". R. M. May, Philos. Trans. R.
Soc. London Ser. B 330, 293 (1990) 330: 293. doi:10.1098/rstb.1990.0200.
http://rstb.royalsocietypublishing.org/content/330/1257/293.abstract?
ijkey=01b04eee73eda3609fb8f928b58db87298a825a0&keytype2=tf_ipsecsha.
14.^ Schloss P, Handelsman J (2004). "Status of the microbial census". Microbiol Mol Biol Rev
68 (4): 686–91. doi:10.1128/MMBR.68.4.686-691.2004. PMID 15590780. PMC 539005.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590780#r6.
15.^ Scientific American; Biology: Is the human race evolving or devolving? retrieved 2007-06-
11
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Evolution of ageing

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improve this article if you can. The talk page may contain suggestions. (May 2008)
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Enquiry into the evolution of ageing aims to explain why almost all living things weaken and die with age.
There is not yet agreement in the scientific community on a single answer. The evolutionary origin of
senescence remains a fundamental unsolved problem in biology.
Historically, ageing was first likened to "wear and tear": living bodies get weaker just as with use a
knife's edge becomes dulled or with exposure to air and moisture iron objects rust. But this idea was
discredited in the 19th century when the second law of thermodynamics was formalized. Entropy (disorder)
must increase inevitably within a closed system, but living beings are not closed systems. It is a defining
feature of life that it takes in free energy from the environment and unloads its entropy as waste. Living
systems can even build themselves up from seed, and routinely repair themselves. There is no
thermodynamic necessity for senescence. In addition, generic damage or "wear and tear" theories could not
explain why biologically similar organisms (e.g. mammals) exhibited such dramatically different life spans.
Contents
[hide]
• 1 History
• 2 Mutation accumulation
• 3 Antagonistic pleiotropy
• 4 Disposable soma theory
• 5 Other problems with the classical ageing theories
• 6 Impact of new evolution concepts on ageing theories
• 6.1 Ageing theories based on group selection
• 6.2 Ageing theories based on evolvability
• 7 Ageing mechanism concepts
• 7.1 Maintenance theories of ageing
• 7.2 Summary of empirical evidence favouring
programmed ageing
• 8 Biogerontology considerations
• 9 See also
• 10 References and notes
[edit] History
August Weismann was responsible for interpreting and formalizing the mechanisms of Darwinian
evolution in a modern theoretical framework. In 1889, he theorized that ageing was part of life's program
because the old need to remove themselves from the theatre to make room for the next generation,
sustaining the turnover that is necessary for evolution.[1] This theory again has much intuitive appeal, but it
suffers from having a teleological or goal-driven explanation. In other words, a purpose for ageing has been
identified, but not a mechanism by which that purpose could be achieved. Ageing may have this advantage
for the long-term health of the community; but that doesn't explain how individuals would acquire the genes
that make them get old and die, or why individuals that had ageing genes would be more successful than
other individuals lacking such genes. (In fact, there is every reason to think that the opposite is true: ageing
decreases individual fitness.) Weismann disavowed his own theory before his life was over.
Theories suggesting that deterioration and death due to ageing are a purposeful result of an
organism's evolved design (such as Weismann's "programmed death" theory) are referred to as theories of
programmed ageing or adaptive ageing. The idea that the ageing characteristic was selected (an adaptation)
because of its deleterious effect was largely discounted for much of the 20th century but is now experiencing
a resurgence because of new empirical evidence as well as new thinking regarding the process of evolution.
[citation needed]
[edit] Mutation accumulation

The first modern, successful theory of mammal ageing was formulated by Peter Medawar in 1952.
His idea was that ageing was a matter of neglect. Nature is a highly competitive place, and almost all animals
in nature die before they attain old age. Therefore, there is not much reason why the body should remain fit
for the long haul - not much selection pressure for traits that would maintain viability past the time when most
animals would be dead anyway, killed by predators or disease or by accident.
Medawar's theory is referred to as Mutation Accumulation. The mechanism of action involves
random, detrimental mutations of a kind that happen to show their effect only late in life. Unlike most
detrimental mutations, these would not be efficiently weeded out by natural selection. Hence they would
'accumulate' and, perhaps, cause all the decline and damage that we associate with ageing.[2][3]
Modern genetics science has disclosed a possible problem with the mutation accumulation concept
in that it is now known that genes are typically expressed in specific tissues at specific times (see regulation
of gene expression). Expression is controlled by some genetic "program" that activates different genes at
different times in the normal growth, development, and day-to-day life of the organism. Defects in genes
cause problems (genetic diseases) when they are not properly expressed when required. A problem late in
life suggests that the genetic program called for expression of a gene only in late life and the mutational
defect prevented proper expression. This implies existence of a program that called for different gene
expression at that point in life. Why, given Medawar's concept, would there exist genes only needed in late
life or a program that called for different expression only in late life? The maintenance mechanism theory
(discussed below) avoids this problem.
Medawar's concept suggested that the evolution process was affected by the age at which an
organism was capable of reproducing. Characteristics that adversely affected an organism prior to that age
would severely limit the organism's ability to propagate its characteristics and thus would be highly "selected
against" by natural selection. Characteristics that caused the same adverse effects that only appeared well
after that age would have relatively little effect on the organism's ability to propagate and therefore might be
allowed by natural selection. This concept fit well with the observed multiplicity of mammal life spans (and
differing ages of sexual maturity) and is important to all of the subsequent theories of ageing discussed
below.
Medawar did not suggest that there were fundamental limitations on life span. Organisms exhibiting
negligible senescence suggest that ageing is not a fundamental limitation, at least not in the scale of
mammal life span.
[edit] Antagonistic pleiotropy

Medawar's theory was further developed by George C. Williams in 1957, who noted that senescence
may be causing many deaths[citation needed], even if animals are not 'dying of old age.' In the earliest
stages of senescence, an animal may lose a bit of its speed, and then predators will seize it first, while
younger animals flee successfully. Or its immune system may decline, and it becomes the first to die of a
new infection. Nature is such a competitive place, said Williams, (turning Medawar's argument back at him),
that even a little bit of senescence can be fatal; hence natural selection does indeed care; ageing isn't cost-
free.
Williams's objection has turned out to be valid: Modern studies of demography in natural
environments demonstrate that senescence does indeed make a substantial contribution to the death rate in
nature. These observations cast doubt on Medawar's theory. Another problem with Medawar's theory
became apparent in the late 1990s, when genomic analysis became widely available. It turns out that the
genes that cause ageing are not random mutations; rather, these genes form tight-knit families that have
been around as long as eukaryotic life. Baker's yeast, worms, fruit flies, and mice all share some of the same
ageing genes.[4]
Williams (1957) proposed his own theory, called antagonistic pleiotropy. Pleiotropy means one gene
that has two or more effects on the phenotype. In antagonistic pleiotropy, one of these effects is beneficial
and another is detrimental. In essence this refers to genes that offer benefits early in life, but exact a cost
later on. If evolution is a race to have the most offspring the fastest, then enhanced early fertility could be
selected even if it came with a price tag that included decline and death later on.[5] Because ageing was a
side effect of necessary functions, Williams considered any alteration of the ageing process to be
"impossible."
Antagonistic pleiotropy is a prevailing theory today, but this is largely by default, and not because the
theory has been well verified. In fact, experimental biologists have looked for the genes that cause ageing,
and since about 1990 the technology has been available to find them efficiently. Of the many ageing genes
that have been reported, some seem to enhance fertility early in life, or to carry other benefits. But there are
other ageing genes for which no such corresponding benefit has been identified. This is not what Williams
predicted. This may be thought of as partial validation of the theory, but logically it cuts to the core premise:
that genetic trade-offs are the root cause of ageing.
Another difficulty with antagonistic pleiotropy and other theories that suppose that ageing is an
adverse side effect of some beneficial function is that the linkage between adverse and beneficial effects
would need to be rigid in the sense that the evolution process would not be able to evolve a way to
accomplish the benefit without incurring the adverse effect even over a very long time span. Such a rigid
relationship has not been experimentally demonstrated and, in general, evolution is obviously able to
independently and individually adjust myriad organism characteristics.
In breeding experiments, Michael R. Rose selected fruit flies for long life span. Based on antagonistic
pleiotropy, Rose expected that this would surely reduce their fertility. His team found that they were able to
breed flies that lived more than twice as long as the flies they started with, but to their surprise, the long-lived,
inbred flies actually laid more eggs than the short-lived flies. This was another setback for pleiotropy theory,
though Rose maintains it may be an experimental artifact.[6]
[edit] Disposable soma theory
This article may contain original research. Please improve it by verifying the claims
made and adding references. Statements consisting only of original research may be
removed. More details may be available on the talk page. (July 2008)
A third mainstream theory of ageing, the Disposable soma theory, proposed in 1977 by Thomas
Kirkwood, presumes that the body must budget the amount of energy available to it. The body uses food
energy for metabolism, for reproduction, and for repair and maintenance. With a finite supply of food, the
body must compromise, and do none of these things quite as well as it would like. It is the compromise in
allocating energy to the repair function that causes the body gradually to deteriorate with age.[7]
The term disposable soma came from the analogy with disposable products—why spend money
making something durable, if it will only be used for a limited amount of time?
The disposable soma theory has great appeal because its basis is so sensible and intuitive, but there
are arguments against it. The theory clearly predicts that a shortage of food should make the compromise
more severe all around; but in many experiments, ongoing since 1930, it has been demonstrated that
animals live longer when fed substantially less than controls. This is the caloric restriction (CR) effect,[8] and
it cannot be easily reconciled with the Disposable Soma theory. Though by decreasing energy expenditure
the damage generated (by free radicals for instance) is expected to be reduced and the total energy budget
might indeed be reduced, but the investment in repair function might still be relatively the same. But dietary
restriction has not been shown to increase lifetime reproductive success (fitness), because when food
availability is lower reproductive output is also lower. So CR does thus not completely dismiss disposable
theory.
Experimentally, some animals lose fertility when their life spans are extended by CR and some suffer
no appreciable loss. Males, for example, typically remain fertile when underfed, while females do not. And,
even females present an enigma because their fertility decline is not tightly coupled to their longevity gain.
For example, in female mice that are restricted to 60% of a free-feeding diet, reproduction is shut down
altogether. But female life span continues to increase linearly right up to the threshold of starvation - around
30% of free-feeding levels.
A difficulty with the disposable soma theory is that the energy required for maintenance and repair
would appear to be relatively minor when compared to the energy required for gestation (repair should take
less energy than producing an entire new organism). Yet gestating animals seem able to perform the
maintenance while post-reproductive animals do not. A similar difficulty is that male animals seem to have
similar life spans as females despite the apparently higher energy requirement for gestation and other
reproductive activities.
[edit] Other problems with the classical ageing theories

This article contains weasel words, vague phrasing that often accompanies biased
or unverifiable information. Such statements should be clarified or removed. (May 2008)
A fundamental shortcoming for all three mainstream theories based on classical evolutionary process
concepts is that there appear to be 'deliberate' metabolic mechanisms that seem to have no other purpose
than to cause death.
One is apoptosis, or programmed cell death. Apoptosis is responsible for killing infected cells,
cancerous cells and cells that are simply in the wrong place during development. There are clear benefits to
apoptosis, so the existence of apoptosis isn't a problem for evolutionary theory. The problem is that apoptosis
seems to ramp up late in life and kill healthy cells, causing weakness and degeneration. And, paradoxically,
apoptosis has been observed as a kind of 'altruistic suicide' in colonies of yeast under stress. This seems to
be a direct hint that senescence arose because it conferred a direct evolutionary advantage, rather than
some kind of side effect of genes that have other evolutionary advantages (pleiotropy).[9]
A second 'deliberate' mechanism is called replicative senescence or cellular senescence.
Metaphorically, a cell may be said to 'count' (with its telomeres) the number of times that it has divided, and
after a set number of replications, it languishes and dies. It has been proposed that this is a last-ditch
protective mechanism against cancer. But this hypothesis fails because replicative senescence is far older
than cancer. Many invertebrates experience replicative senescence, though they never die of cancer.[ citation
needed] Even one-celled organisms count replications, and will die if they don't replenish their telomeres with
conjugation (sex).[10]
More strictly, of course, cells cannot 'count' the number of times they have divided. Telomeres are
not a counting mechanism, though they may be used to indicate the number of times a particular
chromosome has been replicated. Cellular processes for genetic material replication occurs in both directions
along DNA, 5' to 3' and on the other strand, 3' to 5'. As the 3' to 5' end is impossible for DNA polymerase to
grab at the 1 base pair mark, a handful of basepairs (10-15) are cut off each replication. Over time, this
cutting short of the DNA results in no telomeres, and the cell is unable to replicate that chromosome without
cutting into genes.
The dilemma is that classical evolutionary theory says that what is maintained in a lineage is that
which ensures the viability of an organism and its offspring. Ageing can only cut off an individual's capacity to
reproduce. So, according to classical theory, ageing could only evolve as a side effect, or epiphenomenon of
selection. The disposable soma theory and antagonistic pleiotropy theory are examples in which a
compensating individual benefit, compatible with classical evolution theory (See neo-Darwinism and modern
evolutionary synthesis) is proposed. Nevertheless, there is accumulated evidence that ageing looks like an
adaptation in its own right, selected for its own sake.[11][12]
Semelparous organisms and others that die suddenly following reproduction (e.g. salmon, octopus,
marsupial mouse (Brown Antechinus), etc.) also represent instances of organisms who incorporate a life
span limiting feature. Sudden death is more obviously an instance of programmed death or a purposeful
adaptation than gradual ageing. Biological elements clearly associated with evolved mechanisms such as
hormone signalling have been identified in the death mechanisms of organisms such as the octopus.[13]
[edit] Impact of new evolution concepts on ageing theories

At the time most of the non-programmed ageing theories were developed there was very little
scientific disagreement with classical theories (i.e. Neo-Darwinism or modern evolutionary synthesis)
regarding the process of evolution. However, in addition to suicidal behaviour of semelparous species (not
handled by the classical ageing theories) other apparently individually adverse organism characteristics such
as altruism and sexual reproduction were observed. In response to these other conflicts, adjustments to
classical theory were proposed:
• Various group selection theories (beginning in 1962) propose that benefit to a group could
offset the individually adverse nature of a characteristic such as altruism. The same principle could
be applied to characteristics that limited life span and theories proposing group benefits for limited
life spans appeared.
• Evolvability theories (beginning in 1995) suggest that a characteristic that increased an
organism's ability to evolve could also offset an individual disadvantage and thus be evolved and
retained. Multiple evolvability benefits of a limited life span were subsequently proposed in addition to
those originally proposed by Weismann.
[edit] Ageing theories based on group selection
Mitteldorf[14] proposed a group benefit of a limited life span involving regulation of population
dynamics. Populations in nature are subject to boom and bust cycles. Often overpopulation can be punished
by famine or by epidemic. Either one could wipe out an entire population. Senescence is a means by which a
species can 'take control' of its own death rate, and level out the boom-bust cycles. This story may be more
plausible than the Weismann hypothesis as a mechanistic explanation, because it addresses the question of
how group selection can be rapid enough to compete with individual selection.
Libertini[15] also suggests benefits for adaptive ageing.
[edit] Ageing theories based on evolvability

Goldsmith[16] proposed that in addition to increasing the generation rate and thereby evolution rate a
limited life span improves the evolution process by limiting the ability of older individuals to dominate the
gene pool. Further, the evolution of characteristics such as intelligence and immunity may specially require a
limited life span because otherwise acquired characteristics such as experience or exposure to pathogens
would tend to override the selection of the beneficial inheritable characteristic. An older and more
experienced but less intelligent animal would have a fitness advantage over a younger more intelligent
animal except for the effects of ageing.
Skulachev[17] has suggested that programmed ageing assists the evolution process by providing a
gradually increasing challenge or obstacle to survival and reproduction and therefore enhancing the selection
of beneficial characteristics. In this sense ageing would act in a manner similar to that of mating rituals that
take the form of contests or trials that must be overcome in order to mate (another individually adverse
observation). This suggests an advantage of gradual ageing over sudden death as a means of life span
regulation.
Weissmann's 1889 ageing theory was essentially an evolvability theory. Ageing or otherwise
purposely limited life span helps evolution by freeing resources for younger, and therefore presumably better
adapted individuals.
[edit] Ageing mechanism concepts

If organisms purposely limit their life spans via ageing or semelparous behaviour, the associated
evolved mechanisms could be very complex just as mechanisms that provide for mentation, vision, digestion,
or other biological function are typically very complex. Such a mechanism could involve hormones, signalling,
sensing of external conditions, and other complex functions typical of evolved mechanisms. Such complex
mechanisms could explain all of the observations of ageing and semelparous behaviours as described
below.
It is typical for a given biological function to be controlled by a single mechanism that is capable of
sensing the germane conditions and then executing the necessary function. The mechanism signals all the
systems and tissues that need to respond to that function by means of organism-wide signals (hormones). If
ageing is indeed a biological function we would expect all or most manifestations of ageing to be similarly
controlled by a common mechanism. Various observations (listed below) indeed suggest the existence of a
common control mechanism.
It is also typical for biological functions to be modulated by or synchronized to external events or
conditions. The circadian rhythm and synchronization of mating behaviour to planetary cues are examples. In
the case of ageing seen as a biological function, the caloric restriction effect may well be an example of the
ageing function being modulated in order to optimize organism life span in response to external conditions.
Temporary extension of life span under famine conditions would aid in group survival because extending life
span combined with less frequent reproduction would reduce the resources required to maintain a given
population.
Theories to the effect that ageing results by default (mutation accumulation) or is an adverse side
effect of some other function are logically much more limited and suffer when compared to empirical
evidence of complex mechanisms. The choice of ageing theory therefore is logically essentially determined
by one's position regarding evolutionary processes and some theorists reject programmed ageing based
entirely on evolutionary process considerations.[18]
[edit] Maintenance theories of ageing

It is generally accepted that deteriorative processes (wear, other molecular damage) exist and that
living organisms have mechanisms to counter deterioration. Wounds heal; dead cells are replaced; claws
grow.
A non-programmed theory of mammal ageing [19] that fits with classical evolution theory and
Medawar's concept is that different mammal species possess different capabilities for maintenance and
repair. Longer lived species possess many mechanisms for offsetting damage due to causes such as
oxidation, telomere shortening, and other deteriorative processes that are each more effective than those of
shorter lived species. Shorter lived species, having earlier ages of sexual maturity, had less need for
longevity and thus did not evolve or retain the more effective repair mechanisms. Damage therefore
accumulates more rapidly resulting in earlier manifestations and shorter life span. Since there are a wide
variety of ageing manifestations that appear to have very different causes, it is likely that there are many
different maintenance and repair functions.
A corresponding programmed maintenance theory based on evolvability[20] suggests that the repair
mechanisms are in turn controlled by a common control mechanism capable of sensing conditions such as
caloric restriction and also capable of producing the specific life span needed by the particular species. In this
view the differences between short and long lived species are in the control mechanisms as opposed to each
individual maintenance mechanism.
[edit] Summary of empirical evidence favouring programmed ageing

• Existence of complex programmed death mechanisms in semelparous species (e.g. octopus)
including hormone signalling, nervous system involvement, etc. If a limited life span is generally
useful as predicted by the programmed ageing theories, it would be unusual for an octopus to
possess a more complex mechanism for accomplishing that function than a mammal.
• Discovery of "ageing genes" with no other apparent function.
• Caloric restriction effect: reduction of available resources increases life span. This behavior
has a plausible group benefit in enhancing the survival of a group under famine conditions and also
suggests common control.
• Progeria and Werner syndrome are both single-gene genetic diseases that cause
acceleration of many or most symptoms of ageing. The fact that a single gene malfunction can cause
similar effects on many different manifestations of ageing suggests a common mechanism.
• Although mammal life spans vary over an approximately 100:1 range, manifestations of
ageing (cancer, arthritis, weakness, sensory deficit, etc.) are similar in different species. This
suggests that the deterioration mechanisms and corresponding maintenance mechanisms operate
over a short period (less than the life span of a short-lived mammal). All the mammals therefore need
all the maintenance mechanisms. This suggests that the difference between mammals is in a
common control mechanism.
• Life span varies greatly among otherwise very similar species (e.g. different varieties of
salmon 3:1, different fish 600:1) suggesting that relatively few genes control life span and that
relatively minor changes to genotype could cause major differences in life span—suggests common
control mechanism.
[edit] Biogerontology considerations

Theories of ageing affect efforts to understand and find treatments for age-related conditions (see
biogerontology):
• Those who believe in the idea that ageing is an unavoidable side effect of some necessary
function (antagonistic pleiotropy or disposable soma theories) logically tend to believe that attempts
to delay ageing would result in unacceptable side effects to the necessary functions. Altering ageing
is therefore "impossible"[5] and study of ageing mechanisms is of only academic interest.
• Those believing in default theories of multiple maintenance mechanisms tend to believe that
ways might be found to enhance the operation of some of those mechanisms. Perhaps they can be
assisted by anti-oxidants or other agents.
• Those who believe in programmed ageing suppose that ways might be found to interfere with
the operation of the part of the ageing mechanism that appears to be common to multiple symptoms,
essentially "slowing down the clock" and delaying multiple manifestations. Such effect might be
obtained by fooling a sense function. One such effort is an attempt to find a "mimetic" that would
"mime" the anti-ageing effect of calorie restriction without having to actually radically restrict diet.[21]
[edit] See also

• List of life extension-related topics
• Negligible senescence Describes observation of animals without measurable symptoms of
ageing
• Senescence
• Gerontology
[edit] References and notes

1. ^ Weismann A. (1889). Essays upon heredity and kindred biological problems. Oxford:
Clarendon Press. Work that describes Weismann's theory about making room for the young.
2. ^ Medawar, P.B. (1952) (PDF). An Unsolved Problem of Biology. London: H.K. Lewis.
http://www.telomere.org/Downloads/Medawar-UPB.pdf. Edney, E.B. and Gill, R.W. 1968. Delineates
the theory of mutation accumulation.
3. ^ Edney EB, Gill RW (October 1968). "Evolution of senescence and specific longevity".
Nature 220 (5164): 281–2. doi:10.1038/220281a0. PMID 5684860. Further describes theory of
mutation accumulation.
4. ^ Guarente L, Kenyon C (November 2000). "Genetic pathways that regulate ageing in model
organisms". Nature 408 (6809): 255–62. doi:10.1038/35041700. PMID 11089983.
http://www.nature.com/nature/journal/v408/n6809/abs/408255a0.html. Shows similarities between
ageing genes in model organisms.
5. ^ a b Williams, G.C. (1957). "Pleiotropy, natural selection and the evolution of senescence"
(PDF). Evolution 11 (4): 398–411. doi:10.2307/2406060.
http://www.telomere.org/Downloads/Williams_searchable.pdf. Paper in which Williams describes his
theory of antagonistic pleiotropy.
6. ^ Leroi, A.M., Chippindale, A.K., Rose, M.R. (1994). "Long-term laboratory evolution of a
genetic life-history tradeoff in Drosophila melanogaster. 1. The role of genotype-by-environment
interaction". Evolution 48 (4): 1244–57. doi:10.2307/2410382. http://links.jstor.org/sici?sici=0014-
3820(199408)48%3A4%3C1258%3ALLEOAG%3E2.0.CO%3B2-E#abstract.
7. ^ Kirkwood TB (November 1977). "Evolution of ageing". Nature 270 (5635): 301–4.
doi:10.1038/270301a0. PMID 593350.
http://www.nature.com/nature/journal/v270/n5635/abs/270301a0.html. Origin of the disposable soma
theory.
8. ^ Weindruch, R., Walford, R.L. (1986). The Retardation of Aging and Disease by Dietary
Restriction. Springfield, IL: Thomas. Masoro EJ (September 2005). "Overview of caloric restriction
and ageing". Mech. Ageing Dev. 126 (9): 913–22. doi:10.1016/j.mad.2005.03.012. PMID 15885745.
http://linkinghub.elsevier.com/retrieve/pii/S0047-6374(05)00078-3. Overview of caloric restriction
and aging.
9. ^ Gourlay CW, Du W, Ayscough KR (December 2006). "Apoptosis in yeast--mechanisms and
benefits to a unicellular organism". Mol. Microbiol. 62 (6): 1515–21. doi:10.1111/j.1365-
2958.2006.05486.x. PMID 17087770. http://onlinelibrary.wiley.com/resolve/openurl?
genre=article&sid=nlm:pubmed&issn=0950-382X&date=2006&volume=62&issue=6&spage=1515.
10.^ Clark, W.R. (1999). A Means to an End: The biological basis of aging and death . New York:
Oxford University Press. http://wrclarkbooks.com/means_to_an_end.html. About telomeres and
programmed cell death.
11.^ Mitteldorf, J. (2004). "Ageing selected for its own sake" (PDF). Evol. Ecol. Res. 6: 937–53.
http://mathforum.org/~josh/4OwnSake.pdf. On the tension between experimental data and
evolutionary theory.
12.^ Bredesen DE (October 2004). "The non-existent aging program: how does it work?". Aging
Cell 3 (5): 255–9. doi:10.1111/j.1474-9728.2004.00121.x. PMID 15379848.
http://onlinelibrary.wiley.com/resolve/openurl?genre=article&sid=nlm:pubmed&issn=1474-
9718&date=2004&volume=3&issue=5&spage=255. More on the tension between experiment and
theory.
13.^ Wodinsky, J. (1977). "Hormonal Inhibition of Feeding and Death in Octopus: Control by
Optic Gland Secretion". Science 148 (4320): 948–51. doi:10.1126/science.198.4320.948.
PMID 17787564.
14.^ Mitteldorf, J. (2006). "Chaotic population dynamics and the evolution of ageing: proposing a
demographic theory of senescence" (PDF). Evol. Ecol. Res. 8: 561–74.
http://mathforum.org/~josh/LogiSen-EER.pdf. On population dynamics as a mechanism for the
evolution of ageing.
15.^ Libertini, G. (2008). "Empirical evidence for various evolutionary hypotheses on species
demonstrating increasing mortality with increasing chronological age in the wild". Scientific World
Journal 19 (8): 182–93. doi:10.1100/tsw.2008.36. PMID 18301820.
16.^ Goldsmith TC (June 2008). "Aging, evolvability, and the individual benefit requirement;
medical implications of aging theory controversies". J. Theor. Biol. 252 (4): 764–8.
doi:10.1016/j.jtbi.2008.02.035. PMID 18396295. http://linkinghub.elsevier.com/retrieve/pii/S0022-
5193(08)00101-X.
17.^ Skulachev VP (November 1997). "Aging is a specific biological function rather than the
result of a disorder in complex living systems: biochemical evidence in support of Weismann's
hypothesis". Biochemistry Mosc. 62 (11): 1191–5. PMID 9467841.
18.^ Olshansky, SJ; Hayflick, L; Carnes, BA (2002). "No truth to the fountain of youth.".
Scientific American 286 (6): 92–5. PMID 12030096. Article stating that programmed ageing is
"impossible" because of "the way evolution works."
19.^ Holliday R (May 2006). "Aging is no longer an unsolved problem in biology". Ann. N. Y.
Acad. Sci. 1067: 1–9. doi:10.1196/annals.1354.002. PMID 16803964.
http://onlinelibrary.wiley.com/resolve/openurl?genre=article&sid=nlm:pubmed&issn=0077-
8923&date=2006&volume=1067&spage=1.
20.^ Goldsmith, T. (2009). "Mammal aging: active and passive mechanisms". Journal of
Bioscience Hypotheses 2 (2): 59–64. doi:10.1016/j.bihy.2008.12.002. Article compares programmed
and non-programmed maintenance theories of ageing in light of empirical evidence.
21.^ Chen D, Guarente L (February 2007). "SIR2: a potential target for calorie restriction
mimetics". Trends Mol Med 13 (2): 64–71. doi:10.1016/j.molmed.2006.12.004. PMID 17207661.
http://linkinghub.elsevier.com/retrieve/pii/S1471-4914(06)00286-3.

• Evolutionary Theories of Aging and Longevity
• The Evolutionary Theory of Aging by João Pedro de Magalhães.
• Programmed-Aging.Org Site provides comprehensive information on programmed ageing,
the programmed/non-programmed controversy, and underlying evolution controversies.
• How Evolutionary Thinking Affects People's Ideas About Aging Interventions
• AnAge Animal Ageing and Longevity Database Provides maximum observed ages and
sexual maturity ages for many animals.
• The Case for Programmed Mammal Aging Describes empirical data, evolutionary rationale,
and historical perspective supporting programmed ageing in mammals.
• Life Table for USA 2005 Probability of death as a function of age

Processes of
Population genetic
Evolutionary
developmental
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Modes of
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_ageing"
Categories: Aging | Life extension | Death | Evolutionary biology

W000
Origin of avian flight


introducing more precise citations where appropriate. (May 2009)
The Berlin Archaeopteryx, one of the earliest known birds.
"Evolution of flight" redirects here. See also flying and gliding animals and insect flight.
Around 350 BCE, Aristotle and other philosophers of the time were attempting to explain the
aerodynamics of avian flight. Even after the discovery of the ancestral bird Archaeopteryx, over 150 years
ago, debates still persist regarding the evolution of flight. Currently there are three leading hypotheses
pertaining to avian flight: Pouncing Proavis model, Cursorial model, and Arboreal model. Archaeopteryx,
being the oldest known ancestor of modern birds, could provide clues to the origin of avian flight.
Contents
[hide]
• 1 Flight Characteristics
• 2 Theories
• 2.1 Pouncing Proavis model
• 2.2 Cursorial model
• 2.3 Arboreal model
• 3 Footnotes
• 4 References
[edit] Flight Characteristics

For flight to occur in Aves, four physical forces (thrust and drag, lift and weight) must work together.
In order for birds to balance these forces, certain physical characteristics are required. Asymmetrical wings,
found on all flying birds with the exception of hummingbirds, [1] help in the production of thrust and lift.
Anything that moves produces drag due to friction forces. The aerodynamic body of a bird can reduce drag,
but when stopping or slowing down a bird will use its tail and feet to increase drag. Weight is the largest
obstacle birds must overcome in order to fly. Flying birds have evolved reduced weight through several
characteristics. Pneumatic bone is hollow or filled with air sacs, reducing weight. The loss of teeth, gonadal
hypertrophy, and fusion of bones also reduce weight. Teeth have been replaced by a light weight bill made of
keratin, and chewing occurs in the bird's gizzard. Other physical characteristics required for flight are a keel
for the attachment of flight muscles, an enlarged cerebellum for fine motor coordination, and a furcula, which
enhances skeletal bracing for the stresses of flight.
[edit] Theories
The CGI television series Prehistoric Park described a theory that scales turned into contour feathers
for heat insulation, and that later the feathers along the back edges of the arms and legs became bigger and
longer for displaying (e.g. Incisivosaurus), until they were long enough to be used for gliding (e.g.
Microraptor).
[edit] Pouncing Proavis model

A theory of a pouncing proavis was first proposed by Garner, Taylor, and Thomas in 1999:
We propose that birds evolved from predators that specialized in ambush from elevated sites,
using their raptorial hindlimbs in a leaping attack. Drag–based, and later lift-based, mechanisms
evolved under selection for improved control of body position and locomotion during the aerial
part of the attack. Selection for enhanced lift-based control led to improved lift coefficients,
incidentally turning a pounce into a swoop as lift production increased. Selection for greater
swooping range would finally lead to the origin of true flight.
The authors believed that this theory had four main virtues:
• It predicts the observed sequence of character acquisition in avian evolution.
• It predicts an Archaeopteryx-like animal, with a skeleton more or less identical to terrestrial
theropods, with few adaptations to flapping, but very advanced aerodynamic asymmetrical feathers.
• It explains that primitive pouncers (perhaps like Microraptor) could coexist with more
advanced fliers (like Confuciusornis or Sapeornis) since they did not compete for flying niches.
• It explains that the evolution of elongated rachis-bearing feathers began with simple forms
that produced a benefit by increasing drag. Later, more refined feather shapes could begin to also
provide lift.
[edit] Cursorial model

A cursorial, or "running" model was originally proposed by Samuel Wendell Williston in 1879. This
theory states that "flight evolved in running bipeds through a series of short jumps". As the length of the
jumps extended, the wings were used not only for thrust but also for stability, and eventually eliminated the
gliding intermediate. However, this theory was modified in the 1970s by John Ostrom to describe the use of
wings as an insect-foraging mechanism which then evolved into a wing stroke. Research was conducted by
comparing the amount of energy expended by each hunting method with the amount of food gathered. The
potential hunting volume doubles by running and jumping. To gather the same volume of food,
Archaeopteryx would expend less energy by running and jumping than by running alone. Therefore, the
cost/benefit ratio would be more favorable for this model. Due to Archaeopteryx long and erect leg,
supporters of this model say the species was a terrestrial bird. This characteristic allows for more strength
and stability in the hindlimbs. Thrust produced by the wings coupled with propulsion in the legs generates the
minimum velocity required to achieve flight. Thus, through these mechanisms, Archaeopteryx was able to
achieve flight from the ground up.
Although the evidence in favor of this model is scientifically plausible, the evidence against it is
substantial. For instance, a cursorial flight model would be energetically less favorable when compared to the
alternative hypotheses. In order to achieve liftoff, Archaeopteryx would have to run faster than modern birds
by a factor of three, due to its weight. Furthermore, the mass of Archaeopteryx versus the distance needed
for minimum velocity to obtain liftoff speed being proportional., therefore, as mass increases, the energy
required for takeoff increases exponentially. Other research has shown that the physics involved in cursorial
flight would not make this a likely answer to the origin of avian flight. Once flight speed is obtained and
Archaeopteryx is in the air, drag would cause the velocity to instantaneously decrease. In addition, balance
could not be maintained due to this immediate reduction in velocity. Hence, Archaeopteryx would have a very
short and ineffective flight. In contrast to Ostrom’s theory regarding flight as a hunting mechanism, physics
again does not support this model. In order to effectively trap insects with the wings, Archaeopteryx would
require a mechanism such as holes in the wings to reduce air resistance. Without this mechanism, the
cost/benefit ratio would not be feasible.
[edit] Arboreal model

This model was originally proposed in 1880 by Othniel C. Marsh. The theory states Archaeopteryx
was a reptilian bird that soared from tree to tree. After the leap, Archaeopteryx would then use its wings as a
balancing mechanism. According to this model, Archaeopteryx developed a gliding method to conserve
energy. Even though an arboreal Archaeopteryx exerts energy climbing the tree, an arboreal Archaeopteryx
is able to achieve higher velocities and cover greater distances during the gliding phase, which conserves
more energy in the long run than a cursorial bipedal runner. Conserving energy during the gliding phase
makes this a more energy-efficient model. Therefore, the benefits gained by gliding outweigh the energy
used in climbing the tree. A modern behavior model to compare against would be that of the Flying squirrel.
Researchers in support of this model have suggested that Archaeopteryx possessed skeletal
features similar to those of modern birds. The first such feature to be noted was the supposed similarity
between the foot of Archaeopteryx and that of modern perching birds. The hallux, or modified of the first digit
of the foot, was long thought to have pointed posterior to the remaining digits, as in perching birds. Therefore,
researchers once concluded that Archaeopteryx used the hallux as a balancing mechanism on tree limbs.
However, study of the Thermopolis specimen of Archeopteryx, which has the most complete foot of any
known, showed that the hallux was not in fact reversed, limiting the creature's ability to perch on branches
and implying a terrestrial or trunk-climbing lifestyle.[2]
Another skeletal feature that is similar in Archaeopteryx and modern birds is the curvature of the
claws. Archaeopteryx possessed the same claw curvature of the foot to that of perching birds. However, the
claw curvature of the hand in Archaeopteryx was similar to that in basal birds. Based upon the comparisons
of modern birds to Archaeopteryx, perching characteristics were present, signifying an arboreal habitat. The
ability for takeoff and flight was originally thought to require a supracoracoideus pulley system (SC). This
system consists of a tendon joining the humerus and coracoid process of the scapula allowing rotation of the
humerus during the upstroke. However, this system is lacking in Archaeopteryx. Based on experiments
performed by M. Sy in 1936,[3] it was proven that the SC pulley system was not required for flight from an
elevated position but necessary for cursorial takeoff.
[edit] Footnotes
1. ^ http://esotec.org/hbird/HTML/Aero_F.html
2. ^ Mayr, G., Phol, B., Hartman, S. & Peters, D.S. (2007). The tenth skeletal specimen of
Archaeopteryx. Zoological Journal of the Linnean Society, 149, 97–116.
3. ^ M. Sy, "Functionall-anatomische Untersuchungem am Vogelflugel" J Ornithol 1936. 84:199–
296.
[edit] References
• Chatterjee, S. 1997. The Rise of Birds. The Johns Hopkins University Press. Baltimore. p.
150-151, 153, 158.
• Chatterjee, S. and R. J. Templin. 2002. “The flight of Archaeopteryx.” Naturwissenschaften.
90: 27-32.
• Elzanowoski, A. 2000. “The Flying Dinosaurs.” Ed. Paul, G. The Scientific American Book of
Dinosaurs. p. 178.
• Feduccia, A. 1999. The Origin and Evolution of Birds. Yale University Press. London. p. 95,
97, 101, 103-104, 136.
• Garner, J., G. Taylor, and A. Thomas. 1999. “On the origins of birds: the sequence of
character acquisition in the evolution of avian flight.” The Royal Society. 266:
1259-1266.
• Gill, F. 2007. Ornithology. W.H. Freeman and Company. New York. p. 25, 29, 40-41.
• Lewin, R. 1983. “How did vertebrates take to the air?” Science. 221: 38-39.
• Morell, V. 1993. “Archaeopteryx: early bird catches a can of worms.” Science. 259: 764-765.
• Ostrom , J. 1974. “Archaeopteryx and the origin of flight.” The Quarterly Review of Biology.
49: 27-47.
• Paul, G. 2002. Dinosaurs of the Air. The Johns Hopkins University Press. London. p.134-
135.
• Videler, J. 2005. Avian Flight. Oxford University Press. Oxford. P. 2, 91-98.
• Zhou, Z. 2004. “The origin and early evolution of birds: discoveries, disputes, and
Perspectives from fossil evidence.” Naturwissenschaften. 91: 455-471.

• Flight of the Archaeopteryx
• Arboreal argument
Processes of
Population genetic

developmental
biology (Evo-devo)
concepts

Modes of


Retrieved from "http://en.wikipedia.org/wiki/Origin_of_avian_flight"
Categories: Evolution by phenotype | Ornithology | Bird flight | Aerodynamics | Locomotion | Flight

W000
Monogamous pairing in animals


improve this article if you can. The talk page may contain suggestions. (August 2007)
This article requires authentication or verification by an expert. Please assist in

recruiting an expert or improve this article yourself. See the talk page for details. (May 2008)
Close relationships
Types of relationships
Family · Marriage
Husband · Wife
Soulmate · Significant other
Siblings · Cousin
Domestic partnership
Widowhood
Boyfriend · Girlfriend
Cohabitation · Casual
Romantic friendship · Sexual partner
Friendship · Kinship
Monogamy · Same-sex relationship
Non-monogamy · Open marriage
Polyamory · Polyfidelity · Polygamy
Mistress (lover) · Cicisbeo · Concubinage · Courtesan ·
Romantic relationship events
Bonding · Breaking up · Courtship · Dating · Divorce · Infidelity · Mating · Meet market · Romance ·
Separation · Singles event · Transgressing · Wedding
Feelings and emotions
Affinity · Attachment · Compersion · Intimacy · Jealousy · Limerence · Love · Passion · Platonic love ·
Psychology of sexual monogamy
Human practices
Bride price (Dower · Dowry) · Hypergamy · Infidelity · Sexuality
Relationship abuse
Child abuse · Elder abuse · Dating abuse · Infidelity · Spousal abuse ·
v·d·e
Monogamous pairing in animals refers to the natural history of mating systems in which species pair
bond to raise offspring. This is associated, usually implicitly, with sexual monogamy[citation needed].
Contents
[hide]
• 1 Animals
• 1.1 Sexual dimorphism
• 1.2 Testis size
• 1.3 Monogamy as a Best Response
• 2 See also
• 3 References
• 4 Bibliography
[edit] Animals
The evolution of mating systems in animals has received an enormous amount of attention from
biologists. This section briefly reviews three main findings about the evolution of monogamy in animals.
The amount of social monogamy in animals varies across taxa, with over 90 percent of birds
engaging in social monogamy but only 7 percent of mammals engaging in social monogamy.
This list is not complete. Other factors may also contribute to the evolution of social monogamy.
Moreover, different sets of factors may explain the evolution of social monogamy in different species. There
is no one-size-fits-all explanation of why different species evolved monogamous mating systems.
[edit] Sexual dimorphism

Sexual dimorphism refers to differences in body characteristics between males and females. A
frequently studied type of sexual dimorphism is body size. Males typically have larger bodies than females. In
some species, however, females have larger bodies than males. Sexual dimorphism in body size has been
linked to mating behavior. [1] [2] [3] [4] In polygynous species, males compete for control over sexual access
to females. Large males have an advantage in the competition for access to females, and they consequently
pass their genes along to a greater number of offspring. This eventually leads to large differences in body
size between males and females. Polygynous males are often 1.5 to 2.0 times larger in size than females. In
monogamous species, on the other hand, males and females have more equal access to mates, so there is
little or no sexual dimorphism in body size. From a new biological point of view, monogamy could result from
mate guarding and is engaged as a result of sexual conflict[5] following the hypothesis of mutual destruction.
Some researchers have attempted to infer the evolution of human mating systems from the evolution
of sexual dimorphism. Several studies have reported a large amount of sexual dimorphism in
Australopithecus, an evolutionary ancestor of human beings that lived between 2 and 4 million years ago. [2]
[3] [6] [7] These studies raise the possibility that Australopithecus had a polygamous mating system. Sexual
dimorphism then began to decrease. Studies suggest sexual dimorphism reached modern human levels
around the time of Homo Erectus 0.5 to 2 million years ago. [2] [3] [6] [8] This line of reasoning suggests
human ancestors started out polygamous and began the transition to monogamy somewhere between 0.5
million and 2 million years ago.
Attempts to infer the evolution of monogamy based on sexual dimorphism remain controversial for
three reasons:
• The skeletal remains of Australopithecus are quite fragmentary. This makes it difficult to
identify the sex of the fossils. Researchers sometimes identify the sex of the fossils by
their size, which, of course, can exaggerate findings of sexual dimorphism.
• Recent studies using new methods of measurement suggest Australopithecus had the
same amount of sexual dimorphism as modern humans.[9][10] This raises questions
about the amount of sexual dimorphism in Australopithecus.
• Humans may have been partially unique in that selection pressures for sexual
dimorphism might have been related to the new niches that humans were entering at
the time, and how that might have interacted with potential early cultures and tool use. If
these early humans had a differentiation of gender roles, with men hunting and women
gathering, selection pressures in favor of increased size may have been distributed
unequally between the sexes.
• Even if future studies clearly establish sexual dimorphism in Australopithecus, other
studies have shown the relationship between sexual dimorphism and mating system is
unreliable.[1][2] Some polygamous species show little or no sexual dimorphism. Some
monogamous species show a large amount of sexual dimorphism.
Studies of sexual dimorphism raise the possibility that early human ancestors were polygamous
rather than monogamous. But this line of research remains highly controversial. It may be that early human
ancestors showed little sexual dimorphism, and it may be that sexual dimorphism in early human ancestors
had no relationship to their mating systems.
[edit] Testis size

The relative sizes of male testes often reflect mating systems.[11][12][13][14] In species with
promiscuous mating systems, where many males mate with many females, the testes tend to be relatively
large. This appears to be the result of sperm competition. Males with large testes produce more sperm and
thereby gain an advantage impregnating females. In polygynous species, where one male controls sexual
access to females, the testes tend to be small. One male defends exclusive sexual access to a group of
females and thereby eliminates sperm competition.
Studies of primates, including humans, support the relationship between testis size and mating
system.[13][14][15] Chimpanzees, which have a promiscuous mating system, have large testes compared to
other primates. Gorillas, which have a polygynous mating system, have smaller testes than other primates.
Humans, which have a socially monogamous mating system, accompanied by moderate amounts of sexual
non-monogamy (see incidence of monogamy), have moderately sized testes. The moderate amounts of
sexual non-monogamy in humans may result in a low to moderate amount of sperm competition. Also,
notably, in the case of an avowedly sexually monogamous society, the occurrence of sexual nonmonogamy
is typically culturally stigmatized, and therefore detecting its prevalence is inherently difficult, if indeed it is at
all possible. At best, such statistics can be viewed as general approximations with a wide margin of error.
Although testis size in humans is consistent with the modern pattern of social monogamy
accompanied by moderate sexual non-monogamy, this fact reveals little about when the modern pattern
evolved. Did Homo Erectus have testes similar in size to modern humans? What about Australopithecus? It
is not possible to measure the size of testes in the fossil remains of human ancestors. This limits the
usefulness of testis size in understanding the evolution of monogamy in humans.
[edit] Monogamy as a Best Response

In species where the young are particularly vulnerable and may benefit from protection by both
parents, monogamy may be an optimal strategy. The selection factors in favor of different mating strategies
for a species of animal, however, may potentially operate on a large number of factors throughout that
animal's life cycle. For instance, with many species of bear, the female will often drive a male off soon after
mating, and will later guard her cubs from him similar to that of other animals after they are born. It is thought
that this might be due to fact that too many bears close to one another may deplete an area of food resources
for the relatively small but growing cubs. Monogamy could be social but rarely genetic. Thierry Lodé[16]
argued that monogamy should result from conflict of interest between the sexes called sexual conflict.
Organized from territory defense and mate guarding, monogamy appears as a response of male for the
control of female sexuality, but exclusive monogamy would be rare and the biological evolution would
privilege the diversity of sexual behaviors.
[edit] See also

Monogamy topics:
• Monogamy
• Varieties of monogamy
• Incidence of monogamy
• Value of monogamy
• Psychology of monogamy
Evolution topics:
• Evolution
• Evolution of sex
• Animal sexuality
• Human evolution
• History of human sexuality
• r/K selection theory
• Sexual conflict
[edit] References
1. ^ a b Owens, I.P.F. & Hartley, I.R. (1998). "Sexual dimorphism in birds: why are there so
many different forms of dimorphism?" Proceedings of the Royal Society of London B, 265, 397-407.
2. ^ a b c d Frayer, D.W. & Wolpoff, M.H. (1985). "Sexual dimorphism". Annual Review of
Anthropology, 14, 429-473.
3. ^ a b c Geary, D.C., & Flinn, M.V. (2001). "Evolution of human parental behavior and the
human family". Parenting: Science and Practice, 1, 5-61.
4. ^ Dunn, P.O., Whittingham, L.A., & Pitcher, T.E. (2001). "Mating systems, sperm competition,
and the evolution of sexual dimorphism in birds". Evolution, 55, 161–175.
5. ^ T Lodé “la guerre des sexes chez les animaux” Eds O Jacob, Paris, 2006, ISBN 2-7381-
1901-8
6. ^ a b Flinn, M.V. & Ward, C.V. (2004). "Ontogeny and Evolution of the Social Child". In:
Origins of the social mind: Evolutionary psychology and child development , B. Ellis & D. Bjorklund
(Eds.), chapter 2, pp. 19-44. London: Guilford Press.
7. ^ Lockwood, C.A., Richmond, B.G., Jungers, W.L., & Kimbel, W.H. (1996). "Randomization
procedures and sexual dimorphism in Australopithecus afarensis". Journal of Human Evolution, 31,
537-548.
8. ^ Arsuaga, J.L., Carretero, J.M., Lorenzo, C., Gracia, A., Martínez, I., Bermúdez de Castro,
J.M., & Carbonell, E. (1997). "Size variation in Middle Pleistocene humans". Science, 277, 1086-
1088.
9. ^ Reno, P.L., Meindl, R.S., McCollum, M.A., & Lovejoy, C.O. (2003). "Sexual dimorphism in
Australopithecus afarensis was similar to that of modern humans". Proceedings of the National
Academy of Sciences, 100, 9404-9409.
10.^ Larsen, C.S. (2003). "Equality for the sexes in human evolution? Early hominid sexual
dimorphism and implications for mating systems and social behavior". Proceedings of the National
Academy of Sciences, 100, 9103-9104.
11.^ Pitcher, T.E., Dunn, P.O., & Whittingham, L.A. (2005). "Sperm competition and the
evolution of testes size in birds". Journal of Evolutionary Biology, 18, 557–567.
12.^ Simmons, L.W., Firman, R.E.C., Rhodes, G., & Peters, M. (2004). "Human sperm
competition: testis size, sperm production and rates of extrapair copulations". Animal Behaviour, 68,
297-302.
13.^ a b Dixson, A., & Anderson, M. (2001). "Sexual selection and the comparative anatomy of
reproduction in monkeys, apes, and human beings". Annual Review of Sex Research, 12, 121-144.
14.^ a b Harcourt, A.H., Harvey, P.H., Larson, S.G., & Short, R.V. (1981). "Testis weight, body
weight and breeding system in primates". Nature, 293, 55-57.
15.^ T. R. Birkhead (2000), Promiscuity: an evolutionary history of sperm competition. Harvard
University Press, Cambridge, Mass.
16.^ Thierry Lodé "La Guerre des sexes chez les animaux" Eds O Jacob, Paris, 2006
[edit] Bibliography
• Korotayev, Andrey (2004). World Religions and Social Evolution of the Old World Oikumene
Civilizations: A Cross-cultural Perspective (First Edition ed.). Lewiston, New York: Edwin Mellen
Press. ISBN 0-7734-6310-0.
Retrieved from "http://en.wikipedia.org/wiki/Monogamous_pairing_in_animals"
Categories: Evolutionary biology | Monogamy | Mating systems

W000
Evolution of flagella

challenged and removed. (October 2007)
The evolution of flagella is of great interest to biologists because the three known varieties of flagella
(eukaryotic, bacterial, and archaeal) each represent a sophisticated cellular structure that requires the
interaction of many different systems.
Contents
[hide]
• 1 Eukaryotic flagellum
• 1.1 Symbiotic/endosymbiotic/exogenous models
• 1.2 Endogenous, autogenous and direct filiation
models
• 2 Bacterial flagellum
• 3 Archaeal flagellum
• 4 Further research
• 5 References
[edit] Eukaryotic flagellum

There are two competing groups of models for the evolutionary origin of the eukaryotic flagellum
(referred to as cilium below to distinguish it from its bacterial counterpart).
[edit] Symbiotic/endosymbiotic/exogenous models

These models argue some version of the idea that the cilium evolved from a symbiotic spirochete
that attached to a primitive eukaryote or archaebacterium (archaea). The modern version of the hypothesis
was first proposed by Lynn Margulis.[1] The hypothesis, though very well publicized, was never widely
accepted by the experts,[citation needed] in contrast to Margulis' arguments for the symbiotic origin of
mitochondria and chloroplasts.[citation needed]
The primary point in favor of the symbiotic hypothesis is that there are eukaryotes that use symbiotic
spirochetes as their motility organelles (some parabasalids inside termite guts, such as Mixotricha and
Trichonympha). While this is an example of co-option and the flexibility of biological systems, none of the
proposed homologies that have been reported between cilia and spirochetes have stood up to further
scrutiny. The homology of tubulin to the bacterial replication/cytoskeletal protein FtsZ is a major argument
against Margulis, as FtsZ is apparently found native in archaea, providing an endogenous ancestor to tubulin
(as opposed to Margulis' hypothesis, that an archaea acquired tubulin from a symbiotic spirochete).[ citation
needed]
At present the symbiotic hypothesis for the origin of cilia seems to be limited to Margulis and a few of
her associates.[citation needed] Margulis is, though, still strongly promoting and publishing a revised version
of her hypothesis.[2]
[edit] Endogenous, autogenous and direct filiation models
Contrasting with the symbiotic models, these models argue that cilia developed from pre-existing
components of the eukaryotic cytoskeleton (which has tubulin and dynein – also used for other functions) as
an extension of the mitotic spindle apparatus. The connection can still be seen, first in the various early-
branching single-celled eukaryotes that have a microtubule basal body, where microtubules on one end form
a spindle-like cone around the nucleus, while microtubules on the other end point away from the cell and
form the cilium. A further connection is that the centriole, involved in the formation of the mitotic spindle in
many (but not all) eukaryotes, is homologous to the cilium, and in many cases is the basal body from which
the cilium grows.
An apparent intermediate stage between spindle and cilium would be a non-swimming appendage
made of microtubules with a selectable function like increasing surface area, helping the protozoan to remain
suspended in water, increasing the chances of bumping into bacteria to eat, or serving as a stalk attaching
the cell to a solid substrate.
Regarding the origin of the individual protein components, an interesting paper on the evolution of
dyneins[3][4] shows that the more complex protein family of ciliary dynein has an apparent ancestor in a
simpler cytoplasmic dynein (which itself has evolved from the AAA protein family that occurs widely in all
archea, bacteria and eukaryotes). Long-standing suspicions that tubulin was homologous to FtsZ (based on
very weak sequence similarity and some behavioral similarities) were confirmed in 1998 by the independent
resolution of the 3-dimensional structures of the two proteins.
[edit] Bacterial flagellum

An approach to the evolutionary origin of the bacterial flagellum is suggested by the fact that a subset
of flagellar components is similar to the Type III secretory and transport system.
All currently known nonflagellar Type III transport systems serve the function of injecting toxin into
eukaryotic cells. It is hypothesised that the flagellum evolved from the type three secretory system. For
example, the bubonic plague bacterium Yersinia pestis has an organelle assembly very similar to a complex
flagellum, except that is missing only a few flagellar mechanisms and functions, such as a needle to inject
toxins into other cells. It is also a possibility that the flagellum could have evolved from a currently
undiscovered system with similar flagellar traits or a currently extinct organelle/organism.[ citation needed] As
such, the type three secretory system supports the hypothesis that the flagellum evolved from a simpler
bacterial secretion system.
[edit] Archaeal flagellum

The recently elucidated archaeal flagellum is analogous, not homologous, to the bacterial one. In
addition to no sequence similarity being detected between the genes of the two systems, the archaeal
flagellum appears to grow at the base rather than the tip, and is about 15 nanometers (nm) in diameter rather
than 20. Sequence comparison indicates that the archaeal flagellum is homologous to Type IV pili.[5] (pili are
filamentous structures outside the cell). Interestingly, some Type IV pili can retract. Pilus retraction provides
the driving force for a different form of bacterial motility called "twitching" or "social gliding" which allows
bacterial cells to crawl along a surface. Thus Type IV pili can, in different bacteria, promote either swimming
or crawling. Type IV pili are assembled through the Type II transport system. So far, no species of bacteria is
known to use its Type IV pili for both swimming and crawling.
[edit] Further research

Testable outlines exist for the origin of each of the three motility systems, and avenues for further
research are clear; for prokaryotes, these avenues include the study of secretion systems in free-living,
nonvirulent prokaryotes. In eukaryotes, the mechanisms of both mitosis and cilial construction, including the
key role of the centriole, need to be much better understood. A detailed survey of the various nonmotile
appendages found in eukaryotes is also necessary. Finally, the study of the origin of all of these systems
would benefit greatly from a resolution of the questions surrounding deep phylogeny – what are the most
deeply branching organisms in each domain, and what are the interrelationships between the domains (see
Last universal ancestor)?
[edit] References
1. ^ Sagan L (March 1967). "On the origin of mitosing cells". Journal of Theoretical Biology 14
(3): 255–74. doi:10.1016/0022-5193(67)90079-3. PMID 11541392.
2. ^ Margulis, Lynn (1998). Symbiotic planet: a new look at evolution. New York: Basic Books.
ISBN 978-0-465-07271-2. OCLC 39700477. [page needed]
3. ^ Gibbons IR (1995). "Dynein family of motor proteins: present status and future questions".
Cell Motility and the Cytoskeleton 32 (2): 136–44. doi:10.1002/cm.970320214. PMID 8681396.
4. ^ Asai DJ, Koonce MP (May 2001). "The dynein heavy chain: structure, mechanics and
evolution". Trends in Cell Biology 11 (5): 196–202. doi:10.1016/S0962-8924(01)01970-5.
PMID 11316608.
5. ^ Faguy DM, Jarrell KF, Kuzio J, Kalmokoff ML (January 1994). "Molecular analysis of
archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria".
Canadian Journal of Microbiology 40 (1): 67–71. doi:10.1139/m94-011. PMID 7908603.

• Wong, Tim; Amidi, Arezou; Dodds, Alexandra; Siddiqi, Sara; Wang, Jing; Yep, Tracy;
Tamang, Dorjee G.; Saier, Milton H. (2007). "Evolution of the Bacterial Flagellum: Cumulative
evidence indicates that flagella developed as modular systems, with many components deriving from
other systems". Microbe 2 (7): 335–40. http://saier-144-
51.ucsd.edu/~saier/bimm130/reading130/week4/paper4c.pdf.
• Jones, Dan (16 February 2008). "Uncovering the evolution of the bacterial flagellum". New
Scientist. http://www.newscientist.com/article/mg19726431.900-uncovering-the-evolution-of-the-
bacterial-flagellum.html. Retrieved 1 December 2009.
• Hall JL, Ramanis Z, Luck DJ (October 1989). "Basal body/centriolar DNA: molecular genetic
studies in Chlamydomonas". Cell 59 (1): 121–32. doi:10.1016/0092-8674(89)90875-1.
PMID 2571418.
• Pallen MJ, Matzke NJ (October 2006). "From The Origin of Species to the origin of bacterial
flagella". Nature Reviews. Microbiology 4 (10): 784–90. doi:10.1038/nrmicro1493. PMID 16953248.
• Margulis, Lynn (1981). Symbiosis in cell evolution: life and its environment on the early Earth .
San Francisco: W. H. Freeman. ISBN 978-0-7167-1255-8. OCLC 6982472.
• Margulis L (April 1993). "The Inheritance of Acquired Microbes". Citation Classic
Commentaries 36 (16): 9–10.
http://www.garfield.library.upenn.edu/classics1993/A1993KK54300001.pdf.

• Flagellum Evolution at The pandas thumb.
• Matzke NJ (September 2006). "Evolution in (Brownian) space: a model for the origin of the
bacterial flagellum". Talk Reason. http://www.talkdesign.org/faqs/flagellum.html. Retrieved 1
December 2009.
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Categories: Evolution by phenotype

W000
Models of DNA evolution


A number of different Markov models of DNA sequence evolution have been proposed. These
substitution models differ in terms of the parameters used to describe the rates at which one nucleotide
replaces another during evolution. These models are frequently used in molecular phylogenetic analyses. In
particular, they are used during the calculation of likelihood of a tree (in Bayesian and maximum likelihood
approaches to tree estimation) and they are used to estimate the evolutionary distance between sequences
from the observed differences between the sequences.
Contents
[hide]
• 1 Introduction
• 2 DNA evolution as a continuous-time Markov chain
• 2.1 Continuous-time Markov chains
• 2.2 Deriving the dynamics of substitution
• 2.3 Ergodicity
• 2.4 Time reversibility
• 2.5 Scaling of branch lengths
• 3 Most common models of DNA evolution
• 3.1 JC69 model (Jukes and Cantor, 1969)[1]
• 3.2 K80 model (Kimura, 1980)[2]
• 3.3 F81 model (Felsenstein 1981)[3]
• 3.4 HKY85 model (Hasegawa, Kishino and Yano
1985)[4]
• 3.5 T92 model (Tamura 1992)[5]
• 3.6 TN93 model (Tamura and Nei 1993)[6]
• 3.7 GTR: Generalised time-reversible
• 4 References
• 4.1 Further reading
[edit] Introduction
These models are phenomenological descriptions of the evolution of DNA as a string of four discrete
states. These Markov models do not explicitly depict the mechanism of mutation nor the action of natural
selection. Rather they describe the relative rates of different changes. For example, mutational biases and
purifying selection favoring conservative changes are probably both responsible for the relatively high rate of
transitions compared to transversions in evolving sequences. However, in the Kimura (K80) model described
below merely attempts to capture the effect of both forces in a parameter that reflects the relative rate of
transitions to transversions.
Evolutionary analyses of sequences are conducted on a wide variety of time scales. Thus, it is
convenient to express these models in terms of the instantaneous rates of change between different states
(the Q matrices below). If we are given a starting (ancestral) state at one position, the model's Q matrix and a
branch length expressing the expected number of changes to have occurred since the ancestor, then we can
derive the probability of the descendant sequence having each of the four states. The mathematical details of
this transformation from rate-matrix to probability matrix are described in the mathematics of substitution
models section of the substitution model page. By expressing models in terms of the instantaneous rates of
change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or
each comparison if the analysis involves many pairwise sequence comparisons).
The models described on this page describe the evolution of a single site within a sequences. They
are often used to for analyzing the evolution of an entire locus by making the simplifying assumption that
different sites evolve independently and are identically distributed. This assumption may be justifiable if the
sites can be assumed to be evolving neutrally. If the primary effect of natural selection on the evolution of the
sequences is to constrain some sites, then models of among-site rate-heterogeneity can be used. This
approaches allows one to estimate only one matrix of relative rates of substitution, and another set of
parameters describing the variance in the total rate of substitution across sites.
[edit] DNA evolution as a continuous-time Markov chain

[edit] Continuous-time Markov chains
Continuous-time Markov chains have the usual transition matrices which are, in addition,
parameterized by time, . Specifically, if are the states, then the transition matrix
where each individual entry, refers to the probability that state
will change to state in time .

Example: We would like to model the substitution process in DNA sequences (i.e. Jukes–Cantor,
Kimura, etc.) in a continuous-time fashion. The corresponding transition matrices will look like:
where the top-left and bottom-right 2 × 2 blocks correspond to transition probabilities and the top-
right and bottom-left 2 × 2 blocks corresponds to transversion probabilities.
Assumption: If at some time , the Markov chain is in state , then the
probability that at time , it will be in state depends only upon ,
and . This then allows us to write that probability as .

Theorem: Continuous-time transition matrices satisfy:
[edit] Deriving the dynamics of substitution

Consider a DNA sequence of fixed length m evolving in time by base replacement. Assume that the
processes followed by the m sites are Markovian independent, identically distributed and constant in time.
For a fixed site, let
be the column vector of probabilities of states and
at time . Let
be the state-space. For two distinct
, let
be the transition rate from state to state . Similarly, for any ,

let:
The changes in the probability distribution for small increments of time are
given by:
In other words (in frequentist language), the frequency of 's at time is equal
to the frequency at time minus the frequency of the lost 's plus the frequency of the
newly created 's.
Similarly for the probabilities . We can write these compactly as:
where,
or, alternately:
where, is the rate matrix. Note that by definition, the columns of sum to
zero.
[edit] Ergodicity
If all the transition probabilities, are positive, i.e. if all states communicate,
then the Markov chain has a stationary distribution where each is the proportion of
time spent in state after the Markov chain has run for infinite time, and this probability does not
depend upon the initial state of the process. Such a Markov chain is called, ergodic. In DNA evolution, under
the assumption of a common process for each site, the stationary frequencies, correspond to
equilibrium base compositions.
Definition A Markov process is stationary if its current distribution is the stationary distribution, i.e.
Thus, by using the differential equation above,
[edit] Time reversibility

Definition: A stationary Markov process is time reversible if (in the steady state) the amount of
change from state to is equal to the amount of change from to
, (although the two states may occur with different frequencies). This means that:
Not all stationary processes are reversible, however, almost all DNA evolution models assume time
reversibility, which is considered to be a reasonable assumption.
Under the time reversibility assumption, let , then it is easy to see that:
Definition The symmetric term is called the exchangeability between states
and . In other words, is the fraction of the frequency of state
that results as a result of transitions from state to state .
Corollary The 12 off-diagonal entries of the rate matrix, (note the off-diagonal entries
determine the diagonal entries, since the rows of sum to zero) can be completely determined by
9 numbers; these are: 6 exchangeability terms and 3 stationary frequencies , (since the
stationary frequencies sum to 1).
[edit] Scaling of branch lengths

By comparing extant sequences, one can determine the amount of sequence divergence. This raw
measurement of divergence provides information about the number of changes that have occurred along the
path separating the sequences. The simple count of differences (the Hamming distance) between sequences
will often underestimate the number of substitution because of multiple hits (see homoplasy). Trying to
estimate the exact number of changes that have occurred is difficult, and usually not necessary. Instead,
branch lengths (and path lengths) in phylogenetic analyses are usually expressed in the expected number of
changes per site. The path length is the product of the duration of the path in time and the mean rate of
substitutions. While their product can be estimated, the rate and time are not identifiable from sequence
divergence.
The descriptions of rate matrices on this page accurately reflect the relative magnitude of different
substitutions, but these rate matrices are not scaled such that a branch length of 1 yields one expected
change. This scaling can be accomplished by multiplying every element of the matrix by the same factor, or
simply by scaling the branch lengths. If we use the β to denote the scaling factor, and ν to denote the branch
length measured in the expected number of substitutions per site then βν is used the transition probability
formulae below in place of μt. Note that ν is a parameter to be estimated from data, and is referred to as the
branch length, while β is simply a number that can be calculated from the rate matrix (it is not a separate free
parameter).
The value of β can be found by forcing the expected rate of flux of states to 1. The diagonal entries of
the rate-matrix (the Q matrix) represent -1 times the rate of leaving each state. For time-reversible models,
we know the equilibrium state frequencies (these are simply the π i parameter value for state i). Thus we can
find the expected rate of change by calculating the sum of flux out of each state weighted by the proportion of
sites that are expected to be in that class. Setting β to be the reciprocal of this sum will guarantee that scaled
process has an expected flux of 1:
For example, in the Jukes-Cantor, the scaling factor would be 4/(3μ)' because the rate of leaving
each state is 3μ/4.
[edit] Most common models of DNA evolution

[edit] JC69 model (Jukes and Cantor, 1969)[1]
JC69 is the simplest substitution model. There are several assumptions. It assumes equal base
frequencies ( ) and equal mutation rates. The only parameter of this model is therefore μ, the
overall substitution rate.
When branch length, ν, is measured in the expected number of changes per site then:
The Jukes-Cantor estimate of the evolutionary distance (in terms of the expected number of
changes) between two sequences is given by
where p is the proportion of sites that differ between the two sequences. The p in this formula is
frequently referred to as the p-distance. It is a sufficient statistic for calculated the Jukes-Cantor distance
correction, but is not sufficient for the calculation of the evolutionary distance under the more complex
models that follow (also note that p used in subsequent formulae is not identical to the " p-distance").
[edit] K80 model (Kimura, 1980)[2]

The K80 model distinguishes between transitions (A <-> G, i.e. from purine to purine, or C <-> T, i.e.
from pyrimidine to pyrimidine) and transversions (from purine to pyrimidine or vice versa). In Kimura's original
description of the model the α and β were used denote the rates of these types of substitutions, but it is more
now common to set the rate of transversions to 1 and use κ to denote the transition/transversion rate ratio (as
is done below). The K80 model assumes that all of the bases are equally frequent ( πT=πC=πA=πG=0.25).
Rate matrix
The Kimura two-parameter distance is given by:
where p is the proportion of sites that show transitional differences and q is the proportion of sites
that show transversional differences.
[edit] F81 model (Felsenstein 1981)[3]
Felsenstein's 1981 model is an extension of the JC69 model in which base frequencies are allowed
to vary from 0.25 ( )
Rate matrix:
When branch length, ν, is measured in the expected number of changes per site then:
[edit] HKY85 model (Hasegawa, Kishino and Yano 1985)[4]

The HKY85 model can be thought of as combining the extensions made in the Kimura80 and
Felsenstein81 models. Namely, it distinguishes between the rate of transitions and transversions (using the κ
parameter), and it allows unequal base frequencies ( ). Felsenstein described
an equivalent model in 1984 using a different parameterization; thus, the model is sometimes referred to as
the F84 model.
Rate matrix
If we express the branch length, ν in terms of the expected number of changes per site then:
and formula for the other combinations of states can be obtained by substituting in the appropriate
base frequencies.
[edit] T92 model (Tamura 1992)[5]
T92 is a simple mathematical method developed to estimate the number of nucleotide substitutions
per site between two DNA sequences, by extending Kimura’s (1980) two-parameter method to the case
where a G+C-content bias exists. This method will be useful when there are strong transition-transversion
and G+C-content biases, as in the case of Drosophila mitochondrial DNA. (Tamura 1992)
One frequency only πGC
Rate matrix
The evolutionary distance between two noncoding sequences according to this model is given by
where h = 2θ(1 − θ) where is the GC content.
[edit] TN93 model (Tamura and Nei 1993)[6]

The TN93 model distinguishes between the two different types of transition - i.e. (A <-> G) is allowed
to have a different rate to (C<->T). Transversions are all assumed to occur at the same rate, but that rate is
allowed to be different from both of the rates for transitions.
TN93 also allows unequal base frequencies ( ).
Rate matrix
[edit] GTR: Generalised time-reversible

GTR is the most general neutral, independent, finite-sites, time-reversible model possible. It was first
described in a general form by Simon Tavaré in 1986.[ citation needed]
The GTR parameters consist of an equilibrium base frequency vector, Π = (π 1,π2,π3,π4), giving the
frequency at which each base occurs at each site, and the rate matrix
Therefore, GTR (for four characters, as is often the case in phylogenetics) requires 6 substitution rate
parameters, as well as 4 equilibrium base frequency parameters. However, this is usually eliminated down to
9 parameters plus μ, the overall number of substitutions per unit time. When measuring time in substitutions
(μ=1) only 9 free parameters remain.
In general, to compute the number of parameters, one must count the number of entries above the
diagonal in the matrix, i.e. for n trait values per site , and then add n for the equilibrium base
frequencies, and subtract 1 because μ is fixed. One gets
For example, for an amino acid sequence (there are 20 "standard" amino acids that make up
proteins), one would find there are 209 parameters. However, when studying coding regions of the genome,
it is more common to work with a codon substitution model (a codon is three bases and codes for one amino
acid in a protein). There are 43 = 64 codons, but the rates for transitions between codons which differ by
more than one base is assumed to be zero. Hence, there are

parameters.
[edit] References
1. ^ Jukes TH and Cantor CR (1969). Evolution of Protein Molecules. New York: Academic
Press. p. 21–132.
2. ^ Kimura M (1980). "A simple method for estimating evolutionary rates of base substitutions
through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16: 111–120.
3. ^ Felsenstein J (1981). "Evolutionary trees from DNA sequences: a maximum likelihood
approach". Journal of Molecular Evolution 17: 368–376.
4. ^ Hasegawa M, Kishino H, Yano T (1985). "Dating of human-ape splitting by a molecular
clock of mitochondrial DNA". Journal of Molecular Evolution 22: 160–174.
5. ^ Tamura K (1992). "Estimation of the number of nucleotide substitutions when there are
strong transition-transversion and G+C content biases". Molecular Biology and Evolution 9: 678–687.
http://mbe.oxfordjournals.org/cgi/content/abstract/9/4/678.
6. ^ Tamura K, Nei M (1993). "Estimation of the number of nucleotide substitutions in the
control region of mitochondrial DNA in humans and chimpanzees". Molecular Biology and Evolution
10: 512–526. http://mbe.oxfordjournals.org/cgi/content/abstract/10/3/512.
introducing more precise citations where appropriate. (November 2010)
• Gu X, Li W (1992). "Higher rates of amino acid substitution in rodents than in man".
Molecular Phylogenetics and Evolution 1: 211–214. doi:10.1016/1055-7903(92)90017-B.
• Li W-H, Ellsworth DL, Krushkal J, Chang BH-J, Hewett-Emmett D (1996). "Rates of
nucleotide substitution in primates and rodents and the generation-time effect hypothesis". Molecular
Phylogenetics and Evolution 5: 182–187. doi:10.1006/mpev.1996.0012.

• DAWG: DNA Assembly With Gaps — free software for simulating sequence evolution
[hide]v · d · eTopics in molecular evolution
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selection selection · Stabilizing selection · Selective sweep
Models Models of DNA evolution · Models of nucleotide substitution · Allele

frequency · Ka/Ks ratio · Tajima's D
Molecular Gene conversion · Gene duplication · Silent mutation · Synonymous
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W000
Origin of the domestic dog


This article's introduction section may not adequately summarize its contents. To
comply with Wikipedia's lead section guidelines, please consider expanding the lead to
provide an accessible overview of the article's key points. (August 2010)
A dog in Diego Velázquez's Las Meninas
The origin of the domestic dog (Canis lupus familiaris) began with the domestication of the gray wolf
(Canis lupus) several tens of thousands of years ago.[citation needed] Domesticated dogs provided early
humans with a guard animal, a source of food, fur, and a beast of burden. The process continues to this day,
as the intentional cross-breeding of dogs continues, to create the so called "designer dogs".
Contents
[hide]
• 1 Domestication
• 1.1 Possible routes
• 1.2 Archaeology
• 1.3 DNA evidence
• 1.4 Experimental evidence
• 1.5 Before the wolf
• 2 Specialization
• 2.1 Neoteny in the rapid evolution of diverse dog
breeds
• 3 Notes
• 4 References
[edit] Domestication
The earliest fossil carnivores that can be linked with some certainty to canids are the Eocene Miacids
some 56 to 38 million years ago. From the miacids evolved the cat-like (Feloidea) and dog-like (Canoidea)
carnivores. Most important to the ancestry of the dog was the canoid line, leading from the coyote-sized
Mesocyon of the Oligocene (38 to 24 million years ago) to the fox-like Leptocyon and the wolf-like Tomarctus
that wandered North America some 10 million years ago. From the time of Tomarctus, dog-like carnivores
have expanded throughout the world.[1]
[edit] Possible routes
Comparative illustration of wolf and dog tracks

• Orphaned wolf-cubs: Studies have shown that some wolf pups taken at an early age and
reared by humans are easily tamed and socialized.[2] At least one study has demonstrated that adult
wolves can be successfully socialized.[3] However, according to other researchers attempts to
socialize wolves after the pups reach 21 days of age are very time-consuming and seldom practical
or reliable in achieving success.[4] Many scientists believe that humans adopted orphaned wolf cubs
and nursed them alongside human babies.[5][6] Once these early adoptees started breeding among
themselves, a new generation of tame "wolf-like" domestic animals would result which would, over
generations of time, become more dog-like.[7]
• The Promise of Food/Self Domestication : Early wolves would, as scavengers, be attracted to
the refuse left at human campsites. Dr. Raymond Coppinger of Hampshire College (Massachusetts)
argues[8] that those wolves that were more successful at interacting with humans would pass these
traits onto their offspring, eventually creating wolves with a greater propensity to be domesticated.
The "most social and least fearful" dogs were the ones who were kept around the human living
areas, helping to breed those traits that are still recognized in dogs today.[6] Coppinger believes that
a behavioral characteristic called "flight distance" was crucial to the transformation from wild wolf to
the ancestors of the modern dog. It represents how close an animal will allow humans (or anything
else it perceives as dangerous) to get before it runs away. Animals with shorter flight distances will
linger, and feed, when humans are close by; this behavioral trait would have been passed on to
successive generations, and amplified, creating animals that are increasingly more comfortable
around humans. "My argument is that what domesticated—or tame—means is to be able to eat in the
presence of human beings. That is the thing that wild wolves can't do."[9] Furthermore, selection for
domesticity had the side effect of selecting genetically related physical characteristics, and behavior
such as barking. Hypothetically, wolves separated into two populations–the village-oriented
scavengers and the packs of hunters. The next steps have not been defined, but selective pressure
must have been present to sustain the divergence of these populations.
• As a beast of burden: North American Indians used dog-sized travois before adapting the
horse for this purpose, and huskies are famous for pulling sleds for Inuit communities. It is very
probable that the dog was the original beast of burden before the domestication of the horse or ox.
• Dogs as a source of food and fur: While, currently, most societies have difficulty thinking of
dogs (or wolves) as a meat animal, it is conceivable that the human-canine bond was also fostered
by humanity's use of dogs as a source of meat and fur.[10]
[edit] Archaeology
Archaeology has placed the earliest known domestication at potentially 30,000 BC,[11][12] and with
certainty at 7,000 BC.[13] Other evidence suggests that dogs were first domesticated in East Asia.[14]
Due to the difficulty in assessing the structural differences in bones, the identification of a domestic
dog based on cultural evidence is of special value. Perhaps the earliest clear evidence for this domestication
is the first dog found buried together with human from 12,000 years ago in Israel.[15][16]
Domestication of the wolf over time has produced a number of physical changes typical of all
domesticated mammals. These include: a reduction in overall size; changes in coat colouration and
markings; a shorter jaw initially with crowding of the teeth and, later, with the shrinking in size of the teeth; a
reduction in brain size and thus in cranial capacity (particularly those areas relating to alertness and sensory
processing, necessary in the wild); and the development of a pronounced “stop”, or vertical drop in front of
the forehead (brachycephaly). Certain wolf-like behaviors, such as the regurgitation of partially digested food
for the young, have also disappeared.
[edit] DNA evidence
Specialization–Breeds such as the Newfoundland and the Labrador were bred from large black
mixed-breed dogs, such as this one from Atlantic Canada
Prior to the use of DNA, researchers were divided into two schools of thought:
• Most supposed that these early dogs were descendants of tamed wolves, which interbred
and evolved into a domesticated species.
• Other scientists, while believing wolves were the chief contributor, suspected that jackals or
coyotes contributed to the dog's ancestry.
Carles Vila, who has conducted the most extensive study to date, has shown that DNA evidence has
ruled out any ancestor canine species except the wolf. Vila's team analyzed 162 different examples of wolf
DNA from 27 populations in Europe, Asia, and North America. These results were compared with DNA from
140 individual dogs from 67 breeds gathered from around the world. Using blood or hair samples, DNA was
extracted and genetic distance for mitochondrial DNA was estimated between individuals.[17]
Based on this DNA evidence, most of the domesticated dogs were found to be members of one of
four groups. The largest and most diverse group contains sequences found in the most ancient dog breeds,
including the dingo of Australia, the New Guinea Singing Dog, and many modern breeds, like the collie and
retriever. Other groups such as the German shepherd showed a closer relation to wolf sequences than to
those of the main dog group, suggesting that such breeds had been produced by crossing dogs with wild
wolves. It is also possible that this is evidence that dogs may have been domesticated from wolves on
different occasions and at different places. Vilà is still uncertain whether domestication happened once–after
which domesticated dogs bred with wolves from time to time–or whether it happened more than once.
A later study by Peter Savolainen et al. identified mitochondrial DNA evidence suggesting a common
origin from a single East Asian gene pool for all dog populations.[14] However, a more recent study by
Bridgett vonHoldt et al. using a much larger data set of nuclear markers points to the Middle East as the
source of most of the genetic diversity in the domestic dog and a more likely origin of domestication events.
[18]
The most puzzling fact of the DNA evidence is that the variability in molecular distance between dogs
and wolves seems greater than the 10,000–20,000 years assigned to domestication. Yet the process and
economics of domestication by humans only emerged later in this period in any case. Based upon the
molecular clock studies conducted, it would seem that dogs separated from the wolf lineage approximately
100,000 years ago. Although clear evidence for fossil dogs becomes obscure beyond about 14,000 years
ago, there are fossils of wolf bones in association with early humans from well beyond 100,000 years ago.
[19] Tamed wolves might have taken up with hunter-gatherers without changing in ways that the fossil record
could clearly capture. The influx of new genes from those crossings could very well explain the extraordinarily
high number of dog breeds that exist today, the researchers suggest. Dogs have much greater genetic
variability than other domesticated animals, such as cats, asserts Vilà.
Once agriculture took hold, dogs would have been selected for different tasks, their wolf-like natures
becoming a handicap as they became herders and guards. Molecular biologist Elaine Ostrander is of the
view that "When we became an agricultural society, what we needed dogs for changed enormously, and a
further and irrevocable division occurred at that point."[20] This may be the point that stands out in the fossil
record, when dogs and wolves began to develop noticeably different morphologies.
A recent study of African dogs found a high level of mtDNA diversity. The authors suggest that a new
view of the domestication of the dog may be needed.[21] A study by the Kunming Institute of Zoology found
that the domestic dog is descended from wolves tamed less than 16,300 years ago south of the Yangtse river
in China.[22] An older report said that all dog mitochondrial DNA came from three wild Asian female wolves.
[23]
[edit] Experimental evidence
As an experiment in the domestication of wolves, the "farm fox" experiment of Russian scientist
Dmitry Belyaev attempted to reenact of how domestication may have occurred.[24] Researchers working with
selectively breeding wild silver foxes over 35 generations and 40 years for the sole trait of friendliness to
humans, created more dog-like animals. The "domestic elite" foxes are much more friendly to humans and
actually seek human attention, but they also show new physical traits that parallel the selection for tameness,
even though the physical traits were not originally selected for. They include spotted or black-and-white
coats, floppy ears, tails that curl over their backs, the barking vocalization, and earlier sexual maturity. It was
reported "On average, the domestic foxes respond to sounds two days earlier and open their eyes one day
earlier than their non-domesticated cousins. More striking is that their socialization period has greatly
increased. Instead of developing a fear response at 6 weeks of age, the domesticated foxes don't show it
until 9 weeks of age or later. The whimpering and tail wagging is a holdover from puppyhood, as are the
foreshortened face and muzzle. Even the new coat colours can be explained by the altered timing of
development. One researcher found that the migration of certain melanocytes (which determine colour) was
delayed, resulting in a black and white 'star' pattern."
[edit] Before the wolf

There were significantly sized canid carnivores such as Hesperocyon gregarius. The Hesperocyon
was a slender, long tailed animal that inhabited the tropical rainforests of North America (about 37 million
years ago). The Hesperocyon hunted birds and their eggs, eating seeds and fruit as well. Another canid,
Borophaginae, hunted larger animals such as horses and camels. However, the Borophagines met an
untimely end about 5 million years ago when the climate cooled and meat supplies began to dwindle. About
2.5 million years ago, the borophagines became extinct. With the Borophagines gone, the other branch from
Hesperocyon, known as Leptocyon, began to thrive. The Leptocyon was a slender, narrow-snouted carnivore
whose teeth (unlike the Borophagines) had no special bone crushing ability. Leptocyons hunted smaller prey
and used the back lower carnassial teeth to crush plant matter. It was for this reason the Laptocyon surivived
and the Borophagine did not. In a few million years, the Laptocyon split into a number of different species,
leading to the canid family tree: South American Zorros (foxes), wolf-like carnivores (coyotes, jackals,
wolves), and fox-like carnivores (red fox and its relatives).[25][26]
[edit] Specialization
As humans migrated around the planet, a variety of dog forms migrated with them. The agricultural
revolution and subsequent urban revolution led to an increase in the dog population and a demand for
specialization. These circumstances would provide the opportunity for selective breeding to create
specialized types of working dogs and pets.
[edit] Neoteny in the rapid evolution of diverse dog breeds
The Bulldog is well known for its short muzzle and saggy skin on its face
This rapid evolution of dogs from wolves is an example of neoteny or paedomorphism. As with many
species, the young wolves are more social and less dominant than adults; therefore, the selection for these
characteristics, whether deliberate or inadvertent, is more likely to result in a simple retention of juvenile
characteristics into adulthood than to generate a complex of independent new changes in behavior. (This is
true of many domesticated animals, including humans themselves, who have many characteristics similar to
young bonobos.) This paedomorphic selection naturally results in a retention of juvenile physical
characteristics as well. Compared to wolves, many adult dog breeds retain such juvenile characteristics as
soft fuzzy fur, round torsos, large heads and eyes, ears that hang down rather than stand erect, etc.;
characteristics which are shared by most juvenile mammals, and therefore generally elicit some degree of
protective and nurturing behavior cross-species from most adult mammals, including humans, who term such
characteristics "cute" or "appealing".
A hunter with a large pack of beagles, a breed of hunting dogs, 1885

The example of canine neoteny goes even further, in that the various breeds are differently
neotenized according to the type of behavior that was selected.[27]
• Herding dogs exhibit the controlled characteristics of hunting dogs. Members of this group,
such as Border Collies, Belgian Malinois and German Shepherds use tactics of hunter and prey to
intimidate and keep control of herds and flocks. Their natural instinct to bring down an animal under
their charge is muted by training. Other members of the group, including Welsh Corgis, Canaan
dogs, and Cattle dogs herd with a more aggressive demeanor (such as biting and nipping at the
heels of the animals) and make use of body design to elude the defences of their charges.
• Gun dog breeds used in hunting—that is, pointers, setters, spaniels, and retrievers—have an
intermediate degree of paedomorphism; they are at the point where they share in the pack's hunting
behavior, but are still in a junior role, not participating in the actual attack. They identify potential prey
and freeze into immobility, for instance, but refrain from then stalking the prey as an adult predator
would do next; this results in the "pointing" behavior for which such dogs are bred. Similarly, they
seize dead or wounded prey and bring it back to the "pack", even though they did not attack it
themselves, that is, "retrieving" behavior. Their physical characteristics are closer to that of the
mature wild canine than the sheepdog breeds, but they typically do not have erect ears, etc.
The fad for intentionally cross-bred dogs, such as this poodle hybrid, have resulted in the label
"designer dogs"
• Scenthounds maintain an intermediate body type and behavior pattern that causes them to
actually pursue prey by tracking their scent, but tend to refrain from actual individual attacks in favor
of vocally summoning the pack leaders (in this case, humans) to do the job. They often have a
characteristic vocalization called a bay. Some examples are the Beagle, Bloodhound, Basset Hound,
Coonhound, Dachshund, Fox Hound, Otter Hound, and Harrier.
• Sighthounds, who pursue and attack perceived prey on sight, maintain the mature canine
size and some features, such as narrow chest and lean bodies, but have largely lost the erect ears of
the wolf and thick double layered coats. Some examples are the Afghan Hound, Borzoi, Saluki,
Sloughi, Pharaoh Hound, Azawakh, Whippet, and Greyhound.
• Mastiff-types are large dogs, both tall and massive with barrel-like chests, large bones, and
thick skulls. They have traditionally been bred for war, protection, and guardian work.
• Bulldog-types are medium sized dogs bred for combat against both wild and domesticated
animals. These dogs have a massive, square skull and large bones with an extremely muscular build
and broad shoulders.
• Terriers similarly have adult aggressive behavior, famously coupled with a lack of juvenile
submission, and display correspondingly adult physical features such as erect ears, although many
breeds have also been selected for size and sometimes dwarfed legs to enable them to pursue prey
in their burrows.
The least paedomorphic behavior pattern may be that of the basenji, bred in Africa to hunt alongside
humans almost on a peer basis; this breed is often described as highly independent, neither needing nor
appreciating a great deal of human attention or nurturing, often described as "catlike" in its behavior. It too
has the body plan of an adult canine predator. Of course, dogs in general possess a significant ability to
modify their behavior according to experience, including adapting to the behavior of their "pack leaders"—
again, humans. This allows them to be trained to behave in a way that is not specifically the most natural to
their breed; nevertheless, the accumulated experience of thousands of years shows that some combinations
of nature and nurture are quite daunting, for instance, training whippets to guard flocks of sheep.
[edit] Notes
1. ^ Brewer, Douglas J.; Terence, Sir Clark, Adrian Phillips (March 2002). DOGS IN
ANTIQUITY Anubis to Cerberus: The Origins of the Domestic Dog. Aris & Phillips (March 2002).
ISBN 978-0856687044. http://www.arisandphillips.com/ap/Anubis.html.
2. ^ Scott & Fuller 1974, p. 140
3. ^ Scott & Fuller 1974, p. 141
4. ^ Klinghammer, Erich; Goodmann, Patricia Ann (1987). "Chapter 2: Socialization and
management of wolves in captivity". In Frank, Harry. Man and Wolf: Advances, Issues, and Problems
in Captive Wolf Research. Dr W. Junk Publishers. p. 36. ISBN 90-6193-614-4.
5. ^ Grandin, Temple; Johnson, Catherine (2005). Animals in Translation. New York, New York:
Scribner. p. 87. ISBN 0743247698.
6. ^ a b Derr, Mark (2004). Dog's Best Friend. Chicago: University of Chicago Press. p. 21.
ISBN 0226142809.
7. ^ Scott, John Paul (1974). Dog behavior: the genetic basis. University of Chicago Press.
pp. 55–56. ISBN 9780226743387. http://books.google.com/?id=2D3IS1tDFcsC.
8. ^ Human Stars, The Animal Attraction.
9. ^ "Dogs that Changed the World; The Rise of the Dog". PBS-Nature.
http://www.pbs.org/wnet/nature/dog/garbage.html. Retrieved 2007-05-08.
10.^ Derr, Mark (2004). Dog's Best Friend. Chicago: University of Chicago Press. pp. 4, 25, 271.
ISBN 0226142809. http://books.google.com/?id=9_EDbatFH9MC.
11.^ Dienekes' Anthropology Blog : Dog domestication in the Aurignacian (c. 32kyBP )
12.^ MSNBC : World's first dog lived 31,700 years ago, ate big
13.^ Scott & Fuller 1974, p. 54
14.^ a b Savolainen, Peter; Ya-ping Zhang, Jing Luo, Joakim Lundeberg, and Thomas Leitner
(2002-11-22). "Genetic Evidence for an East Asian Origin of Domestic Dogs". Science 298 (5598):
1610–3. doi:10.1126/science.1073906. PMID 12446907.
http://adsabs.harvard.edu/abs/2002Sci...298.1610S.
15.^ James Serpell, The domestic dog: its evolution, behaviour, and interactions with people , pp
10-12. Cambridge University Press, 1995.
16.^ SJM Davis and FR Valla, Evidence for domestication of the dog 12,000 years ago in the
Natufian of Israel, Nature 276, 608-610 (7 December 1978).
17.^ Vila, C.; Peter Savolainen; Jesus E. Maldonado; John E. Rice; Rodney L. Honeycutt (June
13, 1997). "Multiple and ancient origins of the domestic dog". Science 276 (5319): 1687.
doi:10.1126/science.276.5319.1687. PMID 9180076. Archived from the original on 2007-09-26.
http://web.archive.org/web/20070926223204/http://www.idir.net/~wolf2dog/wayne1.htm.
18.^ vonHoldt, Bridgett; et al. (2010-03-17). "Genome-wide SNP and haplotype analyses reveal
a rich history underlying dog domestication". Nature 464 (7290): 898–902. doi:10.1038/nature08837.
PMID 20237475.
19.^ "Humans live a dog's life". abc.net.au. 26 March 2002.
http://www.abc.net.au/science/news/stories/s513072.htm. Retrieved 2007-04-07.
20.^ Mlot, Christine (June 28, 1997). "Stalking the Ancient Dog". Science News Online.
http://www.sciencenews.org/sn_arc97/6_28_97/bob1.htm. Retrieved 2008-07-23.
21.^ "African Dog Genetics Suggest New View of Domestication Needed".
http://www.genomeweb.com/african-dog-genetics-suggest-new-view-domestication-needed.
22.^ Pang et al (September 1, 2009). "mtDNA Data Indicate a Single Origin for Dogs South of
Yangtze River, Less Than 16,300 Years Ago, from Numerous Wolves". Molecular Biology and
Evolution. http://mbe.oxfordjournals.org/cgi/content/full/26/12/2849. Retrieved 2010-01-07.
23.^ Origin of dogs traced, BBC News, November 22, 2002.
24.^ "The Pact for Survival, How wolves became dogs–The Fox Farm Experiment". abc.net.au.
http://abc.net.au/animals/program1/factsheet5.htm. Retrieved 2007-04-11.
25.^ Ascent of the Dog), Discover Magazine, October 1994.
26.^ Christopher Taylor, Dog's Life (8 December 2008), Catalogue of organisms
27.^ Gould 1993, p. 394
[edit] References
• Gould, Stephen Jay (1993). Eight Little Piggies: Reflections in Natural History . New York: W.
W. Norton & Company. ISBN 0393311392. .
• Scott, John Paul; Fuller, John L. (1974). Dog behavior: the genetic basis (2, illustrated ed.).
University of Chicago Press. ISBN 9780226743387. http://books.google.com/?id=2D3IS1tDFcsC.
ISBN 0-226-74338-1, ISBN 978-0-226-74338-7.
• Koler-Matznick, J. (2002). "The origin of the dog revisited". Anthrozoös 15 (2): 98 – 118.
http://newguinea-singing-dog-conservation.org/Tidbits/OriginOfTheDog.pdf.

• Klütsch CFC, Seppälä EH, Lohi H, Fall T, Hedhammar Å, Uhlén M, Savolainen P (2010)
Regional occurrence, high frequency but low diversity of mitochondrial DNA haplogroup d1 suggests
a recent dog-wolf hybridization in Scandinavia. Animal Genetics, online early.
• Morey, Darcy. Dogs: Domestication and the Development of a Social Bond (Cambridge
University Press; 2010) 384 pages; uses zooarchaeology to explores ties between humans and
canines over the past 15,000 years with a focus on the New World and Arctic regions.
• Brisbin Jr., I.L.; T.S. Risch (15 April). "Primitive dogs, their ecology and behavior: Unique
opportunities to study the early development of the human-canine bond.". Journal of the American
Veterinary Medical Association 210 (8): 1122. PMID 9108912.
• Trut, L.N. (1999). "Early Canid Domestication: The Farm-Fox Experiment". American
Scientist, 87: 160-169 87: 160–169. doi:10.1511/1999.2.160.
• Mestel, Rosie (October 1, 1994). "Living World: Ascent of the Dog".
http://discovermagazine.com/1994/oct/ascentofthedog434.
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Categories: Dogs | Upper Paleolithic | Evolution by taxon

W000
Evolution of cells

Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
This article has no lead section. Please help by adding an introductory section to this
article. For more information, see the layout guide, and Wikipedia's lead section guidelines,
and join in a discussion of the issue on the talk page. (November 2009)
"The evolution of modern cells is arguably the most challenging and important problem the field
of Biology has ever faced. In Darwin's day the problem could hardly be imagined. For much of
the 20th century it was intractable. In any case, the problem lay buried in the catch-all rubric
"origin of life"---where, because it is a biological not a (bio)chemical problem, it was effectively
ignored. Scientific interest in cellular evolution started to pick up once the universal phylogenetic
tree, the framework within which the problem had to be addressed, was determined . But it was
not until microbial genomics arrived on the scene that biologists could actually do much about
the problem of cellular evolution." (Carl Woese, 2002) [1]
The First Cell arose in the previously pre-biotic world with the coming together of several entities
that gave a single vesicle the unique chance to carry out three essential and quite different life
processes. These were: (a) to copy informational macromolecules, (b) to carry out specific
catalytic functions, and (c) to couple energy from the environment into usable chemical forms.
These would foster subsequent cellular evolution and metabolism. Each of these three essential
processes probably originated and was lost many times prior to The First Cell, but only when
these three occurred together was life jump-started and Darwinian evolution of organisms
began. (Koch and Silver, 2005)[2]
Contents
[hide]
• 1 The first cells
• 2 Community metabolism
• 3 Genetic code and the RNA world
• 4 Canonical patterns
• 5 Using genomics to infer early lines of evolution
• 6 References
• 7 Bibliography
[edit] The first cells

The origin of cells was the most important step in the evolution of life as we know it. The birth of the
cell marked the passage from pre-biotic chemistry to partitioned units resembling modern cells. The final
transition to living entities that fulfill all the definitions of modern cells depended on the ability to evolve
effectively by natural selection. This transition has been called the Darwinian transition.
If life is viewed from the point of view of replicator molecules, cells satisfy two fundamental
conditions: protection from the outside environment and confinement of biochemical activity. The former
condition is needed to keep complex molecules stable in a varying and sometimes aggressive environment;
the latter is fundamental for the evolution of biological complexity. If freely-floating molecules that code for
enzymes are not enclosed in cells, the enzymes will automatically benefit the neighbouring replicator
molecules. The consequences of diffusion in non-partitioned life forms might be viewed as "parasitism by
default." Therefore the selection pressure on replicator molecules will be lower, as the 'lucky' molecule that
produces the better enzyme has no definitive advantage over its close neighbors. If the molecule is enclosed
in a cell membrane, then the enzymes coded will be available only to the replicator molecule itself. That
molecule will uniquely benefit from the enzymes it codes for; giving it a better chance to multiply.
How did partitioning begin? Biochemically, cell-like spheroids formed by proteinoids are observed by
heating amino acids with phosphoric acid as a catalyst. They bear much of the basic features provided by
cell membranes. Proteinoid-based protocells enclosing RNA molecules could (but not necessarily should)
have been the first cellular life forms on Earth.
Another theory holds that the turbulent shores of the ancient coastal waters may have served as a
mammoth laboratory, aiding in the countless experiments necessary to bring about the first cell. Waves
breaking on the shore create a delicate foam composed of bubbles. Winds sweeping across the ocean have
a tendency to drive things to shore, much like driftwood collecting on the beach. It is possible that organic
molecules were concentrated on the shorelines in much the same way. Shallow coastal waters also tend to
be warmer, further concentrating the molecules through evaporation. While bubbles made mostly of water
tend to burst quickly, oily bubbles happen to be much more stable, lending more time to the particular bubble
to perform these crucial experiments. The phospholipid is a good example of a common oily compound
prevalent in the prebiotic seas.
Phospholipids can be visualized in one's mind as a hydrophilic head on one end, and a hydrophobic
tail on the other. These molecules possess an important characteristic for the construction of cell
membranes; they are able to link together to form a bilayer membrane. A lipid monolayer bubble can only
contain oil, and is therefore not conducive to harbouring water-soluble organic molecules. On the other hand,
a lipid bilayer bubble [1] can contain water, and was a likely precursor to the modern cell membrane. If a
protein came along that increased the integrity of its parent bubble, then that bubble had an advantage, and
was placed at the top of the natural selection waiting list. Primitive reproduction can be envisioned when the
bubbles burst, releasing the results of the experiment into the surrounding medium. Once enough of the 'right
stuff' was released into the medium, the development of the first prokaryotes, eukaryotes, and multi-cellular
organisms could be achieved.[3]
[edit] Community metabolism

The common ancestor of the now existing cellular lineages (eukaryotes, bacteria, and archaea) may
well have been a community of organisms that readily exchanged components and genes. It would have
contained:
• Autotrophs that produced organic compounds from CO2 either photosynthetically or by
inorganic chemical reactions;
• Heterotrophs that obtained organics by leakage from other organisms
• Saprotrophs that absorbed nutrients from decaying organisms
• Phagotrophs that were sufficiently complex to envelop and digest particulate nutrients
including other organisms.
The eukaryotic cell seems to have evolved from a symbiotic community of prokaryotic cells. It
appears that DNA-bearing organelles like mitochondria and chloroplasts are remnants of ancient symbiotic
oxygen-breathing bacteria and cyanobacteria, respectively, where at least part of the rest of the cell may
have been derived from an ancestral archaean prokaryote cell. This concept is often termed the
endosymbiotic theory but is perhaps better considered as an hypothesis. There is still debate about whether
organelles like the hydrogenosome predated the origin of mitochondria, or vice versa: see the hydrogen
hypothesis for the origin of eukaryotic cells.
How the current lineages of microbes evolved from this postulated community is currently unsolved
but subject to intense research by biologists, stimulated by the great flow of new discoveries emerging from
genome science.[4]
File:Genome fusion eukarya.gif
One current hypothesis for the origin of eukaryotic (nucleated) cells, from fusion of two distinct non-
nucleated prokaryotes that were partners of a postulated ancient symbiosis.
[edit] Genetic code and the RNA world

Much modern evidence supports the hypothesis that early cellular evolution occurred in a biological
realm radically distinct from modern biology. It is thought that in this ancient realm, the current genetic role of
DNA was largely filled by RNA, and catalysis also was largely mediated by RNA (that is, by ribozyme
counterparts of enzymes). This remarkable concept is known as the RNA world hypothesis.
According to this hypothesis, the ancient RNA world transitioned into the modern cellular world via
the evolution of forms of protein synthesis akin to modern ribosomal protein synthesis, followed by
replacement of many cellular ribozyme catalysts by protein based enzyme catalysts. Proteins are much more
flexible in catalysis that RNA due to the existence of diverse amino acid side chains with distinct chemical
characteristics. The RNA record in existing cells appears to preserve some 'molecular fossils' from this RNA
world. These RNA fossils include the ribosome itself (in which RNA catalyses peptide-bond formation), the
modern ribozyme catalyst RNase P, and tRNAs.[5][6][7][8]
The universal Genetic code may indeed preserve some evidence for this ancient world. For instance,
recent studies of transfer RNAs , the enzymes that charge them with amino acids (the first step in protein
synthesis) and the way these components recognise and exploit the genetic code, have been used to
suggest that of the universal genetic code emerged before the evolution of the modern amino acid activation
method for protein synthesis.[5][6][9][10][11]
[edit] Canonical patterns

Despite the fact that the evolutionary origins of the major lineages of modern cells are currently hotly
disputed, the primary distinctions between the three major lineages of cellular life (called domains) are clear
cut and firmly established.
In each of these three domains, protein synthesis machinery, DNA replication, and transcription of
RNA from DNA all display distinctive features. There are three versions of ribosomal RNAs, and generally
three versions of each ribosomal protein, one for each domain of life. These three versions of the protein
synthesis apparatus are called the canonical patterns, and it is the existence of these canonical patterns
provide the basis for a definition of the three Domains - Bacteria, Archaea, and Eukarya, (alternatively called
Eukaryota) - of currently existing cells.[12]
[edit] Using genomics to infer early lines of evolution

Instead of relying a single gene such as the small-subunit ribosomal RNA (SSU rRNA) gene to
reconstruct early evolution, or a few genes, scientific effort has shifted to exploiting the comprehensive
information from the many complete genome sequences of organisms that are now available.[13]
From such studies, it is now clear that evolututionary trees based only on SSU rRNA alone do not
capture the events of early eukaryote evolution accurately, and the progenitors of the first nucleated cells are
still uncertain. For instance, careful analysis of the complete genome of the eukaryote yeast shows that many
of its genes are more closely related to bacterial genes than they are to archaea, and it is now clear that
archaea were not the simple progenitors of the eukaryotes, in stark contradiction to the earlier findings based
on SSU rRNA and limited samples of other genes.[14]
One imaginative but disputed hypothesis getting some support from recent computer-assisted
studies of complete genome DNA sequences is that the first nucleated cell arose from two distinctly different
ancient prokaryotic (non-nucleated) species that had formed a symbiotic relationship with one-another to
carry out different aspects of metabolism. One partner of this postulated symbiosis is proposed to be a true
bacterial cell, and the other an archaean cell. It is postulated that this symbiotic partnership progressed via
the cellular fusion of the partners to generate a chimeric or hybrid cell with a membrane bound internal
structure that was the forerunner of the nucleus. The next stage in this scheme was transfer of both partner
genomes into the nucleus and their fusion with one-another. Several variations of this hypothesis for the
origin of nucleated cells have been suggested.[15]
But some biologists dispute this conception[4] and argue for the need for a shift in conceptual
framework if this problem is to be solved. They re-iterate the community metabolism theme, the idea that
early living communities would comprise many different entities to extant cells, and would have shared their
genetic material more extensively than current microbes.[16]
[edit] References
This article incorporates material from the Citizendium article "Evolution of cells", which is licensed
under the Creative Commons Attribution-ShareAlike 3.0 Unported License but not under the GFDL.
1. ^ Woese, CR (2002). "On the evolution of cells". Proceedings of the National Academy of
Sciences of the United States of America 99 (13): 8742–7. doi:10.1073/pnas.132266999.
PMID 12077305. PMC 124369. http://www.pnas.org/cgi/content/full/99/13/8742.
2. ^ Koch, AL; Silver, S (2005). "The first cell". Advances in microbial physiology 50: 227–59.
doi:10.1016/S0065-2911(05)50006-7. PMID 16221582.
3. ^ This theory is expanded upon in The Cell: Evolution of the First Organism by Joseph Panno
4. ^ a b Kurland, CG; Collins, LJ; Penny, D (2006). "Genomics and the irreducible nature of
eukaryote cells". Science 312 (5776): 1011–4. doi:10.1126/science.1121674. PMID 16709776.
5. ^ a b Poole AM, Jeffares DC, Penny D (1998). "The path from the RNA world.". J Mol Evol 46
(1): 1–17. doi:10.1007/PL00006275. PMID 9419221.
6. ^ a b Jeffares DC, Poole AM, Penny D (1998). "Relics from the RNA world.". J Mol Evol 46
(1): 18–36. doi:10.1007/PL00006280. PMID 9419222.
7. ^ Orgel LE (2004). "Prebiotic chemistry and the origin of the RNA world.". Crit Rev Biochem
Mol Biol 39 (2): 99–123. doi:10.1080/10409230490460765. PMID 15217990.
8. ^ Benner SA, Ellington AD, Tauer A (1989). "Modern metabolism as a palimpsest of the RNA
world.". Proc Natl Acad Sci U S A 86 (18): 7054–8. doi:10.1073/pnas.86.18.7054. PMID 2476811.
9. ^ Hohn MJ, Park HS, O'Donoghue P, Schnitzbauer M, Söll D (2006). "Emergence of the
universal genetic code imprinted in an RNA record.". Proc Natl Acad Sci U S A 103 (48): 18095–100.
doi:10.1073/pnas.0608762103. PMID 17110438.
10.^ O'Donoghue P, Luthey-Schulten Z (2003). "On the evolution of structure in aminoacyl-tRNA
synthetases.". Microbiol Mol Biol Rev 67 (4): 550–73. doi:10.1128/MMBR.67.4.550-573.2003.
PMID 14665676.
11.^ Gesteland, RF et al. eds.(2006) The RNA World: The Nature of Modern RNA Suggests a
Prebiotic RNA (2006) (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY,).
12.^ Olsen, GJ; Woese, CR; Ibba, M.; Soll, D. (1997). "Archaeal genomics: an overview.". Cell
89 (7): 991–4. doi:10.1128/MMBR.64.1.202-236.2000. PMID 9215619.
http://mmbr.asm.org/cgi/content/abstract/64/1/202?
ijkey=9104f15d5ac0a9f9f1cf4451691dc8343169a880&keytype2=tf_ipsecsha.
13.^ Daubin, V; Moran, NA; Ochman, H (2003). "Phylogenetics and the cohesion of bacterial
genomes.". Science 301 (5634): 829–32. doi:10.1126/science.1086568. PMID 12907801.
• Eisen, JA; Fraser, CM (2003). "Viewpoint phylogenomics: intersection of evolution
and genomics". Science 300 (5626): 1706–7. doi:10.1126/science.1086292.
PMID 12805538.
• Henz, SR; Huson, DH; Auch, AF; Nieselt-Struwe, K; Schuster, SC (2005). "Whole-
genome prokaryotic phylogeny.". Bioinformatics (Oxford, England) 21 (10): 2329–35.
doi:10.1093/bioinformatics/bth324. PMID 15166018.
http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2329.
14.^ Esser, C; Ahmadinejad, N; Wiegand, C; Rotte, C; Sebastiani, F; Gelius-Dietrich, G; Henze,
K; Kretschmann, E et al. (2004). "A genome phylogeny for mitochondria among alpha-proteobacteria
and a predominantly eubacterial ancestry of yeast nuclear genes.". Molecular biology and evolution
21 (9): 1643–60. doi:10.1093/molbev/msh160. PMID 15155797.
15.^ Esser, C; Ahmadinejad, N; Wiegand, C; Rotte, C; Sebastiani, F; Gelius-Dietrich, G; Henze,
K; Kretschmann, E et al. (2004). "A genome phylogeny for mitochondria among alpha-proteobacteria
and a preedominantly eubacterial ancestry of yeast nuclear genes". Mol Biol Evol 21 (9): 1643–50.
doi:10.1093/molbev/msh160. PMID 15155797.
16.^ Woese, C (2002). "On the evolution of cells". Proc Natl Acad Sci USA 99 (13): 8742–7.
doi:10.1073/pnas.132266999. PMID 12077305. PMC 124369.
[edit] Bibliography
• Kurland, CG; Collins, LJ; Penny, D (2006). "Genomics and the irreducible nature of
eukaryote cells". Science 312 (5776): 1011–4. doi:10.1126/science.1121674. PMID 16709776.
• Woese CR (June 2002). "On the evolution of cells.". Proceedings of the National Academy of
Sciences of the United States of America 99 (13): 8742–7. doi:10.1073/pnas.132266999.
PMID 12077305. . (Open access.)
• Daubin, V; Moran, NA; Ochman, H (2003). "Phylogenetics and the cohesion of bacterial
genomes". Science 301 (5634): 829–32. doi:10.1126/science.1086568. PMID 12907801.
• Eisen, JA; Fraser, CM (2003). "Viewpoint phylogenomics: intersection of evolution and
genomics". Science 300 (5626): 1706–7. doi:10.1126/science.1086292. PMID 12805538.
• Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC (May 2005). "Whole-genome
prokaryotic phylogeny.". Bioinformatics (Oxford, England) 21 (10): 2329–35.
doi:10.1093/bioinformatics/bth324. PMID 15166018.
• Lerat E, Daubin V, Ochman H, Moran NA (2005). "Evolutionary origins of genomic
repertoires in bacteria". PLoS Biology 3 (5): e130. doi:10.1371/journal.pbio.0030130.
PMID 15799709.
• Steenkamp ET, Wright J, Baldauf SL (January 2006). "The protistan origins of animals and
fungi.". Molecular biology and evolution 23 (1): 93–106. doi:10.1093/molbev/msj011.
PMID 16151185. ]
• Forterre P (2006). "Three RNA cells for ribosomal lineages and three DNA viruses to
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doi:10.1073/pnas.0510333103. PMID 16505372.
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Evolution of dinosaurs

challenged and removed. (June 2009)
This article gives an outline and examples of dinosaur evolution. For a detailed list of
interrelationships see Dinosaur classification.
Further information: Evolution of reptiles
Evolution of dinosaurs
Dinosaurs evolved from the archosaurs 232-234 Ma (million years ago) in the Ladinian age, the latter
part of the middle Triassic. Dinosauria is a well-supported clade, present in 98% of bootstraps. It is
diagnosed by many features including loss of the postfrontal on the skull and an elongate deltopectoral crest
on the humerus.[1]
Contents
[hide]
• 1 From archosaurs to dinosaurs
• 2 Earliest dinosaurs
• 3 Saurischia
• 3.1 Sauropodomorpha
• 3.2 Theropoda
• 4 Ornithischia
• 4.1 Thyreophorans
• 4.2 Ornithopoda
• 4.3 Marginocephalia
• 5 Fossil record
• 6 Evolutionary trends
• 6.1 Body size
• 6.2 Mobility
• 6.3 Effect of food sources
• 7 Biogeography
• 8 Extinction
• 9 See also
• 10 References
[edit] From archosaurs to dinosaurs
The process leading up the first dinosaurs can be followed through fossils of the early Archosaurs
such as the Proterosuchidae, Erythrosuchidae and Euparkeria which have fossils dating back to 250 Ma,
through mid-Triassic archosaurs such as Ticinosuchus 232-236 Ma. Crocodiles are also descendants of mid-
Triassic archosaurs.[1]
Dinosaurs can be defined as the last common ancestor of birds (Saurischia) and Triceratops
(Ornithischia) and all the descendants of that ancestor. With that definition, the pterosaurs and several
species of archosaurs narrowly miss out on being classified as dinosaurs. The pterosaurs are famous for
flying through the Mesozoic skies on leathery wings and reaching the largest sizes of any flying animal.
Archosaur genera that narrowly miss out on being classified as dinosaurs include Schleromochlus 220-
225 Ma, Lagerpeton 230-232 Ma and Marasuchus 230-232 Ma.
[edit] Earliest dinosaurs

The first known dinosaurs were bipedal predators that were one to two metres long.
Spondylosoma may or may not be a dinosaur; the fossils (all postcranial) are tentatively dated at
230-232 Ma.[1]
The earliest confirmed dinosaur fossils include saurischian ('lizard-hipped') dinosaurs Saturnalia 225-
232 Ma, Herrerasaurus 220-230 Ma, Staurikosaurus possibly 225-230 Ma, Eoraptor 220-230 Ma and
Alwalkeria 220-230 Ma. Saturnalia may be a basal saurischian or a prosauropod. The others are basal
saurischians.
Among the earliest ornithischian ('bird-hipped') dinosaurs is Pisanosaurus 220-230 Ma. Although
Lesothosaurus comes from 195-206 Ma, skeletal features suggest that it branched from the main
Ornithischia line at least as early as Pisanosaurus.
A. Eoraptor, an early saurischian, B Lesothosaurus, a primitive ornithischian, C Staurikosaurus
(Saurischia) pelvis, D Lesothosaurus pelvis
It is clear from this figure that early saurischians resembled early ornithischians, but not modern
crocodiles. Saurischians are distinguished from the ornithischians by retaining the ancestral configuration of
bones in the pelvis. Another difference is in the skull, the upper skull of the Ornithischia is more solid and the
joint connecting the lower jaw is more flexible; both are adaptations to herbivory and both can already be
seen in Lesothosaurus.
[edit] Saurischia
Setting aside the basal Saurischia, the rest of the Saurischia are split into the Sauropodomorpha and
Theropoda. The Sauropodomorpha is split into Prosauropoda and Sauropoda. The evolutionary paths taken
by the Theropoda are very complicated. The Dinosauria (2004), a major reference work on dinosaurs,[1]
splits the Theropoda into groups Ceratosauria, Basal Tetanurae, Tyrannosauroidea, Ornithomimosauria,
Therizinosauroidea, Oviraptorosauria, Troodontidae, Dromaeosauridae and Basal Avialae in turn. Each
group branches off the main trunk at a later date. See Dinosaur_classification for the detailed
interrelationships between these.
[edit] Sauropodomorpha
The first sauropodomorphs were prosauropods. Prosauropod fossils are known from the late Triassic
to early Jurassic 227-180 Ma.[1] They could be bipedal or quadrupedal and had developed long necks and
tails and relatively small heads. They had lengths of 2.5 to 10 m and were primarily herbivorous. The earliest
prosauropods, such as Thecodontosaurus from 205-220 Ma, still retained the ancestral bipedal stance and
large head to body ratio.
These evolved into the sauropods which became gigantic quadrupedal herbivores, some of which
reached lengths of at least 26 m. Features defining this clade include a ratio of forelimb length to hindlimb
length greater than 0.6. Most sauropods still had hindlimbs larger than forelimbs; one notable exception is
Brachiosaurus whose long forelimbs suggest that it had evolved to feed from tall trees like a modern-day
giraffe.
Sauropod fossils are found from the times of the earliest dinosaurs right up to the K-T extinction
event, from 227 to 65 Ma. Most sauropods are known from the Jurassic, to be more precise between 227 and
121 Ma.
The Cretaceous sauropods form two groups. The Diplodocoidea lived from 121 to 65 Ma. The
Titanosauriformes lived from 132 to 65 Ma. The latter clade consists of series of nested subgoups, the
Titanosauria, the Titanosauridae and Saltasauridae. Both the Diplodocoidea and Titanosauriformes are
descended from the Neosauropoda, the earliest of which lived in about 169 Ma.
The sauropods are famous for being the largest land animals that ever lived, and for having relatively
small skulls. The enlargement of prosauropod and sauropod dinosaurs into these giants and the change in
skull length is illustrated in the following charts.
Dinosaurs used in creating these charts are (in date order): Eo Eoraptor; Prosauropods Ri
Riojasaurus, Pl Plateosaurus, Yu Yunnanosaurus, Ms Massospondylus, Ji Jingshanosaurus, An
Anchisaurus, Lu Lufengosaurus, Yi Yimenosaurus, ; and Sauropods Sh Shunosaurus, Om Omeisaurus, Mm
Mamenchisaurus, Ce Cetiosaurus, Dc Dicraeosaurus, Br Brachiosaurus, Eu Euhelopus, Ap Apatosaurus, Ca
Camarasaurus, Dp Diplodocus,[1] Ha Haplocanthosaurus, Am Amargasaurus, Ar Argentinosaurus (approx),
Bo Bonitasaura, Q Quaesitosaurus, Al Alamosaurus, Sa Saltasaurus, Ra Rapetosaurus, Op
Opisthocoelicaudia, Ne Nemegtosaurus.
With the exception of Argentinosaurus (included to fill a gap in time), these graphs show only the
length of sauropods for whom near-complete fossil skeletons are known. It doesn't show other very large
sauropods (see Dinosaur size#Sauropods) because these are only known from very incomplete skeletons.
The ratio of skull length to body length is much higher in Eoraptor than in sauropods. The longest skull
graphed is of Nemegtosaurus, which is not thought be a particularly large sauropod. The skull of
Nemegtosaurus was found near the headless skeleton of 11 metre long Opisthocoelicaudia, and it has been
suggested that they may be the same species, but see Nemegtosauridae.
The relationship between the evolution of large herbivores and large plants remains uncertain. About
50% of the plants over the time of the dinosaurs were conifers, they increased in number in the Triassic until
stabilising in about 190 Ma. Cycads formed the second largest group until about 120 Ma. Ferns were present
in roughly constant numbers the whole time. Flowering plants began about 120 Ma and by the end of the
period had taken over from the cycads. All dinosaur herbivores appear to have been adversely affected by
the extinction event at the end of the Jurassic.
[edit] Theropoda
By far the earliest fossils of Theropoda (not counting the basal saurischians) are of the
Coelophysoidea, including Coelophysis and others, from late Triassic and early Jurassic 227-180 Ma.[1]
Cladistic analysis sometimes connects these to the group called Ceratosauria. Principal features of both
include changes in the pelvic girdle and hind limb that differ between the sexes. Other ceratosauria first
appear in the late Jurassic of western North America.
These are followed by the basal Tetanurae, of whom fossils have been found from the mid Jurassic
to past the end of the early Cretaceous 180 Ma to 94 Ma. They have a relatively short maxillary tooth row.
They did not all branch off the evolutionary line leading to coelurosaurs at the same time. Basal tetanurans
include Megalosauridae, spinosaurids, a diverse clade of allosaurs, and several genera of less certain
affinities, including Compsognathus. With the exception of Compsognathus they are large-bodied. Allosaurs
form a distinct long-lived clade that share some cranial characters. They include the well known Allosaurus
and Sinraptor among others.
The great radiation of Theropoda into many different clades of Coelurosauria must have happened in
the mid to late Jurassic, because Archaeopteryx was around in about 152-154 Ma, and cladistic analysis has
shown that many other groups of Coelurosauria branched off before that.[2] Fossil evidence from China
suggests that the earliest feathers were found on the primitive Coelurosauria. The most primitive of these,
e.g. on the tyrannosauroid Dilong, were simply hollow-cored fibres that would have been useful for insulation
but useless for flying.
Occasional bones and cladistic analyses point to the Tyrannosauroidea branching off from the other
Theropoda early, in the middle Jurassic, although nearly complete skeletons haven't yet appeared before
Eotyrannus from 121-127 Ma, and the many close relatives of Tyrannosaurus itself don't appear before
84 Ma, near the end of the late Cretaceous.
Ornithomimosauria fossils are known from 127 to 65 Ma. The earliest branch from the main line of
Ornithomimosauria is believed to be Harpymimus.
The Therizinosauroidea are unusual theropods in being almost all vegetarian. Fossil
Therizinosauroidea are known from 127 to 65 Ma.
Maniraptorans include Oviraptorosauria, Deinonychosaurs and birds. They are characterized by an
ulna with a curved shaft.
Oviraptorosaurian fossils are known from 127 to 65 Ma. They have a toothless skull that is extremely
modified. The skeleton has an unusually short tail.
Deinonychosaurs, named after the enlarged sickle-shaped second digit of the hand, are closely
related to birds. They have two distinct families, Troodontidae and Dromaeosauridae. Troodontid fossils are
known from 127 to 65 Ma. They have a more slender build and longer limbs. The earliest named troodontid
fossil known is Sinornithoides. Dromaeosaurid fossils are known from about 127 to 65 Ma with the exception
of Utahraptor. The skeletal remains of Utahraptor are about 127-144 Ma. This is interesting because
according to a recent cladistic analysis,[2] Utahraptor is about as far from the ancestral Theropoda as it is
possible to get, further than Archaeopteryx. Dromaeosaurids have a larger second digit; this family includes
the well known dinosaurs Dromaeosaurus, Deinonychus and Velociraptor.
Ancient birds (Avialae) include both the Aves, which are defined as descendants of the common
ancestor of modern birds and Archaeopteryx, and the more primitive Epidendrosaurus. Fossil birds stretch
down from 154 Ma through the K-T extinction event at 65 Ma to the present day. Scores of complete
skeletons have now been found of the more recent Confuciusornis, which is an early representative of the
Ornithurae. Ornithurans all have a bony pygostyle, to which tail feathers are anchored. For more details on
the evolution of birds, see Evolution of birds.
[edit] Ornithischia
Ornithischia, as the name indicates, was coined for the birdlike pelvic girdle, although they are not
the ancestors of birds.
The ornithischian skull and dentition was modified very early by a herbivorous diet.[3] Lesothosaurus
separated early, but the skull of Lesothosaurus already shows such adaptations, with broad proportions, a
less flexible upper jaw, and a more mobile connection for the lower jaw.
The major clades were already established by the early Jurassic. The ornithischians divided into
armoured thyreophorans and unarmoured ornithopods and marginocephalians.
[edit] Thyreophorans
Surface body armour (scutes) is the most striking feature of the thyreophorans.[3] Scutellosaurus has
these but otherwise differs little from Lesothosaurus. It has a long tail and combined bipedal-quadrupedal
posture that separates it from all later thyreophorans including Stegosauria and Ankylosauria. These two
clades, although quite different in overall appearance, share many unusual features in the skull and skeleton.
Stegosaurs are easily recognised by the prominent row of plates above the spine and ling spines on
the tail. Most stegosaurs, but not Stegosaurus, also have a spine over each shoulder. These spines and
plates have evolved from the earlier surface scutes. Huayangosaurus is the oldest and most primitive known
stegosaur.
Ankylosaurs are easily recognised by their extensive body armour. The skull is heavily ossified. Early
in their evolution, ankylosaurs split into the Nodosauridae and Ankylosauridae, distinguished by features of
the skull.
[edit] Ornithopoda
Ornithopods fall into one of three distinct clades - Heterodontosauridae, Hypsilophodontidae, and
Iguanodontia.[3]
Heterodontosaurids are very small (body length < 1 m) and lived in the early to late Jurassic. Apart
from Abrictosaurus all have a short upper canine and longer lower canine. The forelimbs in known fossils are
unusually long.
Hypsilophodontids more closely resemble their ancestors than the heterodontosaurids do. The most
distinctive features are short scapula and rod-shaped pre-pubic process. The earliest is Agilisaurus from the
middle Jurassic of China.
Iguanodontians are a diverse but morphologically tight knit array of genera known from fossils of the
late Cretaceous. Significant modifications include the evolution of tooth batteries, a ligament-bound
metacarpus and a digitigrade hand posture. Tenontosaurus is the most basal iguanodontian. Others include
Iguanodon, Camptosaurus and Muttaburrasaurus.
[edit] Marginocephalia
Marginocephalia are named for a shelf that projects over the back of the skull.[3] They include the
pachycephalosaurians and ceratopsians.
Pachycephalosaurs are best known for their thick upper fronts to their skull. The oldest known is
Stenopelix, from the early Cretaceous of Europe.
Ceratopsians, famous for Protoceratops, Triceratops and Styracosaurus illustrate the evolution of
frilled and horned skulls. The frills evolved from the shelf common to all Marginocephalia. Ceratopsians are
separated into basal ceratopsians, including the parrot-beaked Psittacosaurus, and neoceratopsians.
Diversity of ceratopsian skulls. A) Skeleton of Protoceratops. B) to I) Skulls. B) & C) Psittacosaurus
side & top. D) & E) Protoceratops side & top. F) & G) Triceratops side & top. H) & I) Styracosaurus side
(without lower jaw) & top.
The sequence of ceratopsian evolution in the Cretaceous is roughly from Psittacosaurus (121
-99 Ma) to Protoceratops (83 Ma) to (Triceratops 67 Ma and Styracosaurus 72 Ma). In side view the skull of
Psittacosaurus bears very little resemblance to that of Styracosaurus but in top view a similar pentagonal
arrangement can be seen.

The first few lines of primitive dinosaurs diversified rapidly through the Triassic period; dinosaur
species quickly evolved the specialised features and range of sizes needed to exploit nearly every terrestrial
ecological niche. During the period of dinosaur predominance, which encompassed the ensuing Jurassic and
Cretaceous periods, nearly every known land animal larger than 1 meter in length was a dinosaur.
One measure of the quality of the fossil record is obtained by comparing the date of first appearance
with the order of branching of a cladogram based on the shape of fossil elements. Close correspondence
exists for ornithiscians, saurischians and subgroups.[3] The cladogram link between coelophysids and
ceratosaurs is an exception, it would place the origin of coelophysids much too late. The simplest explanation
is convergent evolution - ceratosaur bones evolved independently into a shape that resembles that of the
earlier coelophysids. The other possibility is that ceratosaurs evolved much earlier than the fossil record
suggests.
Most dinosaur fossils have been found in the Norian-Sinemurian, Kimmeridgian-Tithonian, and
Campanian-Maastrichtian periods. Continuity of lineages across the intervening gaps shows that those gaps
are artifacts of preservation rather than any reduction in diversity or abundance.
In many instances, cladistic analysis shows that ancestral lineages of varying durations fall in those
gaps. The length of missing ancestral lineages in 1997[3] range from 25 Ma (Lesothosaurus, Genasauria,
Hadrosauroidea, Sauropoda, Neoceratopsia, Coelurosauria) to 85 Ma (Carcharodontosauridae). Because
the dinosaurian radiation began at small body size, the unrecorded early history may be due to less reliable
fossilization of smaller species. However, some missing lineages, notably of Carcharodontosauridae and
Abelisauridae, require alternative explanations because the missing range extends across stages rich in
fossil material.
[edit] Evolutionary trends

[edit] Body size
Body size is important because of its correlation with metabolism, diet, life history, geographic range
and extinction rate.[3] The modal body mass of dinosaurs lies between 1 and 10 tons throughout the
Mesozoic and across all major continental regions. That said, there was a trend towards increasing body size
within many dinosaur clades, including the Thyreophora, Ornithopoda, Pachycephalosauria, Ceratopsia,
Sauropomorpha, and basal Theropoda. Marked decreases in body size have also occurred in some lineages,
but are more sporadic. The best known example is the decrease in body size leading up to the first birds;
Archaeopteryx was below 10 kg in weight, and later birds Confuciusornis and Sinornis are starling- to pigeon-
sized. This occurred for easier flight.
[edit] Mobility
The ancestral dinosaur was a biped. The evolution of a quadrupedal posture occurred four times,
among the ancestors of Euornithopoda, Thyreophora, Ceratopsia and Sauropodomorpha.[3] In all four cases
this was associated with an increase in body size, and in all four cases the trend is unidirectional without
reversal.
Dinosaurs exhibit a pattern of the reduction and loss of fingers on the lateral side of the hand (digits
III, IV and V). The primitive function of the dinosaur hand is grasping with a partially opposable thumb, rather
than weight-bearing. The reduction of digits is one of the defining features of tyrannosaurids, only having two
functional digits on very short forelimbs.
[edit] Effect of food sources

The ancestral dinosaur was a carnivore. Herbivory among dinosaurs arose three times, at the origin
of the ornithischian, sauropodomorph, and therizinosaurid clades. Individual therizinosaurids are herbivorous
or omnivorous. Herbivory among the ornithischians and sauropodomorphs was never reversed.[3]
The potential co-evolution of plants and herbivorous dinosaurs has been subject to extensive
speculation. The appearance of prosauropods in the late Triassic has been tentatively linked either to the
demise or diversification of types of flora at that time. The rise of ceratopsids and iguanodont and
hadrosaurid ornithopods in the Cretaceous has been tentatively linked to the angiosperm radiation.
Unfortunately, there are still no hard data on dietary preferences of herbivorous dinosaurs, apart from data on
chewing technique and gastroliths.
[edit] Biogeography
Dinosaurian faunas, which were relatively uniform in character when Pangaea began to break up,
became markedly differentiated by the close of the Cretaceous. Biogeography is based on the splitting of an
ancestral species by the emplacement of a geographic barrier. Interpretation is limited by a lack of fossil
evidence for eastern North America, Madagascar, India, Antarctica and Australia. No unequivocal proof of
the biogeographical action on Dinosaur species has been obtained,[3] but some authors have outlined
centres of origin for many dinosaur groups, multiple dispersal routes, and intervals of geographic isolation.
Dinosaurs that have been given as evidence of biogeography include abelisaurid theropods from
South America and possibly else where on Gondwana.
Relationships between dinosaurs show abundant evidence of dispersal from one region of the globe
to another. Tetanuran theropods travelled widely through western North America, Asia, South America, Africa
and Antarctica. Pachycephalosaurs and ceratopsians show clear evidence of multiple bidirectional dispersion
events across Beringa.
[edit] Extinction
The Cretaceous–Tertiary extinction event, which occurred 65.5 million years ago at the end of the
Cretaceous period, caused the extinction of all dinosaurs except for the line that had already given rise to the
first birds.
[edit] See also

Dinosaurs portal
• Dinosaur classification
• Origin of birds
• List of fossil birds
[edit] References
1. ^ a b c d e f g Weishampel, Dodson & Osmolska, 2004, The Dinosauria
2. ^ a b Senter, P. (2007). "A new look at the phylogeny of Coelurosauria (Dinosauria:
Theropoda)." Journal of Systematic Palaeontology, (doi:10.1017/S1477201907002143)
3. ^ a b c d e f g h i j PC Sereno (1997) "The origin and evolution of dinosaurs" Annu. Rev. Earth
Planet. Sci. 25:435-489
Paul C. Sereno (1999) The evolution of dinosaurs, Science, Vol 284, pp. 2137–2146
http://www.sciencemag.org/cgi/content/abstract/284/5423/2137

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Evolution of spiders

A spider in Baltic amber
The evolution of spiders has been going on for at least 400 million years, since the first true spiders
(thin-waisted arachnids) evolved from crab-like chelicerate ancestors. Today, there are over 40,000
described spider species within the diverse phylum of arthropods.
Major developments in spider evolution include the development of spinnerets and silk secretion, as
well as different adaptions for its use.
[edit] Early spider-like arachnids

Among the oldest known land arthropods are Trigonotarbids, members an extinct order of spider-like
arachnids.
Sharing many superficial characteristics with spiders, Trigonotarbida were terrestrial, respired
through book lungs, and walked on eight legs with two additional legs adapted to use around their mouth.
Arguments still remain open as to whether they possessed the ability to create silk. This had been popular
thought for quite some time, until an unpublished fossil was described with distinct microtubercles on its hind
legs, akin to those used by spiders to direct and manipulate their silk.
Regardless Trigonotarbida are not considered true-spiders. They are generally accepted as an
independent early offshoot within the Arachnida clade, and not directly ancestral to modern spiders.
[edit] Emergence of true spiders

At one stage the oldest fossil spider was believed to be Attercopus which lived 380 million years ago
during the Devonian. Attercopus was placed as the sister-taxon to all living spiders, but has now been
reinterpreted as a member of a separate, extinct order Uraraneida which could produce silk, but did not have
true spinnerets.
Microscopic structure of spider silk, possibly the most important adaption developed during the
evolution of these arachnids
The oldest true spiders are thus Carboniferous in age, or about 300 million years. Most of these early
segmented fossil spiders from the Coal Measures of Europe and North America probably belonged to the
Mesothelae, or something very similar, a group of primitive spiders with the spinnerets placed underneath the
middle of the abdomen, rather than at the end as in modern spiders. They were probably ground dwelling
predators, living in the giant clubmoss and fern forests of the mid-late Palaeozoic, where they were
presumably predators of other primitive arthropods. Silk may have been used simply as a protective covering
for the eggs, a lining for a retreat hole, and later perhaps for simple ground sheet web and trapdoor
construction.
As plant and insect life diversified so also did the spider's use of silk. Spiders with spinnerets at the
end of the abdomen (Mygalomorphae and Araneomorphae) appeared more than 250 million years ago,
presumably promoting the development of more elaborate sheet and maze webs for prey capture both on
ground and foliage, as well as the development of the safety dragline. The oldest mygalomorph,
Rosamygale, was described from the Triassic of France and belongs to the modern family Hexathelidae.
Megarachne servinei from the Permo-Carboniferous was once thought to be a giant mygalomorph spider
and, with its body length of 1 foot (34 cm) and leg span of above 20 inches (50 cm), the largest known spider
ever to have lived on Earth, but subsequent examination by an expert revealed that it was actually a
middling-sized sea scorpion.
By the Jurassic, the sophisticated aerial webs of the orb-weaver spiders had already developed to
take advantage of the rapidly diversifying groups of insects. A spider web preserved in amber, thought to be
110 million years old, shows evidence of a perfect "orb" web, the most famous, circular kind one thinks of
when imagining spider webs. An examination of the drift of those genes thought to be used to produce the
web-spinning behavior suggests that orb spinning was in an advanced state as many as 136 million years
ago.
The 110-million-year-old amber-preserved web is also the oldest to show trapped insects, containing
a beetle, a mite, a wasp's leg, and a fly.[1] The ability to weave orb webs is thought to have been "lost", and
sometimes even re-evolved or evolved separately, in different breeds of spiders since its first appearance.
A complete list of fossil spiders, down to species level, can be found at the American Museum of
Natural History's website.[1]
[edit] See also

• Spider taxonomy
• Insect evolution
[edit] References
1. ^ "LiveScience.com - Oldest Known Spider Web Discovered in Amber".
http://www.livescience.com/animalworld/060622_spider_webs.html. Retrieved June 25, 2006.
• Brunetta, Leslie and Craig, Catherine L. (2010). Spider silk : evolution and 400 million years
of spinning, waiting, snagging, and mating. New Haven: Yale University Press.
ISBN 9780300149227.
• Penney, D. (2008). Dominican Amber Spiders: a comparative neontological approach to
identification faunistics ecology and biogeography. Manchester: Siri Scientific Press. ISBN 978-0-
9558636-0-8.
• Penney, D. & Selden P.A. (2011). Fossil Spiders: the evolutionary history of a mega-diverse
order. Manchester: Siri Scientific Press. ISBN 978-0-9558636-5-3.
• Picture of spider fossil
[hide]v · d · eSpiders
Arachnology Ballooning · Behavior · Cannibalism ·

Evolution · Classification
Araneomorphae · Mesothelae ·
Taxonomy Mygalomorphae · Opisthothelae · List of
families of spiders · Lists of spider species
Arthropod leg · Book lung ·

Calamistrum · Cephalothorax · Chelicerae ·
Anatomy Cheliceral fang · Cribellum · Epigyne ·
Exuvia · Opisthosoma · Pedipalp · Scopulae ·
Silk · Spinneret · Urticating hair
Human Arachnophobia · Cultural depictions ·

interaction Spider bite · Spider fighting
Webs Spider web · Web decorations

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Evolution of fungi

The evolution of fungi has been going on since fungi diverged from other life around 1,500 million
years ago, (Wang et al., 1999)[1] with the glomaleans branching from the "higher fungi" at ~570 million years
ago, according to DNA analysis. (Schüßler et al., 2001; Tehler et al., 2000)[1] Fungi probably colonised the
land during the Cambrian, over 500 million years ago, (Taylor & Osborn, 1996)[1] but fossils only become
uncontroversial and common during the Devonian, 400 million years ago.[1]
[edit] Early fungi

A rich diversity of fungi is known from the lower Devonian Rhynie chert, an earlier record is absent.
Since fungi do not biomineralise, they do not readily enter the fossil record; there are only three claims of
early fungi. One from the Ordovician[2] has been dismissed on the grounds that it lacks any distinctly fungal
features, and is held by many to be contamination;[3] the position of a "probable" Proterozoic fungus is still
not established,[3] and it may represent a stem group fungus. There is also a case for a fungal affinity for the
enigmatic microfossil Ornatifilum. Since the fungi form a sister group to the animals, the two lineages must
have diverged before the first animal lineages, which are known from fossils as early as the Ediacaran.[4]
In contrast to plants and animals, the early fossil record of the fungi is meager. Factors that likely
contribute to the under-representation of fungal species among fossils include the nature of fungal fruiting
bodies, which are soft, fleshy, and easily degradable tissues and the microscopic dimensions of most fungal
structures, which therefore are not readily evident. Fungal fossils are difficult to distinguish from those of
other microbes, and are most easily identified when they resemble extant fungi.[5] Often recovered from a
permineralized plant or animal host, these samples are typically studied by making thin-section preparations
that can be examined with light microscopy or transmission electron microscopy.[6] Compression fossils are
studied by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to
examine surface details.[7]
The earliest fossils possessing features typical of fungi date to the Proterozoic eon, some 1,430
million years ago (Ma); these multicellular benthic organisms had filamentous structures with septa, and were
capable of anastomosis.[3] More recent studies (2009) estimate the arrival of fungal organisms at about 760–
1060 Ma on the basis of comparisons of the rate of evolution in closely related groups.[8] For much of the
Paleozoic Era (542–251 Ma), the fungi appear to have been aquatic and consisted of organisms similar to the
extant Chytrids in having flagellum-bearing spores.[9] The evolutionary adaptation from an aquatic to a
terrestrial lifestyle necessitated a diversification of ecological strategies for obtaining nutrients, including
parasitism, saprobism, and the development of mutualistic relationships such as mycorrhiza and
lichenization.[10] Recent (2009) studies suggest that the ancestral ecological state of the Ascomycota was
saprobism, and that independent lichenization events have occurred multiple times.[11]
The fungi probably colonized the land during the Cambrian (542–488.3 Ma), long before land plants.
[1] Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460 Ma) resemble modern-
day Glomerales, and existed at a time when the land flora likely consisted of only non-vascular bryophyte-like
plants.[12] Prototaxites, which was probably a fungus or lichen, would have been the tallest organism of the
late Silurian. Fungal fossils do not become common and uncontroversial until the early Devonian (416–
359.2 Ma), when they are abundant in the Rhynie chert, mostly as Zygomycota and Chytridiomycota.[1][13]
[14] At about this same time, approximately 400 Ma, the Ascomycota and Basidiomycota diverged,[15] and
all modern classes of fungi were present by the Late Carboniferous (Pennsylvanian, 318.1–299 Ma).[16]
Lichen-like fossils have been found in the Doushantuo Formation in southern China dating back to
635–551 Ma.[17] Lichens were a component of the early terrestrial ecosystems, and the estimated age of the
oldest terrestrial lichen fossil is 400 Ma;[18] this date corresponds to the age of the oldest known sporocarp
fossil, a Paleopyrenomycites species found in the Rhynie Chert.[19] The oldest fossil with microscopic
features resembling modern-day basidiomycetes is Palaeoancistrus, found permineralized with a fern from
the Pennsylvanian.[20] Rare in the fossil record are the homobasidiomycetes (a taxon roughly equivalent to
the mushroom-producing species of the agaricomycetes). Two amber-preserved specimens provide
evidence that the earliest known mushroom-forming fungi (the extinct species Archaeomarasmius legletti)
appeared during the mid-Cretaceous, 90 Ma.[21][22]
Some time after the Permian-Triassic extinction event (251.4 Ma), a fungal spike (originally thought
to be an extraordinary abundance of fungal spores in sediments) formed, suggesting that fungi were the
dominant life form at this time, representing nearly 100% of the available fossil record for this period.[23]
However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to
assess,[24] the spike did not appear worldwide,[25][26] and in many places it did not fall on the Permian-
Triassic boundary.[27]
[edit] References
Fungi portal
1. ^ a b c d e f in Brundrett, M.C. (2002). "Coevolution of roots and mycorrhizas of land plants".

New Phytologist 154 (2): 275–304. doi:10.1046/j.1469-8137.2002.00397.x.
2. ^ Redecker, D.; Kodner, R.; Graham, L.E. (2000). "Glomalean Fungi from the Ordovician".
Science 289 (5486): 1920. doi:10.1126/science.289.5486.1920. PMID 10988069.
3. ^ a b c Butterfield, N.J. (2005). "Probable Proterozoic fungi". Paleobiology 31 (1): 165–182.
doi:10.1666/0094-8373(2005)031.
4. ^ Miller, A.J. (2004). "A Revised Morphology of Cloudina with Ecological and Phylogenetic
Implications". http://ajm.pioneeringprojects.org/files/CloudinaPaper_Final.pdf. Retrieved 2007-04-24
5. ^ Donoghue MJ, Cracraft J. (2004). Assembling the tree of life. Oxford (Oxfordshire): Oxford
University Press. p. 187. ISBN 0-19-517234-5.
6. ^ Taylor and Taylor, p. 19.
7. ^ Taylor and Taylor, pp. 7–12.
8. ^ Lucking R, Huhndorf S, Pfister D, Plata ER, Lumbsch H. (2009). "Fungi evolved right on
track". Mycologia 101 (6): 810–822. doi:10.3852/09-016. PMID 19927746.
http://www.mycologia.org/cgi/content/abstract/09-016v1.
9. ^ James TY, et al. (2006). "Reconstructing the early evolution of Fungi using a six-gene
phylogeny". Nature 443 (7113): 818–22. doi:10.1038/nature05110. PMID 17051209.
10.^ Taylor and Taylor, pp. 84–94 and 106–107.
11.^ Schoch CL, Sung G-H, López-Giráldez F et al. (2009). "The Ascomycota tree of life: A
phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological
traits". Systematic Biology 58 (2): 224–39. doi:10.1093/sysbio/syp020. PMID 20525580.
12.^ Redecker D, Kodner R, Graham LE. (2000). "Glomalean fungi from the Ordovician".
Science 289 (5486): 1920–21. doi:10.1126/science.289.5486.1920. PMID 10988069.
13.^ Taylor TN, Taylor EL. (1996). "The distribution and interactions of some Paleozoic fungi".
Review of Palaeobotany and Palynology 95 (1–4): 83–94. doi:10.1016/S0034-6667(96)00029-2.
14.^ Dotzler N, Walker C, Krings M, Hass H, Kerp H, Taylor TN, Agerer R. (2009).
"Acaulosporoid glomeromycotan spores with a germination shield from the 400-million-year-old
Rhynie chert". Mycological Progress 8 (1): 9–18. doi:10.1007/s11557-008-0573-1.
15.^ Taylor JW, Berbee ML. (2006). "Dating divergences in the Fungal Tree of Life: review and
new analyses". Mycologia 98 (6): 838–49. doi:10.3852/mycologia.98.6.838. PMID 17486961.
16.^ Blackwell M, Vilgalys R, James TY, Taylor JW. (2009). "Fungi. Eumycota: mushrooms, sac
fungi, yeast, molds, rusts, smuts, etc.". Tree of Life Web Project. http://tolweb.org/Fungi/2377.
17.^ Yuan X, Xiao S, Taylor TN. (2005). "Lichen-like symbiosis 600 million years ago". Science
308 (5724): 1017–20. doi:10.1126/science.1111347. PMID 15890881.
http://www.sciencemag.org/cgi/pmidlookup?view=long&pmid=15890881.
18.^ Karatygin IV, Snigirevskaya NS, Vikulin SV. (2009). "The most ancient terrestrial lichen
Winfrenatia reticulata: A new find and new interpretation" . Paleontological Journal 43 (1): 107–14.
doi:10.1134/S0031030109010110.
http://www.springerlink.com/content/g8l8708r5gr36646/fulltext.pdf.
19.^ Taylor TN, Hass H, Kerp H, Krings M, Hanlin RT. (2005). "Perithecial Ascomycetes from
the 400 million year old Rhynie chert: an example of ancestral polymorphism". Mycologia 97 (1): 269–
85. doi:10.3852/mycologia.97.1.269. PMID 16389979.
20.^ Dennis RL. (1970). "A Middle Pennsylvanian basidiomycete mycelium with clamp
connections". Mycologia 62 (3): 578–84. doi:10.2307/3757529. http://jstor.org/stable/3757529.
21.^ Hibbett DS, Grimaldi D, Donoghue MJ. (1995). "Cretaceous mushrooms in amber". Nature
487: 487.
22.^ Hibbett DS, Grimaldi D, Donoghue MJ. (1997). "Fossil mushrooms from Miocene and
Cretaceous ambers and the evolution of homobasidiomycetes". American Journal of Botany 84 (7):
23.^ Eshet Y, Rampino MR, Visscher H. (1995). "Fungal event and palynological record of
ecological crisis and recovery across the Permian-Triassic boundary". Geology 23 (1): 967–70.
doi:10.1130/0091-7613(1995)023<0967:FEAPRO>2.3.CO;2.
24.^ Foster CB, Stephenson MH, Marshall C, Logan GA, Greenwood PF. (2002). "A revision of
Reduviasporonites Wilson 1962: description, illustration, comparison and biological affinities".
Palynology 26 (1): 35–58. doi:10.2113/0260035.
http://palynology.geoscienceworld.org/cgi/content/abstract/26/1/35.
25.^ López-Gómez J, Taylor EL. (2005). "Permian-Triassic transition in Spain: a
multidisciplinary approach". Palaeogeography, Palaeoclimatology, Palaeoecology 229 (1–2): 1–2.
doi:10.1016/j.palaeo.2005.06.028. http://www.sciencedirect.com/science?
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1&_urlVersion=0&_userid=1495569&md5=537a1a5b0a8e04cca2221ecb12afb1e9.
26.^ Looy CV, Twitchett RJ, Dilcher DL, Van Konijnenburg-van Cittert JHA, Visscher H. (2005).
"Life in the end-Permian dead zone". Proceedings of the National Academy of Sciences USA 162 (4):
653–59. doi:10.1073/pnas.131218098. PMID 11427710. "See image 2".
27.^ Ward PD, Botha J, Buick R, De Kock MO, Erwin DH, Garrison GH, Kirschvink JL, Smith R.
(2005). "Abrupt and gradual extinction among late Permian land vertebrates in the Karoo Basin,
South Africa". Science 307 (5710): 709–14. doi:10.1126/science.1107068. PMID 15661973.
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Categories: Evolution by taxon

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Evolutionary history of cephalopods


The cephalopods have a long geological history, with the first nautiloids found in late Cambrian
strata,[1] and purported stem-group representatives present in the earliest Cambrian lagerstätten.[2]
The class developed during the middle Cambrian, and underwent pulses of diversification during the
Ordovician period[3] to become diverse and dominant in the Paleozoic and Mesozoic seas. Small shelly
fossils such as Tommotia were once interpreted as early cephalopods, but today these tiny fossils are
recognized as sclerites of larger animals,[4] and the earliest accepted cephalopods date to the Middle
Cambrian Period. During the Cambrian, cephalopods are most common in shallow near-shore environments,
but they have been found in deeper waters too.[5] Cephalopods were thought to have "undoubtedly" arisen
from within the tryblidiid monoplacophoran clade.[6] However genetic studies suggest that they are more
basal, forming a sister group to the Scaphopoda but otherwise basal to all other major mollusc classes.[7]
The internal phylogeny of Mollusca, however, is wide open to interpretation – see mollusc phylogeny.
Contents
[hide]
• 1 Traditional view of origins
• 2 Early shelly record
• 2.1 Cambrian cephalopods
• 2.1.1 Knightoconus
• 2.1.2 Plectronoceras
• 2.1.3 Yochelcionellids
• 2.1.4 Ellesmerocerida
• 2.2 Early Ordovician diversity
• 2.3 Fossils mistaken for cephalopods
• 2.3.1 Volborthella
• 2.3.2 Shelbyoceras
• 2.3.3 Kirengellids
• 3 Coleoidea
• 4 Organ origins
• 5 Exceptional preservation
• 6 Notes
• 7 References
[edit] Traditional view of origins
The cephalopods were once thought to have evolved from a monoplacophoran-like ancestor[8] with
a curved, tapering shell,[9] and to be closely related to the gastropods (snails).[10] The similarity of the early
shelled cephalopod Plectronoceras to some gastropods was used in support of this view. The development
of a siphuncle would have allowed the shells of these early forms to become gas-filled (thus buoyant) in order
to support them and keep the shells upright while the animal crawled along the floor, and separated the true
cephalopods from putative ancestors such as Knightoconus, which lacked a siphuncle.[10] Negative
buoyancy (i.e. the ability to float) would have come later, followed by swimming in the Plectronocerida and
eventually jet propulsion in more derived cephalopods.[11] However, because chambered shells are found in
a range of molluscs – monoplacophora and gastropods as well as cephalopods – a siphuncle is essential to
ally a fossil shell conclusively to the cephalopoda.[9]:57 Chambered gastropods can be distinguished from
cephalopod shells by the absence of a siphuncle, the irregular spacing of septa, the layering of the shell and
(in younger or unmetamorphosed rocks) its microstructure, and the relatively thick width of the shell.[12] The
earliest such shells do not have the muscle scars which would be expected if they truly had a
monoplacophoran affinity.[9]:57 Additionally, the discovery that Nectocaris pteryx, which did not have a shell
and appeared to possess jet propulsion in the manner of "derived" cephalopods, complicated the question of
the order in which cephalopod features developed[2] – provided it is in fact a cephalopod and not an
arthropod.[13]
[edit] Early shelly record
Fossil orthoconic nautiloid from the Ordovician of Kentucky; an internal mold showing siphuncle and
half-filled camerae, both encrusted.
Understanding of early cephalopod origins is by necessity biased by the available fossil material,
which on the whole consists of shelly fossils. Critical fossils are detailed below; since their stratigraphic age
has guided the interpretation of the fossils,[14] they are listed in descending order of age.
[edit] Cambrian cephalopods

With the exception of the shelly genera Ectenolites and Eoclarkoceras, none of the 30+ Cambrian
cephalopod genera are known to have survived into the Ordovician.[15] Cambrian cephalopods differ from
their descendants by account of their small size (a few centimetres in length); long, tapering shells; smooth
shell surfaces; closely-spaced septa; and lack of deposits in their body chamber; several more specific
features are also only seen in certain groups of Cambrian cephalopod.[15]
[edit] Knightoconus
Knightoconus is a Cambrian monoplacophoran[16] thought to represent an ancestor to the
cephalopods. It had a chambered, conical shell, but lacked a siphuncle.[10] Although earlier molluscan
fossils are also septate, Knightoconus is the latest septate mollusc before the first sipunculate cephalopods –
a point that has been taken to prove its relevance to the Cephalopoda.[14] The absence of this siphuncle has
been taken as evidence against cephalopod ancestry – how, it is argued, could a siphuncle evolve to
penetrate existing septa? The prevailing argument suggests that a strand of tissue remained attached to the
previous septum as the mollusc moved forwards and deposited its next septum, producing an obstacle to the
complete closure of the septum and becoming mineralised itself.[17] 10 or more septa are found in mature
individuals, occupying around a third of the shell – septa form very early and have been found in specimens
as small as 2 mm in length.[14] Septa are uniformly spaced,[14] which is inconsistent with a gastropod
affinity.[12] Unlike monoplacophoran fossils, there is no evidence of muscle scarring in Knightoconus fossils.
[14]
[edit] Plectronoceras
Plectronoceras is arguably the earliest known crown-group cephalopod, dating to the Upper
Cambrian.[1] Its 14 known specimens hail from the basal Fengshan Formation (north-east China) of the
earliest Fengshanian stage.[6] None of the fossils are complete, and none show the tip or opening of the
shell.[6] Approximately half of its shell was filled with septa; 7 were recorded in a 2 cm shell.[14] Its shell
contains transverse septa separated by about half a millimetre, with a siphuncle on its concave side.[6] Its
morphology matches closely to that hypothesised for the last common ancestor of all cephalopods,[6] and
the Plectronocerida have been said to be the ancestors of the Ellesmerocerids, the first "true cephalopods".
[edit] Yochelcionellids
The Yochelcionellids have given rise to the "snorkel hypothesis". These fossils are aseptate
helcionellids with a snorkel-like tube on one surface. The snorkel has been seized upon as characteristic of a
cephalopod-like water circulatory system, or perhaps as a precursor to the siphuncle. However, neither of
these theories have been borne out.[14]
[edit] Ellesmerocerida
Sketch of the soft-part anatomy of early ellesmeroceridans

The earliest true cephalopod order to emerge was the Ellesmerocerida, which were quite small
organisms; their shells were slightly curved, and the internal chambers were closely spaced. The siphuncle
penetrated the septa with meniscus-like holes.[3] This marks an important difference from the earlier
cephalopods, whose siphuncle was positioned at the edge of the septum and against the shell wall.[14] On
the basis of muscle scars preserved in such genera as Paradakeoceras and Levisoceras, these animals are
reconstructed with a straight body and dorsal shell, with the head at the anterior, concave surface of the
shell, and the funnel – consisting of a pair of folds in the foot – at the rear — not juxtaposed with the head as in
later, oncocerid-like forms.[11]
[edit] Early Ordovician diversity

The Ellesmerocerids were the only shelled cephalopods that survived the end-Cambrian extinction,
and all subsequent cephalopods, which diversified throughout the Ordovician period, are thus thought to be
derived from these forms.
Early cephalopods had fine shells that could not cope with the pressures of deep water.[3] In the mid
Tremadoc, these were supplemented by larger shells around 20 cm in length; these larger forms included
straight and coiled shells, and fall into the orders Endocerida (with wide siphuncles) and Tarphycerida (with
narrow siphuncles).[3]
By the mid Ordovician these orders are joined by the Orthocerids, whose first chambers are small
and spherical, and Lituitids, whose siphuncles are thin. The Oncocerids also appear during this time; they are
restricted to shallow water and have short exogastric conchs.[3] The mid Ordovician saw the first
cephalopods with septa strong enough to cope with the pressures associated with deeper water, and could
inhabit depths greater than 100–200 m.[3] The wide-siphuncled Actinocerida and the Discocerida both
emerged during the Darriwilian.[3] The direction of coiling would prove to be crucial to the future success of
the lineages; endogastric coiling would only permit large size to be attained with a straight shell, whereas
exogastric coiling – initially rather rare – permitted the spirals familiar from the fossil record to develop, with
their corresponding large size and diversity.[17] (Endogastric mean the shell is curved so as the ventral or
lower side is longitudinally concave (belly in); exogastric means the shell is curved so as the ventral side is
longitudinally convex (belly out) allowing the funnel to be pointed backwards beneath the shell.)[17]
Curved shells brought a number of benefits. Firstly, minerals are not required in as large quantities,
as each successive whorl builds on the one before. Also, the organism is more stable (its centre of mass
coincides with its centre of buoyancy) and more manoeuvrable.[18]
Early cephalopods were likely predators near the top of the food chain.[19] In the Early Palaeozoic,
their range was far more restricted than today; they were mainly constrained to sub-littoral regions of shallow
shelves of the low latitudes, and usually occur in association with thrombolites.[20] A more pelagic habit was
gradually adopted as the Ordovician progressed.[20] Deep-water cephalopods, whilst rare, have been found
in the Lower Ordovician – but only in high-latitude waters.[20]
[edit] Fossils mistaken for cephalopods

A number of fossils have historically been considered to represent components of the cephalopods'
history, but been reinterpreted on the basis of additional material.
[edit] Volborthella
When it was discovered in 1888,[14] it was thought that the early Cambrian Volborthella was a
cephalopod. However discoveries of more detailed fossils showed that Volborthella’s small, conical shell was
not secreted but built from grains of the mineral silicon dioxide (silica); neither was it septate.[21] This illusion
was a result of the laminated texture of the organisms' tests.[22] Therefore, Volborthella’s classification is
now uncertain.[23]
[edit] Shelbyoceras
Because the characters differentiating monoplacophora from cephalopods are few, several
monoplacophora have been mistaken for cephalopod ancestors. One such genus is Shelbyoceras, which
was reclassified based on a depressed groove that forms a band around the shell, which is similar to a
feature seen in Hypseloconus.[24] The septa in this genus are either closely or irregularly spaced.[24]
[edit] Kirengellids
The Kirengellids are a group of shells that, whilst originally aligned to the monoplacophoran ancestry
of the cephalopods, have been reinterpreted as brachiopods.[25]
[edit] Coleoidea
An ammonitic ammonoid with the body chamber missing, showing the septal surface (especially at
right) with its undulating lobes and saddles.
The ancestors of coleoids (including most modern cephalopods) and the ancestors of the modern
nautilus, had diverged by the Floian Age of the Early Ordovician Period, over 470 million years ago. We know
this because the orthocerids were the first known representatives of the neocephalopoda,[26] were ultimately
the ancestors of ammonoids and coleoids, and had appeared by the Floian.[20] It is widely held that the
Bactritida, an Silurian–Triassic group of orthocones, are paraphyletic to the coleoids and ammonoids – that is,
the latter groups arose from within the Bactritida.[27]:393 An increase in the diversity of the coleoids and
ammonoids is observed around the start of the Devonian period, and corresponds with a profound increase
in fish diversity. This could represent the origin of the two derived groups.[27]
Unlike most modern cephalopods, most ancient varieties had protective shells. These shells at first
were conical but later developed into curved nautiloid shapes seen in modern nautilus species. It is thought
that competitive pressure from fish forced the shelled forms into deeper water, which provided an
evolutionary pressure towards shell loss and gave rise to the modern coleoids, a change which led to greater
metabolic costs associated with the loss of buoyancy, but which allowed them to recolonise shallow waters.
[10]:36 However, some of the straight-shelled nautiloids evolved into belemnites, out of which some evolved
into squid and cuttlefish.[verification needed] The loss of the shell may also have resulted from evolutionary
pressure to increase manoeuvrability, resulting in a more fish-like habit.[28]:289 This pressure may have
increased as a result of the increased complexity of fish in the late Palaeozoic, increasing the competitive
pressure.[28]:289 Internal shells still exist in many non-shelled living cephalopod groups but most truly
shelled cephalopods, such as the ammonites, became extinct at the end of the Cretaceous.
[edit] Organ origins
The tentacles of the ancestral cephalopod developed from the mollusc's foot;[29] the ancestral state
is thought to have had five pairs of tentacles which surrounded the mouth.[29] Smell-detecting organs
evolved very early in the cephalopod lineage.[29]
The earliest cephalopods,[note 1] like Nautilus and some coeloids, appeared to be able to propel
themselves forwards by directing their jet backwards.[28]:289 Because they had an external shell, they would
not have been able to generate their jets by contracting their mantle, so must have used alternate methods:
such as by contracting their funnels or moving the head in and out of the chamber.[28]:289
[edit] Exceptional preservation

The preservation of cephalopod soft parts is not entirely unusual; soft-bodied fossils, especially of
coeloids (squid), are relatively widespread in the Jurassic,[30] but phosphatized remains are unknown before
this period.[31] On the other hand, soft parts – including a possible ink sac — are known from the Paleozoic
Hunsrück Slate and Francis Creek shale.[32]
[edit] Notes
1. ^ Ordovician orthocone nautiloids are the first for which trace fossil evidence is available
[edit] References
1. ^ a b Dzik, J. (1981). "Origin of the cephalopoda" (PDF). Acta Palaeontologica Polonica 26
(2): 161–191. http://www.paleo.pan.pl/people/Dzik/Publications/Cephalopoda.pdf.
2. ^ a b Smith, M. R.; Caron, J. B. (2010). "Primitive soft-bodied cephalopods from the
Cambrian". Nature 465 (7297): 469. doi:10.1038/nature09068. PMID 20505727.
Bibcode: 2010Natur.465..469S. http://individual.utoronto.ca/martinsmith/nectocaris.html. edit
3. ^ a b c d e f g Kröger, B.; Yun-bai, Y. B. (2009). "Pulsed cephalopod diversification during the
Ordovician". Palaeogeography Palaeoclimatology Palaeoecology 273: 174–201.
doi:10.1016/j.palaeo.2008.12.015. edit
4. ^ Begtson, Stefan (1970). "The Lower Cambrian fossil Tommotia". Lethaia 3 (4): 363–392.
doi:10.1111/j.1502-3931.1970.tb00829.x.
5. ^ Landing, Ed; Kröger, Björn (2009). "The Oldest Cephalopods from East Laurentia". Journal
of Paleontology 83: 123–127. doi:10.1666/08-078R.1.
6. ^ a b c d e Clarke, M.R.; Trueman, E.R., ed (1988). "Main features of cephalopod evolution".
The Mollusca. 12: Palaeontology and Neontology of Cephalopods. Orlando, Fla.: Acad. Pr..
ISBN 0127514120.
7. ^ Giribet; Okusu, A; Lindgren, A.R.; Huff, S.W.; Schrödl, M; Nishiguchi, M.K. (May 2006).
"Evidence for a clade composed of molluscs with serially repeated structures: monoplacophorans are
related to chitons" (Free full text). Proceedings of the National Academy of Sciences of the United
States of America 103 (20): 7723–7728. doi:10.1073/pnas.0602578103. PMID 16675549.
PMC 1472512. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=16675549. edit
8. ^ Lemche, H; Wingstrand, K.G. (1959). "The anatomy of Neopilina galatheae Lemche, 1957
(Mollusca, Tryblidiacea)." (Link to free full text + plates). Galathea Rep. 3: 9–73.
http://www.zmuc.dk/inverweb/Galathea/index.html.
9. ^ a b c Wingstrand, KG (1985). "On the anatomy and relationships of Recent
Monoplacophora" (Link to free full text + plates). Galathea Rep. 16: 7–94.
http://www.zmuc.dk/inverweb/Galathea/Galathea_p5.html.
10.^ a b c d "Origin and Evolution". Cephalopods – ecology and fisheries. 2005. pp. 36.
doi:10.1002/9780470995310.ch3. ISBN 0632060484.
11.^ a b Kroger, B. (2007). "Some Lesser Known Features of the Ancient Cephalopod Order
Ellesmerocerida (nautiloidea, Cephalopoda)". Palaeontology 50 (3): 565–572. doi:10.1111/j.1475-
4983.2007.00644.x.
12.^ a b Otto P. Majewske (1974). Recognition of Invertebrate Fossil Fragments in Rocks and
Thin Sections. Leiden, Netherlands: E.J. Brill. p. 76. http://books.google.com/?
id=m8gUAAAAIAAJ&pg=PA76.
13.^ Mazurek, D.; Zatoń, M. (2011). "Is Nectocaris pteryx a cephalopod?". Lethaia.
doi:10.1111/j.1502-3931.2010.00253.x. edit
14.^ a b c d e f g h i Webers, G. F.; Yochelson, E. L. (1989). "Late Cambrian molluscan faunas
and the origin of the Cephalopoda". In Crame, J. A.. Origins and Evolution of the Antarctic Biota . 47.
Geological Society, London: Special Publications. pp. 29. doi:10.1144/GSL.SP.1989.047.01.04. edit
15.^ a b Chen, J. Y.; Teichert, C. (1983). "Cambrian cephalopods". Geology 11: 647-650.
doi:10.1130/0091-7613(1983)11<647:CC>2.0.CO;2. ISSN 0091-7613. edit
16.^ doi:10.1111/j.1502-3931.1973.tb01199.x
17.^ a b c Holland, C. H. (1987). "The nautiloid cephalopods: a strange success: President's
anniversary address 1986". Journal of the Geological Society 144: 1–0.
doi:10.1144/gsjgs.144.1.0001. edit
18.^ Wells, M.J.; O'Dor, R.K.. "Jet Propulsion and the Evolution of the Cephalopods". Bulletin of
Marine Science, Volume 49, Number 1, July 1991 , pp. 419-432(14).
19.^ Boyle, Peter; Rodhouse, Paul (2004). Cephalopods : ecology and fisheries. Ames, Iowa:
Blackwell. doi:10.1002/9780470995310.ch2. ISBN 0632060484. http://books.google.com/?
id=4UtCi2B4VnoC.
20.^ a b c d Kröger, B. R.; Servais, T.; Zhang, Y.; Kosnik, M. (2009). "The Origin and Initial Rise
of Pelagic Cephalopods in the Ordovician". PLoS ONE 4 (9): e7262.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007262. Retrieved 2009-
10-30. edit
21.^ Lipps, J. H.; Sylvester, A. G. (1 March 1968). "The Enigmatic Cambrian Fossil Volborthella
and Its Occurrence in California". Journal of Paleontology (Journal of Paleontology, Vol. 42, No. 2) 42
(2): 329–336. ISSN 00223360. http://jstor.org/stable/1302218. edit
22.^ "Lower Cambrian fossil Volborthella: the whole truth or just a piece of the beast?". Geology
21: 805. 1993. doi:10.1130/0091-7613(1993)021<0805:LCFVTW>2.3.CO;2. edit
23.^ Hagadorn, J.W.; Waggoner, B.M. (2002). "The Early Cambrian problematic fossil
Volborthella: New insights from the Basin and Range". In Corsetti, F.A.. Proterozoic-Cambrian of the
Great Basin and Beyond, Pacific Section SEPM Book 93 . SEPM (Society for Sedimentary Geology).
pp. 135–150. http://www3.amherst.edu/~jwhagadorn/publications/volb.pdf
24.^ a b Stinchcomb, B. L. (1980). "New Information on Late Cambrian Monoplacophora
Hypseloconus and Shelbyoceras (Mollusca)". Journal of Paleontology (Paleontological Society) 54
(1): 45–49. http://jstor.org/stable/1304159. edit
25.^ Dzik, Jerzy (2010). "BRACHIOPOD IDENTITY OF THE ALLEGED MONOPLACOPHORAN
ANCESTORS OF CEPHALOPODS". Malacologia %V 52 %N 1 %P 97-113.
http://www.paleo.pan.pl/people/Dzik/Publications/Angarella.pdf.
26.^ Kröger, Björn (2006). "Early growth-stages and classification of orthoceridan Cephalopods
of the Darriwillian (Middle Ordovician) of Baltoscandia". Lethaia 39 (2): 129–139.
doi:10.1080/00241160600623749. http://www3.interscience.wiley.com/journal/119918421/abstract.
27.^ a b Young, R.E.; Vecchione, M.; Donovan, D.T.. "The evolution of coleoid cephalopods and
their present biodivesity and ecology". In Payne, AIL; Lipin'ski, M.R.; Clarke, M.R.; Roeleveld, M.A.C.
Cephalopod biodiversity, ecology & evolution. South Afriocan journal of Marine Sciences. 20.
pp. 393–420.
28.^ a b c d Wilbur, Karl M.; Trueman, E.R.; Clarke, M.R., eds. (1985), The Mollusca, 11. Form
and Function, New York: Academic Press, ISBN 0-12-728702-7
29.^ a b c Shigeno, S.; Sasaki, T.; Moritaki, T.; Kasugai, T.; Vecchione, M.; Agata, K. (2008).
"Evolution of the cephalopod head complex by assembly of multiple molluscan body parts: Evidence
from Nautilus Embryonic Development". Journal of Morphology 269 (1): 1–17.
doi:10.1002/jmor.10564. PMID 17654542.
30.^ Kear, A.J.; Briggs, D.E.G.; Donovan, D.T. (1995). "Decay and fossilization of non-
mineralized tissue in coleoid cephalopods". Palaeontology 38 (1): 105–132.
http://palaeontology.palass-pubs.org/pdf/Vol%2038/Pages%20105-131.pdf. Retrieved 2009-04-21.
31.^ Briggs, D. E. G.; Kear, A. J.; Martill, D. M.; Wilby, P. R. (1993). "Phosphatization of soft-
tissue in experiments and fossils". Journal of the Geological Society 150: 1035–1033.
doi:10.1144/gsjgs.150.6.1035. edit
32.^ Allison, P. A. (1987). "A new cephalopod with soft parts from the Upper Carboniferous
Francis Creek Shale of Illinois, USA". Lethaia 20 (78): 117–121. doi:10.1111/j.1502-
3931.1987.tb02028.x. http://www3.interscience.wiley.com/journal/120019493/abstract. edit

• Chen, J. Y.; Teichert, C. (1983). "Cambrian cephalopods". Geology 11: 647-650.
doi:10.1130/0091-7613(1983)11<647:CC>2.0.CO;2. ISSN 0091-7613. edit
[hide]v · d · eNotable fossil cephalopods (listed by first occurrence)

Cenozoic The belemnite-cuttlefish-like Belosaepia
• advanced nautiloids; Nautilaceae • true

ammonites;
Mesozoic • early coleoids: Proteroctopus, Styletoctopus,
Keuppia, Palaeoctopus, Paleocirroteuthis
• ceratitid ammonoids; • late Nautilida Evolutionary history of
cephalopods
• Long-lasting lineages: Belemnites • Goniatite

and ceratite ammonoids • Probable coleoid ancestor
Bactritida
• Early forms: the earliest cephalopod group
Palaeozoic Ellesmerocerida • Orthocones: Endocerida,
Orthocerida, Actinocerida • Brevicones: Ascocerida,
Oncocerida • Earliest coiled cephalopods:
Tarphycerida • Spirulid?: Shimanskya
• Octopus: Pohlsepia
Cambrian • earliest unambiguous cephalopods;

Plectronocerida • Plectronoceras
• Monoplacophoran-like ancestral forms: •
Knightoconus
• possible, nude, "stem-group cephalopods":
Nectocarididae
Retrieved from "http://en.wikipedia.org/wiki/Evolutionary_history_of_cephalopods"
Categories: Extinct cephalopods | Evolution by taxon | Cephalopods

W000
Evolution of the Vertebrates


This article may not meet the general notability guideline. Please help to establish
notability by adding reliable, secondary sources about the topic. If notability cannot be
established, the article is likely to be merged, redirected, or deleted. (June 2008)
Colbert's Evolution of the Vertebrates

5th Edition Book Cover
Author Edwin H. Colbert, Michael Morales, Eli C. Minkoff,
Language English, Japanese
Subject(s) Vertebrate Evolution
Publisher Wiley-Liss
Publication date December 15, 2001

Pages 576
ISBN 0-471-38461-5
OCLC Number 46504406
Dewey Decimal 566 21
LC Classification QE841 .C68 2001

Evolution of the Vertebrates, subtitled "A History of the Backboned Animals Through Time" is a basic
paleontology textbook by Edwin H. Colbert, published by John Wiley & Sons.
[edit] Overview
The first and second editions (1955 and 1969) provide an overview of the entire range of vertebrate
evolution, and are illustrated by the distinctive drawings of Lois Darling. The style of writing is very light and
readable, and technical concepts kept to a minimum. In the book vertebrate evolution is studied utilizing
comparative anatomy & functional morphology of existing vertebrates, and fossil records. The book is
"considered a classic" (New York Times, 25 November 2001) and was used very frequently as a college-
level text on the subjects of basic paleontology and vertebrate evolution.
These editions predate the cladistic revolution and so contain a number of chapters and sections
dedicated to paraphyletic taxa (Labyrinthodonts, Thecodonts, Condylarths, etc.) which nevertheless
constituted an important part of the understanding of the time.
[edit] Latest Publishing
The latest edition, the fifth edition, was cowritten with Michael Morales and Eli C. Minkoff, and has
been revised to incorporate recent discoveries and current developments in the field of vertebrate evolution.
This new addition includes entirely new sections. Some examples of these are conodonts, primates, and
dinosaurs. Some new topics that the fifth edition discuss are:
• Analysis of morphological and molecular data
• Early ruling reptiles
• Basic adaptation of ungulates
• Early diversification of vertebrates
• The evolution of dinosaurs
• The origin of mammals
The fifth edition has generally received praise from both professors and students using this textbook
on the college level. It has, however, received mild criticism for its out-of-date material. Others however
argue that the broad scope of the edits in the fifth edition make up for any generalizations pertaining to
specific details related to geological palentology.
[edit] Bibliography
• Edwin H. Colbert, (1969), Evolution of the Vertebrates, John Wiley & Sons (2nd ed.)
• Edwin H. Colbert, Michael Morales, Eli C. Minkoff, 2001 Colbert's Evolution of the
Vertebrates: A History of the Backboned Animals Through Time , 5th Edition, Wiley, ISBN 0-471-
38461-5
• Publisher's Website and Book Overview
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_the_Vertebrates"
Categories: Paleontology books

W000
Evolution of influenza

Influenza (Flu)
Types
Avian (A/H5N1 subtype) · Canine
Equine · Swine (A/H1N1 subtype)
Vaccines
2009 pandemic (Pandemrix)
ACAM-FLU-A · Fluzone · Influvac
Live attenuated (FluMist) · Optaflu
Treatment
Amantadine · Arbidol · Laninamivir
Oseltamivir · Peramivir · Rimantadine
Vitamin D · Zanamivir
Pandemics
2009 Swine · 1968–1969 Hong Kong · 1918
Outbreaks
2008 West Bengal
2007 Bernard Matthews H5N1
2007 Australian equine
2006 H5N1 India · 1976 swine flu
See also
Flu season · Influenza evolution
Influenza research
Influenza-like illness
v·d·e
To comply with Wikipedia's guidelines, the introduction of this article may need to be
rewritten. Please discuss this issue on the talk page and read the layout guide to make sure
the section will be inclusive of all essential details. (April 2010)
The virus causing influenza is one of the best known pathogens found in various species. In
particular, the virus is found in birds as well as mammals including horses, pigs, and humans.[1] The
phylogeny, or the evolutionary history of a particular species, is an important component when analyzing the
evolution of influenza. Phylogenetic trees are graphical models of the relationships between various species.
They can be used to trace the virus back to particular species and show how organisms that look so different
may be so closely related.[1]
Contents
[hide]
• 1 Mechanisms of evolution
• 1.1 Reassortment
• 1.2 Drift
• 2 Transmission
• 2.1 Species and barriers
• 2.2 Geographic differences
• 3 Phylogenetic analysis
• 4 Future impact
• 5 References
[edit] Mechanisms of evolution

Two common mechanisms by which viruses evolve are reassortment and genetic drift.[2]
[edit] Reassortment
Reassortment allows new viruses to evolve under both natural conditions and in artificial cultures.[2]
In fact, the 1957 evolution of the H2N2 virus is thought to be a result of reassortment.[2] In this case, human
H1N1 strains and avian influenza A genes were mixed.[2] Infecting tissue cultures can demonstrate how
pathogenic qualities can evolve for a particular species even though the reassorted virus may be
nonpathogenic for another species.[2] A prime example of evolution under natural conditions is the
reassortment of two avian influenza strains that were discovered in dead seals back in 1979.[2]
[edit] Drift
New viruses can also emerge by drift. Drift can refer to genetic drift or antigenic drift.[2] Mutation and
selection for the most advantageous variation of the virus takes place during this form of evolution.[2]
Antigenic mutants can evolve quickly due to the high mutation rate in viruses. Influenza antigenic drift
happens when two influenza viruses infect on cell. When new ones come out they have a segment from the
others genome that could let som but not enoygh antibodies to bind. Also the receptor could not bind to
antibodies.[2] This evolution occurs under the pressure of antibodies or immune system responses.[2]
[edit] Transmission
[edit] Species and barriers
The transmission, or how the influenza virus is passed from one species to another, varies. There are
barriers that prevent the flow of the virus between some species ranging from high to low transmission. For
example, there is no direct pathway between humans and birds.[2] Pigs however, serve as an open pathway.
There is a limited barrier for them to spread the virus.[2] Therefore, pigs act as a donator of the virus
relatively easily.
[edit] Geographic differences

Phylogenetic maps are a graphical representation of the geographic relationships among species.
They indicate that the human influenza virus is minimally impacted by geographic differences.[1] However,
both swine and avian influenza does appear to be geographically dependent.[1] All three groups (avian,
swine, and human) show chronological differences. The human influenza virus is retained in humans only,
meaning it does not spread to other species.[1] Some lineages and sublineages of the virus emerge and may
be more prevalent in certain locations. For instance, many human influenza outbreaks begin in Southeast
Asia.[2]
[edit] Phylogenetic analysis

Phylogenetic analysis can help determine past viruses and their patterns as well as determining a
common ancestor of the virus. Past studies reveal that an avian virus spread to pigs and then to humans
approximately 100 years ago.[2] This resulted in human lineages further evolving and becoming more
prominent and stable.[2]
Analysis can also feature relationships between species. The 1918 Spanish influenza virus
demonstrates this. Even though the hemagglutinin (HA) gene was closer in relation to avian strains than
mammalian ones, it was, in fact, mammalian.[3] The gene may have been adapting in humans even prior to
1918.[3] Breaking down the phylogenetic history of the influenza virus shows that there is a common
ancestor that reaches back before the 1918 outbreak that links the current human virus to the swine virus.[4]
The ancestor was derived from an avian host.[2]
[edit] Future impact

Looking at the past phylogenetic relationships of the influenza virus can help lead to information
regarding treatment resistance, selecting vaccine strains, and future influenza strains.
In current years, there has been a huge increase in the amount of resistance to certain drugs,
including the antiviral compound adamantine.[5] In fact, its resistance has recently climbed from 2 percent to
nearly 90 percent.[5] These records of built up resistance infer that drugs, such as adamantine, will not be
useful against the influenza virus in the future.
Various lineages may continue their presence and reassort indicating the importance of a complete-
genome approach to determine new influenza strains and future epidemics.[6][7] In terms of vaccine strain
selection, antigenic clades evolve by reassortment, not by antigenic drift.[6] This was shown in the 2003-
2004 influenza outbreak.[6]
Phylogenetic trees can help determine what codons in the HA gene of the influenza A virus have
changed in past outbreaks.[8] The more mutations there are in a virus strain, the more likely that strain is to
be a generator of a new lineage in future influenza seasons.[8]
[edit] References
1. ^ a b c d e Liu, S; Kang, J; Chen, J; Tai, D; Jiang, W; Hou, G; Chen, J; Li, J et al. (2009).
"Panorama phylogenetic diversity and distribution of type A influenza virus". PLoS ONE 4: 1–20.
doi:10.1371/journal.pone.0005022. http://www.plosone.org/article/info:doi
%2F10.1371%2Fjournal.pone.0005022.
2. ^ a b c d e f g h i j k l m n o p Scholtissek, C (1995). "Molecular evolution of influenza viruses".
Virus Genes 11 (2-3): 209–215. doi:10.1007/BF01728660. PMID 8828147.
http://springerlink.metapress.com/content/v5747t6n11622627/fulltext.pdf.
3. ^ a b Reid, A; Fanning, T; Hultin, J; Taubenberger, J (1999). "Origin and evolution of the 1918
‘‘Spanish’' influenza virus hemagglutinin gene". Proceedings of the National Academy of Sciences
USA 96: 1651–1656. doi:10.1073/pnas.96.4.1651. http://www.pnas.org/content/96/4/1651.full.pdf.
4. ^ Gorman, O; Donis, R; Kawaoka, Y; Webster, R (1990). "Evolution of influenza A virus PB2
genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A
virus". Journal of Virology 64 (10): 4893–4902. PMID 2398532. PMC 247979.
http://jvi.asm.org/cgi/content/abstract/64/10/4893.
5. ^ a b Simonsen, L; Viboud, C; Grenfell, B; Dushoff, J; Jennings, L; Smit, M; Macken, C; Hata,
M et al. (2007). "The genesis and spread of reassortment human influenza A/H3N2 viruses
conferring adamantane resistance". Molecular Biology and Evolution 24 (8): 24.
doi:10.1093/molbev/msm103. PMID 17522084.
http://mbe.oxfordjournals.org/cgi/content/full/24/8/1811#SEC4.
6. ^ a b c Holmes, E; Ghedin, E; Miller, N; Taylor, J; Bao, Y; St George, K; Grenfell, B; Salzberg,
S et al. (2005). "Whole-genome analysis of human influenza A virus reveals multiple persistent
lineages and reassortment among recent H3N2 viruses". Plos Biology 3: 1579–1589.
doi:10.1371/journal.pbio.0030300.
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030300.
7. ^ Vana, G; Westover, K (2008). "Origin of the 1918 Spanish influenza virus: A comparative
genomic analysis". Molecular Phylogenetics and Evolution 3: 1100–1110.
8. ^ a b Fitch, W; Bush, R; Bender, C; Subbarao, K; Cox, N year=2000 (2000). "Predicting the
evolution of human influenza A". Journal of Heredity 91 (3): 183–185. doi:10.1093/jhered/91.3.183.
PMID 10833042. http://jhered.oxfordjournals.org/cgi/reprint/91/3/183.
Processes of Adaptation · Macroevolution · Microevolution · Speciation

evolution
Population genetic
Evolutionary
developmental
concepts

Modes of

Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_influenza"
Categories: Influenza | Mutation | Evolution by taxon

W000
Evolution of hair

A recent study by scientists from Medical University of Vienna traced the origins of hair to the
common ancestor of mammals, birds and lizards that lived 310 million years ago. The study found chickens,
lizards and humans all possessed a similar set of genes that was involved in the production of alpha keratin.
In chickens and lizards, the α-keratin produced was found in their claws, but in mammals it was used to
produce hair. The scientists involved were still searching for the mechanisms that allowed mammals to use
the α-keratins of animal claws to produce hair.[1][2]
[edit] References
1. ^ Human hair linked to dinosaur claws Origins of hair go back 310 million years to common
ancestor
2. ^ Eckhart L, Valle LD, Jaeger K, et al. (November 2008). "Identification of reptilian genes
encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair".
Proceedings of the National Academy of Sciences of the United States of America 105 (47): 18419–
23. doi:10.1073/pnas.0805154105. PMID 19001262.
Processes of
Population genetic
Evolutionary
developmental Canalisation · Inversion · Modularity · Phenotypic plasticity
biology (Evo-devo)
concepts

Modes of


This evolution-related article is a stub. You can help Wikipedia by expanding it.v · d
·e
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_hair"
Categories: Hair | Evolution by phenotype | Mammal anatomy | Evolution stubs

W000
The Evolution of Melanism


The Evolution of Melanism: a study of recurring necessity; with special reference to industrial
melanism in the Lepidoptera is a 1973 science book by the lepidopterist Bernard Kettlewell.
The book includes Kettlewell's original papers in the journal Heredity on his classic predation
experiments on the peppered moth. It also covers Kettlewell's experiments in the Hebrides.
[edit] See also

• Industrial melanism
[edit] References
• The Evolution of Melanism: A study of recurring necessity; with special reference to industrial
melanism in the Lepidoptera. Oxford, Clarendon Press, 1973. ISBN 0-19-857370-7
[hide]v · d · ePeppered moth
Biology Overview, ecology, and genetics · Evolution of · Experiments on
Writers and Bernard Kettlewell · Mike Majerus · Cyril Clarke · Bruce Grant · E. B.
researchers Ford · Jonathan Wells · Judith Hooper
Works The Evolution of Melanism · Melanism: Evolution in Action · Icons of

Evolution · Of Moths and Men
W000
Evolution of the Hippocampus

This article is an orphan, as few or no other articles link to it. Please introduce links
to this page from related articles; suggestions may be available. (April 2010)
Contents
[hide]
• 1 Earliest spatial recognition centers
• 2 Fish and reptiles
• 3 The olfactory connection
• 4 Comparison of mammalian and avian hippocampus
• 4.1 Structurally
• 4.2 Functionally
• 5 Notes
• 6 References
[edit] Earliest spatial recognition centers

Until recently, mushroom bodies in insects had been thought to be the center of voluntary control,
evidence that insects were not just innate creatures.[1] Much research has found that mushroom bodies are
closely involved in learning and memory, especially in regard to spatial memory and olfaction.[2] While it
might have been assumed that mushroom bodies were the ancient precursor to the mammalian
hippocampus, it is highly unlikely that the structures are shared derived traits, due to the major structural and
neuronal differences between mushroom bodies and the hippocampus.[2] In addition, mammals and insects
share a very distant ancestor that probably did not possess mushroom bodies. However, there are interesting
analogies in spatial function between mushroom bodies and the hippocampus. Mushroom bodies are
primarily involved in olfactory memory, just as the hippocampus is in close connection with the olfactory bulb.
[3] Mizunami et al.. (1993)[4] also found many similarities in place memory between cockroaches and
vertebrates.
Another distant relative of vertebrates, the octopus has the ability to navigate and use spatial
landmarks,[5] suggesting it possess a brain structure specializing in spatial memory. However, octopuses
have no brain structures like that of vertebrates, once again suggesting a convergent evolution, and, more
importantly a universal need for spatial recognition.
[edit] Fish and reptiles

The fish pallium is the earliest vertebrate predecessor to the mammalian and avian cerebrum. Even
jawless fish, the most primitive vertebrates, possess a pallium.[6] It has been shown that lesioning the lateral
pallium of goldfish disrupts spatial and temporal learning,[7] indicating that the lateral pallium evolved into the
hippocampus. Portavella and Vargas (2005)[8] believe that there is enough evidence to suggest that a
vertebrate ancestor 400 million years ago possessed a pallium with modern-day spatial functions present.
The reptile’s medial pallium, the closest vertebrate related to birds and mammals, evolved from the
fish lateral pallium, and has been shown to be homologous to the hippocampus in spatial functioning.[9][10]
Further evidence of homology includes findings that similar neurotransmitters found in the hippocampus are
also found in the medial pallium of reptiles.[7][11] Reptiles also possess a high zinc area, the medial small-
celled cortex that seems to be homologous to the mammalian dentate gyrus.[12]
[edit] The olfactory connection

The hippocampus has a strong connection to the olfactory bulb, the results of which have been
experienced by most people: when one encounters a particular odor, one might have an unusually vivid
memory of experiencing that smell at another time. The memory is often so strong that one has an
experience of actually being in that original place. This may be a retained mechanism for pre-mammal
(reptile precursors to mammals). Vision in these creatures was not highly developed, and olfaction was the
main sense, so the organisms relied strongly on olfaction for spatial memory.[7] Even now, in rodents such
as rats, olfaction is used when visual-spatial information isn’t available.[13]
[edit] Comparison of mammalian and avian hippocampus

In birds, a region called the medial telencephalon is considered to be homologous to the mammalian
hippocampus, and is often referred to as the ‘avian hippocampus’. The avian hippocampus might be the most
highly developed close relative of the mammalian hippocampus, both of them evolving from the reptile
medial pallium. Comparison between the two structures can lead to insights in the evolution of the
hippocampus, as well as an overall ability for spatial learning and memory.
[edit] Structurally
The mammalian hippocampus uniquely possesses the dentate gyrus, which is thought to aid in
distinguishing new memories from old memories by amplifying the signal sent from the entorhinal cortex.[12]
The mammalian denate gyrus and the reptilian medial small-celled cortex both have a high zinc content
which shows up in stains, but the avian hippocampus doesn’t have any area of high zinc concentration.[14]
However, researchers believe that the ventro-medial region in birds is the avian dentate gyrus due to the
similar connectivity of the areas.[15]
The mammalian hippocampus receives visual information as well as olfactory and auditory
information, but the visual information in birds goes to the avian equivalent of the amygdala instead.[16]
However, this difference doesn’t appear in memory and learning tasks.[17] Other comparisons include an
experiment in chicks on memory consolidation that shows noradrenaline is released in the hippocampus
early on after the training stage[18] much like in mammals.[19][20] Also, both the CA3 region of the
mammalian hippocampus and the medio-dorsal pallium of birds and reptiles serve as memory storage
centers for spatial representations.[21]
[edit] Functionally
There is much debate over how similar the avian hippocampus is to the mammalian hippocampus in
function. Visual memory is thought to be a part of the mammalian hippocampus abilities only,[16] but
comparison of past experiments shows that visual memory is not impaired by hippocampal lesioning in either
mammals or birds.[22] Similarly, Aboitiz et al. (2003)[6] suggested that birds—and not mammals—can still use
visual landmarks to find rewards, but Pearce et al. (1998)[23] found that rats with a damaged hippocampus
can find a platform in a water maze when relying on landmarks just as easily as an undamaged rat can.
Place cells, originally discovered in rats, have been one of the most important discoveries of the
mammalian hippocampus. Place cells are hippocampus neurons that fire clearly at high rates when an
animal is in a certain location.[24] Free-moving pigeons in a maze have also been found to have cell
responses in the hippocampus when the animal was in a certain location, but it wasn’t as specific to
particular spaces, nor was it as reliable or as strong.[25]
[edit] Notes
1. ^ Dujardin, 1850
2. ^ a b Strausfeld et al., 1998
3. ^ Mizunami et al., 1997
4. ^ Mizunami et al., 1993
5. ^ Mather, 1991
6. ^ a b Aboitiz et al., 2003
7. ^ a b c Vargas et al., 2009
8. ^ Portavella and Vargas, 2005
9. ^ Lopez et al., 2000
10.^ Lopez et al., 2001
11.^ Guirado and Davila, 1994
12.^ a b Treves et al., 2008
13.^ Save et al., 2000
14.^ Faber et al., 1989
15.^ Atoji and Wild, 2006
16.^ a b Rodriguez et al., 2002
17.^ Colombo, 2003
18.^ Gibbs et al., 2008
19.^ Sara et al., 1994
20.^ Yavich et al., 2005
21.^ Papp et al., 2007
22.^ Colombo and Broadbend, 2000
23.^ Pearce et al., 1998
24.^ O’Keefe and Nadel, 1978
25.^ Siegel et al., 2005
[edit] References
• Aboitiz, F; Morales D, Montiel J (2003). "The evolutionary origin of the mammalian isocortex:
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Karten, Harvey; Kuenzel, Wayne; Medina, Loreta; Paxinos, George et al. (2005). "Avian brains and a
new understanding of vertebrate evolution". Nature Reviews Neurosci. 6: 151–159.
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• Colombo, M; Broadbent N (2000). "Is the avian hippocampus a functional homologue of the
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the chick brain: a light- and electron-microscopic study using the Timm method". Cell Tissue Res.
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learning in turtles". Animal Learn. Behav. 28: 360–372.
• Lopez, J C; Rodriguez F, Gomez Y, Vargas J P, Broglio C, Salas C (2001). "Spatial learning
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mushroom body of the cockroach". Neurosci. Letters 229: 153–156. doi:10.1016/S0304-
3940(97)00438-2.
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networks in invertebrate neuroethology and robotics. Academic Press. ISBN 9780120847280.
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• Papp, G; Witter M P, Treves A (2007). "The CA3 network as a memory storage for spatial
representation". Learn. Memory 14: 732–744. doi:10.1101/lm.687407.
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PMID 9817202.
• Portavella, M; Vargas J P (2005). "Emotional and spatial learning in goldfish is dependent on
different telencephalic pallial systems". Euro. Journal of Neurosci. 21: 2800–2806.
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• Sara, S J; Vankov A, Herve A (1994). "Locus-coeruleus-evoked responses in behaving rats;
a clue to the role of noradrenaline in memory". Brain Res. Bull. 35 (5-6): 457–465. doi:10.1016/0361-
9230(94)90159-7. PMID 7859103.
• Save, E; Nerad L, Poucet B (2000). "Contribution of multiple sensory information to place
field stability in hippocampal place cells". Hippocampus 10 (1): 64–76. doi:10.1002/(SICI)1098-
1063(2000)10:1<64::AID-HIPO7>3.0.CO;2-Y. PMID 10706218.
• Siegel, J J; Nitz D, Bingman V P (2005). "Spatial-specificity of single-units in the
hippocampal formation of freely moving homing pigeons". Hippocampus 15 (1): 26–40.
doi:10.1002/hipo.20025. PMID 15390167.
• Strausfeld, N J; Hansen L, Li Y, Gomez S, Ito K (1998). "Evolution, discovery, and
interpretations of arthropod mushroom bodies". Learn. Memory 5: 11–37.
• Rodriguez, F; Lopez J C, Vargas J P, Broglio C, Gomez Y, Salas C (2002). "Spatial memory
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• Treves, A; Tashiro A, Witter M P, Moser E I (2008). "What is the mammalian dentate gyrus
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• Vargas, J P; Lopez J C, Portavella M (2009). "What are the functions of fish brain pallium?".
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Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_the_Hippocampus"
Categories: Limbic system | Cerebrum

W000
Mammal

For other uses, see Mammal (disambiguation).
Mammal
Mammals
Temporal range: Late Triassic – Recent, 220–0 Ma
PreЄ
g
Kingdom: Animalia
Phylum: Chordata
Superclass: Tetrapoda
(unranked): Mammaliaformes
Mammalia
Class:
Linnaeus, 1758
Subgroups
• Subclass †Allotheria*
• Subclass Prototheria
• Subclass Theria
• Infraclass †Trituberculata
• Infraclass Metatheria
• Infraclass Eutheria
challenged and removed. (August 2009)
Mammals (formally Mammalia) are a class of air-breathing vertebrate animals characterized by the
possession of hair, three middle ear bones, a neocortex, and mammary glands functional in mothers with
young. Most mammals also possess sweat glands and specialized teeth, and the largest group of mammals,
the placentals, have a placenta which feeds the offspring during gestation. The mammalian brain regulates
endothermic and circulatory systems, including a four-chambered heart. Mammals range in size from the 30–
40 millimeter (1- to 1.5-inch) Bumblebee Bat to the 33-meter (108-foot) Blue Whale.
Depending on classification scheme, there are approximately 5,500 species (5,490, according to the
IUCN Red List) of mammals, distributed in about 1,200 genera, 153 families, 29 orders[1] divided into three
infraclasses in two subclasses: the monotremes of the sublclass Prototheria, and the marsupials and
placentals or the subclass Theria. Except for the five species of monotremes (which lay eggs), all mammal
species give birth to live young. Most mammals, including the six largest orders, belong to the placental
group. The three largest orders, in descending order, are Rodentia (mice, rats, porcupines, beavers,
capybaras, and other gnawing mammals), Chiroptera (bats), and Soricomorpha (shrews, moles and
solenodons). The next three largest orders include the Carnivora (dogs, cats, weasels, bears, seals, and their
relatives), the Cetartiodactyla (including the even-toed hoofed mammals and the whales) and the Primates to
which the human species belongs.
The early synapsid mammalian ancestors, a group which included pelycosaurs such as Dimetrodon,
diverged from the amniote line that would lead to reptiles at the end of the Carboniferous period. Although
they were preceded by many diverse groups of non-mammalian synapsids (sometimes misleadingly referred
to as mammal-like reptiles), the first true mammals appeared 220 million years ago in the Triassic period.
Modern mammalian orders appeared in the Palaeocene and Eocene epochs of the Palaeogene period.
Phylogenetically, the clade Mammalia is defined as all descendants of the most recent common ancestor of
monotremes (e.g., echidnas and platypuses) and therian mammals (marsupials and placentals).[2] This
means that some extinct groups of "mammals" are not members of the crown group Mammalia, even though
most of them have all the characteristics that traditionally would have classified them as mammals.[3] These
"mammals" are now usually placed in the unranked clade Mammaliaformes.
Contents
[hide]
• 2.1 Standardized textbook classification
• 2.2 McKenna/Bell classification
• 2.3 Molecular classification of placentals
• 3.1 Evolution
• 3.2 Earliest appearances of features
• 4 Anatomy and morphology
• 4.1 Skeletal system
• 4.2 Respiratory system
• 4.3 Nervous system
• 4.4 Integumentary system
• 4.5 Reproductive system
• 5 Physiology
• 5.1 Endothermy
• 5.2 Intelligence
• 5.3 Social structure
• 5.4 Locomotion
• 5.4.1 Terrestrial
Living mammal species can be identified by the presence of sweat glands, including those that are
specialized to produce milk. However, other features are required when classifying fossils, since soft tissue
glands and some other features are not visible in fossils. Paleontologists use a distinguishing feature that is
shared by all living mammals (including monotremes), but is not present in any of the early Triassic
synapsids: mammals use two bones for hearing that were used for eating by their ancestors. The earliest
synapsids had a jaw joint composed of the articular (a small bone at the back of the lower jaw) and the
quadrate (a small bone at the back of the upper jaw). Most reptiles including lizards, crocodilians, dinosaurs
(and their descendants the birds) use this system, as did non-mammalian synapsids such as therapsids.
Mammals have a different jaw joint, however, composed only of the dentary (the lower jaw bone which
carries the teeth) and the squamosal (another small skull bone). In mammals the quadrate and articular
bones have become the incus and malleus bones in the middle ear.
Mammals also have a double occipital condyle: they have two knobs at the base of the skull which fit
into the topmost neck vertebra, and other vertebrates have a single occipital condyle. Paleontologists use
only the jaw joint and middle ear as criteria for identifying fossil mammals, since it would be confusing if they
found a fossil that had one feature, but not the other.
Main article: Mammal classification
Over 70% of mammal species are in the orders Rodentia (blue), Chiroptera (red), and Soricomorpha
(yellow)
George Gaylord Simpson's "Principles of Classification and a Classification of Mammals" (AMNH
Bulletin v. 85, 1945) was the original source for the taxonomy listed here. Simpson laid out a systematics of
mammal origins and relationships that was universally taught until the end of the 20th century. Since
Simpson's classification, the paleontological record has been recalibrated, and the intervening years have
seen much debate and progress concerning the theoretical underpinnings of systematization itself, partly
through the new concept of cladistics. Though field work gradually made Simpson's classification outdated, it
remained the closest thing to an official classification of mammals.
[edit] Standardized textbook classification

A somewhat standardized classification system has been adopted by most current mammalogy
classroom textbooks. The following taxonomy of extant and recently extinct mammals is from Vaughan et al.
(2000).
Class Mammalia
• Subclass Prototheria: monotremes: platypuses and echidnas
• Subclass Theria: live-bearing mammals
• Infraclass Metatheria: marsupials
• Infraclass Eutheria: placentals
[edit] McKenna/Bell classification

In 1997, the mammals were comprehensively revised by Malcolm C. McKenna and Susan K. Bell,
which has resulted in the "McKenna/Bell classification".
McKenna and Bell, Classification of Mammals: Above the species level , (1997) is the most
comprehensive work to date on the systematics, relationships, and occurrences of all mammal taxa, living
and extinct, down through the rank of genus. The new McKenna/Bell classification was quickly accepted by
paleontologists, though recent molecular genetic data challenge several of the higher level groupings. The
authors work together as paleontologists at the American Museum of Natural History, New York. McKenna
inherited the project from Simpson and, with Bell, constructed a completely updated hierarchical system,
covering living and extinct taxa that reflects the historical genealogy of Mammalia.
The McKenna/Bell hierarchical listing of all of the terms used for mammal groups above the species
includes extinct mammals as well as modern groups, and introduces some fine distinctions such as legions
and sublegions (ranks which fall between classes and orders) that are likely to be glossed over by the
nonprofessionals.
The published re-classification forms both a comprehensive and authoritative record of approved
names and classifications and a list of invalid names.
Extinct groups are represented by a cross (†).
Class Mammalia
• Subclass Prototheria: monotremes: echidnas and the Platypus
• Subclass Theriiformes: live-bearing mammals and their prehistoric relatives
• Infraclass †Allotheria: multituberculates
• Infraclass †Triconodonta: triconodonts
• Infraclass Holotheria: modern live-bearing mammals and their prehistoric relatives
• Supercohort Theria: live-bearing mammals
• Cohort Marsupialia: marsupials
• Magnorder Australidelphia: Australian marsupials and the
Monito del Monte
• Magnorder Ameridelphia: New World marsupials
• Cohort Placentalia: placentals
• Magnorder Xenarthra: xenarthrans
• Magnorder Epitheria: epitheres
• Grandorder Anagalida: lagomorphs, rodents, and
elephant shrews
• Grandorder Ferae: carnivorans, pangolins,
†creodonts, and relatives
• Grandorder Lipotyphla: insectivorans
• Grandorder Archonta: bats, primates, colugos, and
treeshrews
• Grandorder Ungulata: ungulates
• Order Tubulidentata incertae sedis: aardvark
• Mirorder Eparctocyona: †condylarths,
whales, and artiodactyls (even-toed ungulates)
• Mirorder †Meridiungulata: South American
ungulates
• Mirorder Altungulata: perissodactyls (odd-
toed ungulates), elephants, manatees, and hyraxes
[edit] Molecular classification of placentals

Molecular studies based on DNA analysis have suggested new relationships among mammal
families over the last few years. Most of these findings have been independently validated by retrotransposon
presence/absence data. The most recent classification systems based on molecular studies have proposed
four groups or lineages of placental mammals. Molecular clocks suggest that these clades diverged from
early common ancestors in the Cretaceous, but fossils have not yet been found to corroborate this
hypothesis. These molecular findings are consistent with mammal zoogeography:
Following molecular DNA sequence analyses, the first divergence was that of the Afrotheria 110–100
million years ago. The Afrotheria proceeded to evolve and diversify in the isolation of the African-Arabian
continent. The Xenarthra, isolated in South America, diverged from the Boreoeutheria approximately 100–95
million years ago. According to an alternative view, the Xenarthra has the Afrotheria as closest allies, forming
the Atlantogenata as sistergroup to Boreoeutheria. The Boreoeutheria split into the Laurasiatheria and
Euarchontoglires between 95 and 85 mya; both of these groups evolved on the northern continent of
Laurasia. After tens of millions of years of relative isolation, Africa-Arabia collided with Eurasia, exchanging
Afrotheria and Boreoeutheria. The formation of the Isthmus of Panama linked South America and North
America, which facilitated the exchange of mammal species in the Great American Interchange. The
traditional view that no placental mammals reached Australasia until about 5 million years ago when bats and
murine rodents arrived has been challenged by recent evidence and may need to be reassessed. These
molecular results are still controversial because they are not reflected by morphological data, and thus not
accepted by many systematists. Further there is some indication from retrotransposon presence/absence
data that the traditional Epitheria hypothesis, suggesting Xenarthra as the first divergence, might be true.
With the old order Insectivora shown to be polyphylectic and more properly subdivided (as Afrosoricida,
Erinaceomorpha, and Soricomorpha), the following classification for placental mammals contains 21 orders:
• Clade Atlantogenata
• Group I: Afrotheria
• Clade Afroinsectiphilia
• Order Macroscelidea: elephant shrews (Africa)
• Order Afrosoricida: tenrecs and golden moles (Africa)
• Order Tubulidentata: aardvark (Africa south of the Sahara)
• Clade Paenungulata
• Order Hyracoidea: hyraxes or dassies (Africa, Arabia)
• Order Proboscidea: elephants (Africa, Southeast Asia)
• Order Sirenia: dugong and manatees (cosmopolitan tropical)
• Group II: Xenarthra
• Order Pilosa: sloths and anteaters (Neotropical)
• Order Cingulata: armadillos (Americas)
• Clade Boreoeutheria
• Group III: Euarchontoglires (Supraprimates)
• Superorder Euarchonta
• Order Scandentia: treeshrews (Southeast Asia).
• Order Dermoptera: flying lemurs or colugos (Southeast Asia)
• Order Primates: lemurs, bushbabies, monkeys, apes (cosmopolitan),
humans
• Superorder Glires
• Order Lagomorpha: pikas, rabbits, hares (Eurasia, Africa, Americas)
• Order Rodentia: rodents (cosmopolitan)
• Group IV: Laurasiatheria
• Order Erinaceomorpha: hedgehogs
• Order Soricomorpha: moles, shrews, solenodons
• Clade Ferungulata
• Clade Cetartiodactyla
• Order Cetacea: whales, dolphins and porpoises
• Order Artiodactyla: even-toed ungulates, including pigs,
hippopotamus, camels, giraffe, deer, antelope, cattle, sheep, goats
• Clade Pegasoferae
• Order Chiroptera: bats (cosmopolitan)
• Clade Zooamata
• Order Perissodactyla: odd-toed ungulates, including
horses, donkeys, zebras, tapirs, and rhinoceroses
• Clade Ferae
• Order Pholidota: pangolins or scaly
anteaters (Africa, South Asia)
• Order Carnivora: carnivores (cosmopolitan)

For more details on this topic, see Evolution of mammals.
Mammaliaformes
Adelobasileus
void
Sinocodon
void
Morganucodon
void
Docodonta
void
––
Hadrocodium
––Mammalia
Synapsida, the group which contains mammals and their extinct relatives, originated during the
Pennsylvanian epoch, when they split from the lineage that led to reptiles and birds. Non-mammalian
synapsids were once called "mammal-like reptiles", although they are usually no longer considered reptiles.
Mammals evolved from non-mammalian synapsids during the Early Jurassic.
[edit] Evolution
The original synapsid skull structure contains one temporal opening behind the orbitals, in a fairly low
position on the skull (lower right in this image). This might have assisted in the containing the jaw muscles of
these organisms that could have increased their biting strength.
The first fully terrestrial vertebrates were amniotes. Like amphibians, they have lungs and limbs.
Amniotes' eggs, however, have internal membranes which allow the developing embryo to breathe but keep
water in. Hence amniotes can lay eggs on dry land, while amphibians generally need to lay their eggs in
water.
The first amniotes apparently arose in the late Carboniferous. They descended from earlier
tetrapods,[4] which lived on land already inhabited by insects, and other invertebrates, and by ferns, mosses,
and other plants. Within a few million years two important amniote lineages became distinct: the synapsids,
which include mammals; and the sauropsids, which include lizards, snakes, crocodilians, dinosaurs and
birds.[5] Synapsids have a single hole (temporal fenestra) low on each side of the skull.
One synapsid group, the pelycosaurs, were the most common land vertebrates of the early Permian
and included the largest land animals of the time.[6]
Therapsids descended from pelycosaurs in the middle Permian, about 260M years ago, and took
over their position as the dominant land vertebrates. They differ from pelycosaurs in several features of the
skull and jaws, including: larger temporal fenestrae and incisors which are equal in size.[7] The therapsids
went through a series of stages, beginning with animals which were very like their pelycosaur ancestors and
ending with the Triassic cynodonts, some of which could easily be mistaken for mammals. Those stages
were characterized by:
• gradual development of a bony secondary palate.[8]
• progress towards an erect limb posture, which would increase the animals' stamina by
avoiding Carrier's constraint. But this process was slow and erratic – for example: all herbivorous
non-mammaliaform therapsids retained sprawling limbs (some late forms may have had semi-erect
hind limbs); Permian carnivorous therapsids had sprawling forelimbs, and some late Permian ones
also had semi-sprawling hindlimbs. In fact modern monotremes still have semi-sprawling limbs.
• the dentary gradually becoming the main bone of the lower jaw; and in the Triassic, progress
towards the fully mammalian jaw (the lower consisting only of the dentary) and middle ear (which is
constructed by the bones that were previously used to construct the jaws of Reptiles)
• there is possible evidence of hair in Triassic therapsids, but none for Permian therapsids.
• some scientists have argued that some Triassic therapsids show signs of lactation.
The Permian–Triassic extinction event ended the dominance of the therapsids, and in the Early
Triassic all the medium to large land animal niches were taken over by early archosaurs, which were the
ancestors of crocodilians, pterosaurs, dinosaurs and birds. After this "Triassic Takeover" the cynodonts and
their descendants could only survive as small, mainly nocturnal insectivores.[9]
The first true mammals appeared in the Late Triassic (ca. 200 million years ago), over 70 million
years after the first therapsids and approximately 30 million years after the first mammaliaformes.
Hadrocodium appears to be in the middle of the transition to true mammal status — it had a mammalian jaw
joint (formed by the dentary and squamosal bones), but there is some debate about whether its middle ear
was fully mammalian.[10] The majority of the mammal species that existed in the Mesozoic Era were
characterized by Multituberculates.
The earliest known monotreme is Teinolophos, which lived about 123M years ago in Australia.
Monotremes have some features which may be inherited from the original amniotes:
• they use the same orifice to urinate, defecate and reproduce ("monotreme" means "one
hole") – as lizards and birds also do.
• they lay eggs which are leathery and uncalcified, like those of lizards, turtles and
crocodilians.
Unlike other mammals, female monotremes do not have nipples and feed their young by "sweating"
milk from patches on their bellies.
The oldest known marsupial is Sinodelphys, found in 125M-year old early Cretaceous shale in
China's northeastern Liaoning Province. The fossil is nearly complete and includes tufts of fur and imprints of
soft tissues.[11]
Reconstruction based on Megalonyx jeffersonii, Iowa Museum of Natural History, University of Iowa.
The living Eutheria ("true beasts") are all placentals. But the earliest known eutherian, Eomaia, found
in China and dated to 125M years ago, obtained some features which are more like those of marsupials,
which suggested it was perhaps a transitional fossil that eventually give rise to the placental lineage (the
surviving metatherians):[12]
• Epipubic bones extending forwards from the pelvis, which are not found in any modern
placental, but are found in marsupials, monotremes and mammaliformes such as multituberculates.
In other words, they appear to be an ancestral feature which subsequently disappeared in the
placental lineage. These epipubic bones seem to function by stiffening the muscles of these animals
during locomotion, reducing the amount of space being presented, which placentals require to
contain their fetus during gestation periods.
• A narrow pelvic outlet, which indicates that the young were very small at birth and therefore
pregnancy was short, as in modern marsupials. This suggests that the placenta was a later
development.
It is not certain when true placental mammals evolved – the earliest undisputed fossils of placentals
come from the early Paleocene, after the extinction of the dinosaurs.[13]
Mammals and near-mammals expanded out of their nocturnal insectivore niche from the mid
Jurassic onwards – for example Castorocauda had adaptations for swimming, digging and catching fish.[14]
The traditional view is that: mammals only took over the medium- to large-sized ecological niches in
the Cenozoic, after the extinction of the dinosaurs; but then they diversified very quickly; for example the
earliest known bat dates from about 50M years ago, only 15M years after the extinction of the dinosaurs.[15]
On the other hand recent molecular phylogenetic studies suggest that most placental orders diverged
about 100M to 85M years ago, but that modern families first appeared in the late Eocene and early
Miocene[16] But paleontologists object that no placental fossils have been found from before the end of the
Cretaceous.[13]
During the Cenozoic several groups of mammals appeared which were much larger than their
nearest modern equivalents – but none was even close to the size of the largest dinosaurs with similar
feeding habits.
[edit] Earliest appearances of features

Hadrocodium, whose fossils date from the early Jurassic (approx. 195 million years ago), provides
the first clear evidence of fully mammalian jaw joints.
It has been suggested that the original function of lactation (milk production) was to keep eggs moist.
Much of the argument is based on monotremes (egg-laying mammals):[17][18][19]
The earliest clear evidence of hair or fur is in fossils of Castorocauda, from 164M years ago in the
mid Jurassic. From 1955 onwards some scientists have interpreted the foramina (passages) in the maxillae
(upper jaws) and premaxillae (small bones in front of the maxillae) of cynodonts as channels which supplied
blood vessels and nerves to vibrissae (whiskers), and suggested that this was evidence of hair or fur.[20][21]
But foramina do not necessarily show that an animal had vibrissae – for example the modern lizard
Tupinambis has foramina which are almost identical to those found in the non-mammalian cynodont
Thrinaxodon.[22][23]
American Lion was one of the abundant Pleistocene megafauna, a wide variety of very large
mammals that lived during the Pleistocene and went extinct about 10,000 years ago.[24]
The evolution of erect limbs in mammals is incomplete — living and fossil monotremes have sprawling
limbs. In fact some scientists think that the parasagittal (non-sprawling) limb posture is a synapomorphy
(distinguishing characteristic) of the Boreosphenida, a group which contains the Theria and therefore
includes the last common ancestor of modern marsupial and placentals – and therefore that all earlier
mammals had sprawling limbs.[25] Sinodelphys (the earliest known marsupial) and Eomaia (the earliest
known eutherian) lived about 125M years ago, so erect limbs must have evolved before then.
It is currently very difficult to be confident when endothermy first appeared in the evolution of
mammals. Modern monotremes have a lower body temperature and more variable metabolic rate than
marsupials and placentals.[26] So the main question is when a monotreme-like metabolism evolved in
mammals. The evidence found so far suggests Triassic cynodonts may have had fairly high metabolic rates,
but is not conclusive. In particular it is difficult to see how small animals can maintain a high and stable body
temperature without fur.
[edit] Anatomy and morphology
[edit] Skeletal system
The majority of mammals have seven cervical vertebrae (bones in the neck); this includes bats,
giraffes, whales, and humans. The few exceptions include the manatee and the two-toed sloth, which have
only six cervical vertebrae, and the three-toed sloth with nine cervical vertebrae.[27]
[edit] Respiratory system

The lungs of mammals have a spongy texture and are honeycombed with epithelium having a much
larger surface area in total than the outer surface area of the lung itself. The lungs of humans are typical of
this type of lung.
Breathing is largely driven by the muscular diaphragm which divides the thorax from the abdominal
cavity, forming a dome with its convexity towards the thorax. Contraction of the diaphragm flattens the dome
increasing the volume of the cavity in which the lung is enclosed. Air enters through the oral and nasal
cavities; it flows through the larynx, trachea and bronchi and expands the alveoli. Relaxation of the
diaphragm has the opposite effect, passively recoiling during normal breathing. During exercise, the
abdominal wall contracts, increasing visceral pressure on the diaphragm, thus forcing the air out more quickly
and forcefully. The rib cage itself also is able to expand and contract the thoracic cavity to some degree,
through the action of other respiratory and accessory respiratory muscles. As a result, air is sucked into or
expelled out of the lungs, always moving down its pressure gradient. This type of lung is known as a bellows
lung as it resembles a blacksmith's bellows.
[edit] Nervous system
All mammalian brains possess a neocortex, a brain region that is unique to mammals. Placental
mammals have a corpus callosum unlike monotremes and marsupials. The size and number of cortical areas
(Brodmann's areas) is least in monotremes (about 8-10) and most in placentals (up to 50).
[edit] Integumentary system

The integumentary system is made up of three layers: the outermost epidermis, the dermis, and the
hypodermis.
The epidermis is typically ten to thirty cells thick, its main function being to provide a waterproof layer.
Its outermost cells are constantly lost; its bottommost cells are constantly dividing and pushing upward. The
middle layer, the dermis, is fifteen to forty times thicker than the epidermis. The dermis is made up of many
components such as bony structures and blood vessels. The hypodermis is made up of adipose tissue. Its
job is to store lipids, and to provide cushioning and insulation. The thickness of this layer varies widely from
species to species.
Although mammals and other animals have cilia that superficially may resemble it, no other animals
except mammals have hair. It is a definitive characteristic of the class. Some mammals have very little, but
nonetheless, careful examination reveals the characteristic, often in obscure parts of their bodies. None are
known to have hair that naturally is blue or green in color[ citation needed] although some cetaceans, along
with the mandrills appear to have shades of blue skin. Many mammals are indicated as having blue hair or
fur, but in all known cases, it has been found to be a shade of gray. The two-toed sloth and the polar bear
may seem to have green fur, but this color is caused by algae growths.
[edit] Reproductive system
Goat kids will stay with their mother until they are weaned
Most mammals give birth to live young (vivipary), but a few, namely the monotremes, lay eggs. The
platypus and the echidna present a particular sex determination system that is different from other
vertebrates.[28]
Certain glands of mammals known as mammary glands are specialized to produce milk, a liquid
used by newborns as their primary source of nutrition. The monotremes branched early from other mammals
and do not have the nipples seen in most mammals, but they do have mammary glands.
Viviparous mammals are classified into the subclass Theria and are divided into two infraclasses:
Metatheria (of which only the Marsupialia survive), and Eutheria. Marsupialia, or marsupials, have short
gestation periods and give birth to undeveloped young which are contained within a pouch-like sac
(marsupium) located in front of the mothers' abdomen. Eutherians, commonly known as placentals, are
mammals that give birth to complete and fully developed young. This is usually characterized by long
gestation periods. The majority of mammal species are classified as eutherians.
[edit] Physiology
[edit] Endothermy
Nearly all mammals are endothermic ("warm-blooded"). Most mammals also have hair to help keep
them warm. Like birds, mammals can forage or hunt in cold weather and climates where non-avian reptiles
and large insects cannot.
Endothermy requires plenty of food energy, so pound for pound mammals eat more food than most
reptiles. Small insectivorous mammals eat prodigious amounts for their size.
A rare exception, the naked mole rat produces little metabolic heat, so it is considered an operational
poikilotherm . Birds are also endothermic, so endothermy is not a defining mammalian feature.
[edit] Intelligence
In intelligent mammals, such as primates, the cerebrum is larger relative to the rest of the brain.
Intelligence itself is not easy to define, but indications of intelligence include the ability to learn, matched with
behavioral flexibility. Rats, for example, are considered to be highly intelligent as they can learn and perform
new tasks, an ability that may be important when they first colonize a fresh habitat. In some mammals, food
gathering appears to be related to intelligence: a deer feeding on plants has a brain smaller than a cat, which
must think to outwit its prey.[29]
[edit] Social structure
This section is empty. You can help by adding to it.
[edit] Locomotion
See also: Animal locomotion
Mammals evolved from four-legged ancestors. They use their limbs to walk, climb, swim, and fly.
Some land mammals have toes that produce claws and hooves for climbing and running. Aquatic mammals
such as whales and dolphins have flippers which evolved from legs.
[edit] Terrestrial
See also: Terrestrial locomotion
The fastest land animal, the cheetah can reach 120 kmh (75 mph)
[edit] Arboreal
See also: Arboreal locomotion
Sloths travel slowly along branches rather than swinging energetically like monkeys.
[edit] Aquatic
Buoyed by their aquatic environment, whales have evolved into the largest mammals and indeed the
largest animals ever.
[edit] Aerial
Townsend's Big-eared Bat, Corynorhinus townsendii

See also: Aerial locomotion
[edit] Feeding
To maintain a high constant body temperature is energy expensive – mammals therefore need a
nutritious and plentiful diet. While the earliest mammals were probably predators, different species have
since adapted to meet their dietary requirements in a variety of ways. Some eat other animals – this is a
carnivorous diet (and includes insectivorous diets). Other mammals, called herbivores, eat plants. A
herbivorous diet includes sub-types such as fruit-eating and grass-eating. An omnivore eats both prey and
plants. Carnivorous mammals have a simple digestive tract, because the proteins, lipids, and minerals found
in meat require little in the way of specialized digestion. Plants, on the other hand, contain complex
carbohydrates, such as cellulose. The digestive tract of an herbivore is therefore host to bacteria that ferment
these substances, and make them available for digestion. The bacteria are either housed in the multi-
chambered stomach or in a large cecum. The size of an animal is also a factor in determining diet type. Since
small mammals have a high ratio of heat-losing surface area to heat-generating volume, they tend to have
high-energy requirements and a high metabolic rate. Mammals that weigh less than about 18 oz (500 g) are
mostly insectivorous because they cannot tolerate the slow, complex digestive process of a herbivore. Larger
animals on the other hand generate more heat and less of this heat is lost. They can therefore tolerate either
a slower collection process (those that prey on larger vertebrates) or a slower digestive process (herbivores).
Furthermore, mammals that weigh more than 18 oz (500 g) usually cannot collect enough insects during their
waking hours to sustain themselves. The only large insectivorous mammals are those that feed on huge
colonies of insects (ants or termites).[29]
Specializations in herbivory include: Granivory "seed eating", folivory "leaf eating", fruivory "fruit
eating", nectivory "nectar eating", gumivory "gum eating", and mycophagy "fungus eating".
[edit] See also

Mammals portal
• List of African mammals

• List of extinct mammals
• List of Indian mammals
• List of mammalogists
• List of mammals
• Lists of mammals by region
• List of prehistoric mammals
• Mammal classification
• Mammals discovered in the 2000s
• Prehistoric mammals
[edit] References
1. ^ Wilson, Don E.; Reeder, DeeAnn M., eds (2005). Mammal Species of the World (3rd ed.).
Baltimore: Johns Hopkins University Press, 2 vols. (2142 pp.). ISBN 978-0-8018-8221-0.
OCLC 62265494. http://www.bucknell.edu/msw3.
2. ^ Rose, Kenneth D. (2006). The beginning of the age of mammals. Baltimore: Johns Hopkins
University Press. p. 43. ISBN 0-8018-8472-1.
3. ^ McKenna, Malcolm C.; Bell, Susan Groag. Classification of Mammals. Columbia University
Press. p. 32. ISBN 0-231-11013-8.
4. ^ Ahlberg, P. E. and Milner, A. R. (April 1994). "The Origin and Early Diversification of
Tetrapods". Nature 368: 507–514. doi:10.1038/368507a0.
5. ^ "Amniota – Palaeos". http://www.palaeos.org/Amniota.
6. ^ "Synapsida overview – Palaeos".
http://www.palaeos.com/Vertebrates/Units/Unit390/000.html.
7. ^ "Therapsida – Palaeos".
http://www.palaeos.com/Vertebrates/Units/400Therapsida/100.html.
8. ^ Kermack, D.M.; Kermack, K.A. (1984). The evolution of mammalian characters. Croom
Helm. ISBN 079915349.
9. ^ "Cynodontia: Overview – Palaeos".
http://www.palaeos.com/Vertebrates/Units/410Cynodontia/410.000.html.
10.^ "Symmetrodonta – Palaeos".
http://www.palaeos.com/Vertebrates/Units/Unit420/420.300.html.
11.^ "Oldest Marsupial Fossil Found in China". National Geographic News. December 15, 2003.
http://news.nationalgeographic.com/news/2003/12/1215_031215_oldestmarsupial.html.
12.^ "Eomaia scansoria: discovery of oldest known placental mammal".
http://www.evolutionpages.com/Eomaia%20scansoria.htm.
13.^ a b "Dinosaur Extinction Spurred Rise of Modern Mammals".
News.nationalgeographic.com. http://news.nationalgeographic.com/news/2007/06/070620-
mammals-dinos.html. Retrieved 2009-03-08.
14.^ "Jurassic "Beaver" Found; Rewrites History of Mammals".
http://news.nationalgeographic.com/news/2006/02/0223_060223_beaver.html.
15.^ "Rogue finger gene got bats airborne". Newscientist.com.
http://www.newscientist.com/news/news.jsp?id=ns99996647. Retrieved 2009-03-08.
16.^ Bininda-Emonds, O.R.P.; Cardillo, M.; Jones, K.E.; 'et al.', Ross D. E.; Beck, Robin M. D.;
Grenyer, Richard; Price, Samantha A.; Vos, Rutger A. et al. (2007). "The delayed rise of present-day
mammals". Nature 446 (446): 507–511. doi:10.1038/nature05634. PMID 17392779.
http://scienceblogs.com/pharyngula/2007/03/dont_blame_the_dinosaurs.php.
17.^ Oftedal, O.T. (2002). "The mammary gland and its origin during synapsid evolution".
Journal of Mammary Gland Biology and Neoplasia 7 (3): 225–252. doi:10.1023/A:1022896515287.
PMID 12751889.
18.^ Oftedal, O.T. (2002). The origin of lactation as a water source for parchment-shelled
eggs=Journal of Mammary Gland Biology and Neoplasia. 7. pp. 253–266.
19.^ "Lactating on Eggs". Nationalzoo.si.edu. 2003-07-14.
http://nationalzoo.si.edu/ConservationAndScience/SpotlightOnScience/oftedalolav20030714.cfm.
20.^ Brink, A.S. (1955). "A study on the skeleton of Diademodon". Palaeontologia Africana 3: 3–
39.
21.^ Kemp, T.S. (1982). Mammal-like reptiles and the origin of mammals. London: Academic
Press. p. 363. ISBN 0124041205.
22.^ Bennett, A. F. and Ruben, J. A. (1986) "The metabolic and thermoregulatory status of
therapsids"; pp. 207–218 in N. Hotton III, P. D. MacLean, J. J. Roth and E. C. Roth (eds), "The
ecology and biology of mammal-like reptiles", Smithsonian Institution Press, Washington.
23.^ Estes, R. (1961). "Cranial anatomy of the cynodont reptile Thrinaxodon liorhinus". Bulletin
of the Museum of Comparative Zoology (1253): 165–180.
24.^ Ice Age Animals, Illinois State Museum
25.^ Kielan−Jaworowska, Z.; Hurum, J.H.. (2006). "Limb posture in early mammals: Sprawling
or parasagittal" (–Scholar search). Acta Palaeontologica Polonica 51 (3): 10237–10239.
http://www.app.pan.pl/acta51/app51-393.pdf. [dead link]
26.^ Paul, G.S. (1988). Predatory Dinosaurs of the World. New York: Simon and Schuster.
p. 464. ISBN 0671619462.
27.^ http://books.google.com/books?
id=FIIgDk9i_GkC&pg=PA154&lpg=PA154&dq=mammal+cervical+vertebrae+sloth&source=bl&ots=a
whUXef5uS&sig=fisiFeMccFCbEGLkKE91m2QU7e0&hl=en&ei=8jqvTKH-
C8L38Ab1uNCoCQ&sa=X&oi=book_result&ct=result&resnum=5&ved=0CCcQ6AEwBA#v=onepage
&q&f=false
28.^ Wallis, M.C., Waters, P.D., Delbridge, M.L., Kirby, P.J., Pask, A.J., Grützner, F., Rens, W.,
Ferguson-Smith, M.A., and Graves, J.A.M. (December 2007). Sex determination in platypus and
echidna: autosomal location of SOX3 confirms the absence of SRY from monotremes. Chromosome
Research 15(8): 949–959. ISSN 0967-3849 (Print) 1573–6849 (Online). doi:10.1007/s10577-007-
1185-3.
29.^ a b Don E. Wilson & David Burnie, ed (2001). Animal: The Definitive Visual Guide to the
World's Wildlife (1st ed.). DK Publishing. pp. 86–89. ISBN 978-0789477644.
[edit] Bibliography
• Bergsten, Johannes. February 2005. "A review of long-branch attraction". Cladistics 21:163–
193. (pdf version)
• Brown, W.M. (2001). Natural selection of mammalian brain components. Trends in Ecology
and Evolution, 16, 471–473.
• Khalaf-von Jaffa, Norman Ali Bassam Ali Taher (2006). Mammalia Palaestina: The Mammals
of Palestine. Gazelle: The Palestinian Biological Bulletin. Number 55, July 2006. pp. 1–46.
• McKenna, Malcolm C., and Bell, Susan K. 1997. Classification of Mammals Above the
Species Level. Columbia University Press, New York, 631 pp. ISBN 0-231-11013-8
• Nowak, Ronald M. 1999. Walker's Mammals of the World, 6th edition. Johns Hopkins
University Press, 1936 pp. ISBN 0-8018-5789-9
• Simpson, George Gaylord (1945). "The principles of classification and a classification of
mammals". Bulletin of the American Museum of Natural History 85: 1–350.
• William J. Murphy, Eduardo Eizirik, Mark S. Springer et al., Resolution of the Early Placental
Mammal Radiation Using Bayesian Phylogenetics,Science, Vol 294, Issue 5550, 2348–2351 , 14
December 2001.
• Springer, Mark S., Michael J. Stanhope, Ole Madsen, and Wilfried W. de Jong. 2004.
"Molecules consolidate the placental mammal tree". Trends in Ecology and Evolution, 19:430–438.
(PDF version)
• Vaughan, Terry A., James M. Ryan, and Nicholas J. Capzaplewski. 2000. Mammalogy:
Fourth Edition. Saunders College Publishing, 565 pp. ISBN 0-03-025034-X (Brooks Cole, 1999)
• Jan Ole Kriegs, Gennady Churakov, Martin Kiefmann, Ursula Jordan, Juergen Brosius,
Juergen Schmitz. (2006) Retroposed Elements as Archives for the Evolutionary History of Placental
Mammals. PLoS Biol 4(4): e91."PLoS Biology – Retroposed Elements as Archives for the
Evolutionary History of Placental Mammals". Biology.plosjournals.org.
doi:10.1371/journal.pbio.0040091. http://biology.plosjournals.org/perlserv/?request=get-
document&doi=10.1371/journal.pbio.0040091. Retrieved 2009-03-08.
• David MacDonald, Sasha Norris. 2006. The Encyclopedia of Mammals, 3rd edition. Printed
in China, 930 pp. ISBN 0-681-45659-0.

Find more about Mammal on Wikipedia's sister projects:

Wikispecies has information related to: Mammalia

Mammalia
External identifiers for Mammalia
NCBI Taxonomy 40674

ITIS 179913
Encyclopedia of Life 1642
uBio NameBank 2478620
Also found in: Wikispecies, Arctos

• BBC Wildlife Finder – video clips from the BBC's natural history archive
• GlobalTwitcher.com – All species in the world with distribution maps and images
• Paleocene Mammals, a site covering the rise of the mammals, paleocene-mammals.de
• Evolution of Mammals, a brief introduction to early mammals, enchantedlearning.com
• Tree of Life poster – Shows mammals' evolutionary relation to other organisms,
tellapallet.com
• The Evolution of Mesozoic Mammals, a Rough Sketch , an informal introduction,
home.arcor.de
• Carnegie Museum of Natural History, some discoveries of early mammal fossils,
carnegiemnh.org
• High-Resolution Images of various Mammalian Brains, brainmaps.org
• Mammal Species, collection of information sheets about various mammal species,
learnanimals.com
• Summary of molecular support for Epitheria , biology.plosjournals.org
• Mikko's Phylogeny Archive, fmnh.helsinki.fi
• European Mammal Atlas EMMA from Societas Europaea Mammalogica, european-
mammals.org
• Marine Mammals of the World—An overview of all marine mammals, including descriptions,
multimedia and a key, eti.uva.nl
• Mammalogy.org The American Society of Mammalogists was established in 1919 for the
purpose of promoting the study of mammals, and this website includes a mammal image library

Cephalochordata
(Lancelets) Leptocardii

Mammalia (Mammals)
[hide]v · d · eExtant mammal orders by infraclass
Kingdom Animalia · Phylum Chordata · Subphylum Vertebrata · (unranked) Amniota
Australosphenida Monotremata (Platypus and echidnas)
Paucituberculata (Shrew opossums) ·

Ameridelphia
Didelphimorphia (Opossums)
Metatheria
(Marsupial inclusive) Microbiotheria (Monito del Monte) ·
Notoryctemorphia (Marsupial moles) · Dasyuromorphia
Australidelphia
(Quolls and dunnarts) · Peramelemorphia (Bilbies and
bandicoots) · Diprotodontia (Kangaroos and relatives)
Eutheria Cingulata (Armadillos) · Pilosa (Anteaters and

(Placental inclusive) Xenarthra
sloths)
Afrosoricida (Tenrecs and golden moles) ·

Macroscelidea (Elephant shrews) · Tubulidentata
Afrotheria
(Aardvark) · Hyracoidea (Hyraxes) · Proboscidea
(Elephants) · Sirenia (Dugongs and manatees)
Soricomorpha (Shrews and moles) ·
Erinaceomorpha (Hedgehogs and relatives) ·
Chiroptera (Bats) · Pholidota (Pangolins) · Carnivora ·
Laurasiatheria
Perissodactyla (Odd-toed ungulates) · Artiodactyla
(Even-toed ungulates) · Cetacea (Whales and
dolphins)
Rodentia (Rodents) · Lagomorpha (Rabbits

Euarchontoglires and relatives) · Scandentia (Treeshrews) ·
Dermoptera (Colugos) · Primates
Retrieved from "http://en.wikipedia.org/wiki/Mammal"
Categories: Mammals
W000
Herbivore

A deer and two fawns feeding on some foliage
Herbivores are organisms that are adapted to eat plants. Herbivory is a form of predation in which an
organism consumes principally autotrophs[1][page needed] such as plants, algae and photosynthesizing
bacteria. More generally, organisms that feed on autotrophs in general are known as primary consumers.
Comes from the Greek suffix "vora" (Greek -βόρα) meaning "which eat".
By strict interpretation of this definition, many fungi, some bacteria, many animals, some protists and
a small number of parasitic plants might be considered herbivores. However, herbivory generally refers to
animals eating plants. Fungi, bacteria and protists that feed on living plants are usually termed plant
pathogens (plant diseases). Microbes that feed on dead plants are saprotrophs. Flowering plants that obtain
nutrition from other living plants are usually termed parasitic plants.
Contents
[hide]
• 1 Evolution of herbivory
• 2 Food Chain
• 3 Predator-prey Theory (herbivore-plant interactions)
• 4 Feeding strategies
• 5 Attacks and Counter-Attacks
• 5.1 Plant Defense
• 5.2 Herbivore Offense
• 6 The Adaptation Dance
• 7 Impacts of Herbivores
• 8 See also
• 9 References
[edit] Evolution of herbivory
A fossil Viburnum lesquereuxii leaf with evidence of insect herbivory; Dakota Sandstone
(Cretaceous) of Ellsworth County, Kansas. Scale bar is 10 mm.
Our understanding of herbivory in geological time comes from three sources: fossilized plants, which
may preserve evidence of defence (such as spines), or herbivory-related damage; the observation of plant
debris in fossilised animal faeces; and the construction of herbivore mouthparts.[2]
Long thought to be a Mesozoic phenomenon, evidence for herbivory is found almost as soon as
fossils which could show it. Within under 20 million years of the first fossils of sporangia and stems towards
the close of the Silurian, around 420 million years ago, there is evidence that plants were being consumed by
insects.[3] Insects fed on the spores of early Devonian plants, and the Rhynie chert also provides evidence
that organisms fed on plants using a "pierce and suck" technique.[2]
Herbivory among terrestrial vertebrates (tetrapods) came much later. Early tetrapods were large
amphibious piscivores. While amphibians continued to feed on fish and later insects, reptiles began exploring
two new food types, tetrapods (carnivory), and later, plants (herbivory). Carnivory was a natural transition
from insectivory for medium and large tetrapods, requiring minimal adaptation. In contrast, a complex set of
adaptations was necessary for feeding on highly fibrous plant materials).[4]
During the ensuing 75 million years[citation needed], plants evolved a range of more complex organs
- from roots to seeds. There is no evidence for these being fed upon until the middle-late Mississippian, 326.4
million years ago. There was a gap of 50 to 100 million years between each organ evolving, and it being fed
upon; this may be due to the low levels of oxygen during this period, which may have suppressed evolution.
[3] Further than their arthropod status, the identity of these early herbivores is uncertain.[3] Hole feeding and
skeletonisation are recorded in the early Permian, with surface fluid feeding evolving by the end of that
period.[2]
Arthropods have evolved herbivory in four phases, changing their approach to herbivory in response
to changing plant communities.[5]
Another stage of herbivore evolution is characterized by the evolution of tetrapod herbivores, with the first
appearance in the fossil record near the Permio-Carboniferous boundary approximately 300 MYA. The
earliest evidence of herbivory by tetrapod organisms is seen in fossils of jawbones where dental occlusion
(process by which teeth from the upper jaw come in contact with those in the lower jaw) is present. The
evolution of dental occlusion lead to a drastic increase in food processing associated with herbivory and
provides direct evidence about feeding strategies based on tooth wear patterns. Examination of phylogenetic
frameworks reveals that dental occlusion developed independently in several lineages through dental and
mandibular morphologes, suggesting that the evolution and radiation of tetrapod herbivores occurred
simultaneously within various lineages.[6]
[edit] Food Chain
Leaf miners feed on leaf tissue between the epidermal layers, leaving visible trails
Herbivores form an important link in the food chain as they consume plants in order to receive the
carbohydrates produced by a plant from photosynthesis. Carnivores in turn consume herbivores for the same
reason, while omnivores can obtain their nutrients from either plants or herbivores. Due to an herbivore's
ability to survive solely on tough and fibrous plant matter, they are termed the primary consumers in the food
cycle(chain). Herbivory, carnivory, and omnivory and call be regarded as special cases of Consumer-
Resource Systems [7].
[edit] Predator-prey Theory (herbivore-plant interactions)
According to the theory of predator-prey interactions, the relationship between herbivores and plants
is cyclic.[8] When prey (plants) are numerous their predators (herbivores) increase in numbers, reducing the
prey population, which in turn causes predator number to decline.[9] The prey population eventually
recovers, starting a new cycle. This suggests that the population of the herbivore fluctuates around the
carrying capacity of the food source, in this case the plant.
Several factors play into these fluctuating populations and help stabilize predator-prey dynamics. For
example, spatial heterogeneity is maintained, which means there will always be pockets of plants not found
by herbivores. This stabilizing dynamic plays an especially important role for specialist herbivores that feed
on one species of plant and prevents these specialists from wiping out their food source.[10] Prey defenses
also help stabilize predator-prey dynamic, and for more information on these relationships see the section on
Plant Defenses. Eating a second prey type helps herbivores’ populations stabilize.[11] Alternating between
two or more plant types provides population stability for the herbivore, while the populations of the plants
oscillate.[12] This plays an important role for generalist herbivores that eat variety of plants. Keystone
herbivores keep vegetation populations in check and allow for a greater diversity of both herbivores and
plants.[11] When an invasive herbivore or plant enters the system, the balance is thrown off and the diversity
can collapse to a monotaxon system.[11]
[edit] Feeding strategies

Herbivores are limited in their feeding ability by either time or resources. Animals that are time
limited, meaning they have a limited amount of time to consume the food they need, use a feeding strategy of
grazing and browsing, while those animals that are resource limited, meaning that they are limited in the type
of food they eat, use a selective feeding strategy. Grazers/browsers tend to be either very large herbivores
that need to consume a lot of food in order to maintain their metabolism, or herbivores that have a very short
amount of time to eat as much as possible before reproducing, like many generalist insects. Several theories
attempt to explain and quantify the relationship between animals and their food, such as Kleiber's law,
Holling's disk equation and Marginal Value Theorem.
Kleiber’s law explains the relationship between the size of the animal and the feeding strategy it
uses. In essence, it says that larger animals need to eat less food, per unit weight, than smaller animals.[13]
Kleiber’s law states that the metabolic rate (q0) of an animal is the mass of the animal (M) raise to the 3/4th
power:
q0=M3/4
Therefore, the mass of the animal increases at a faster rate then the metabolic rate.[14]
There are many types of feeding strategies employed by herbivores. Many herbivores do not fall into one
specific feeding strategy, but instead employ several strategies and eat a variety of plant parts.
Types of feeding strategies:
Feeding Strategy Diet Example
Frugivores Fruit Ruffed lemurs
Folivores Leaves Koalas
Nectarivores Nectar Honey Possum
Granivores Seeds Hawaiian Honeycreepers

Palynivores Pollen Bees
Mucivores Plant fluids, i.e. sap Aphids
Xylophages Wood Termites
Optimal Foraging Theory is a model for predicting animal behavior while looking for food or other resource,
such as shelter or water. This model assesses both individual movement, such as animal behavior while
looking for food, and distribution within a habitat, such as dynamics at the population and community level.
For example, the model would be used to look at the browsing behavior of a deer while looking for food, as
well as that deer’s specific location and movement within the forested habitat and its interaction with other
deer while in that habitat.
This model can be controversial, where critics say that the theory is circular and untestable. Critics say that
the theory uses examples that fit the theory, but that researchers do not use the theory when it does not fit
the reality.[15] [16] Other critics point out that animals do not have the ability to assess and maximize their
potential gains, therefore the optimal foraging theory is irrelevant and derived to explain trends that do not
exist in nature.[17][18]
Holling’s disk equation models the efficiency at which predators consume prey. The model predicts
that as the number of prey increases, the amount of time predators spend handling prey also increases and
therefore the efficiency of the predator decreases.[19] In 1959 S. Holling proposed an equation to model the
rate of return for an optimal diet: Rate (R ) = Energy gained in foraging (Ef)/(time searching (Ts) + time
handling (Th))
R = Ef / (Ts + Th)
Where s = cost of search per unit time f = rate of encounter with items, h = handling time, e = energy gained
per encounter
In effect, this would indicate that an herbivore in a dense forest would spend more time getting handling
(eating) the vegetation because there was so much vegetation around than an herbivore in a sparse forest,
who could easily browse through the forest vegetation. Therefore, according to the Holling's disk equation,
the herbivore in the sparse forest would be more efficient at eating than the herbivore in the dense forest
Marginal Value Theorem describes the balance between eating all the food in a patch for immediate
energy, or moving to a new patch and leaving the plants in the first patch to regenerate for future use. The
theory predicts that absent complicating factors, an animal should leave a resource patch when the rate of
payoff (amount of food) falls below the average rate of payoff for the entire area.[20] According to this theory,
therefore, locus should move to a new patch of food when the patch they are currently feeding on requires
more energy to obtain food than an average patch. Within this theory, two subsequent parameters emerge,
the Giving Up Density (GUD) and the Giving Up Time (GUT). The Giving Up Density (GUD) quantifies the
amount of food that remains in a patch when a forager moves to a new patch.[21] The Giving Up Time (GUT)
is used when an animal continuously assesses the patch quality.[22]
[edit] Attacks and Counter-Attacks

[edit] Plant Defense
Main article: Plant defense against herbivory
A plant defense is a trait that increases plant fitness when faced with herbivory. This is measured
relative to another plant that lacks the defensive trait. Plant defenses increase survival and/or reproduction
(fitness) of plants under pressure of predation from herbivores.
Defense can be divided into two main categories, tolerance and resistance. Tolerance is the ability of
a plant to withstand damage without a reduction in fitness. This can occur by diverting herbivory to non-
essential plant parts or by rapid regrowth and recovery from herbivory. Resistance refers to the ability of a
plant to reduce the amount of damage it receives from an herbivore. This can occur via avoidance in space
or time,[23] physical defenses, or chemical defenses. Defenses can either be constitutive, always present in
the plant, or induced, produced or translocated by the plant following damage or stress.[24]
Physical, or mechanical, defenses are barriers or structures designed to deter herbivores or reduce
intake rates, lowering overall herbivory. thorns such as those found on roses or acacia trees are one
example, as are the spines on a cactus. Smaller hairs known as trichomes may cover leaves or stems and
are especially effective against invertebrate herbivores.[25] In addition, some plants have waxes or resins
that alter their texture, making them difficult to eat. Finally, some plants sequester silica inside their tissues.
These are basically small pieces of glass that wear down the teeth of herbivores.
Chemical defenses are secondary metabolites produced by the plant that deter herbivory. There are
a wide variety of these in nature and a single plant can have hundreds of different chemical defenses.
Chemical defenses can be divided into two main groups, carbon-based defenses and nitrogen-based
defenses.
Carbon-based defenses include terpenes and phenolics. Terpenes are derived from 5-carbon
isoprene units and comprise essential oils, carotenoids, resins, and latex. They can have a number of
functions that disrupt herbivores such as inhibiting adenosine triphosphate (ATP) formation, molting
hormones, or the nervous system.[26] Phenolics combine an aromatic carbon ring with a hydroxyl group.
There are a number of different phenolics such as lignins, which are found in cell walls and are very
indigestible except for specialized microorgamisms; tannins, which have a bitter taste and bind to proteins
making them indigestible; and furanocumerins, which produce free radicals disrupting DNA, protein, and
lipids, and can cause skin irritation.
Nitrogen-based defenses are synthesized from amino acids and primarily come in the form of
alkaloids and cyanogens. Alkaloids include commonly recognized substances such as caffeine, nicotine, and
morphine. These compounds are often bitter and can inhibit DNA or RNA synthesis or block nervous system
signal transmission. Cyanogens get their name from the cyanide stored within their tissues. This is released
when the plant is damaged and inhibits cellular respiration and electron transport.
Plants have also changed features that enhance the probability of attracting natural enemies to
herbivores. Some emit semiochemicals, odors that attract natural enemies, while others provide food and
housing to maintain the natural enemies’ presence (eg. ants that reduce herbivory[27]). A given plant species
often has many types of defensive mechanisms, mechanical or chemical, constitutive or induced, which
additively serve to protect the plant, and allow it to escape from herbivores.
[edit] Herbivore Offense
Aphids are fluid feeders on plant sap.

Main article: Herbivore adaptations to plant defense
The myriad of defenses displayed by plants means that their herbivores need a variety of techniques
to overcome these defenses and obtain food. These allow herbivores to increase their feeding and use of a
host plant. Herbivores have three primary strategies for dealing with plant defenses: choice, herbivore
modification, and plant modification.
Feeding choice involves which plants an herbivore chooses to consume. It has been suggested that
many herbivores feed on a variety of plants to balance their nutrient uptake and to avoid consuming too much
of any one type of defensive chemical. This involves a tradeoff however, between foraging on many plant
species to avoid toxins or specializing on one type of plant that can be detoxified.[28]
Herbivore modification is when various adaptations to body or digestive systems of the herbivore
allow them to overcome plant defenses. This might include detoxifying secondary metabolites,[29]
sequestering toxins unaltered,[30] or avoiding toxins, such as through the production of large amounts of
saliva to reduce effectiveness of defenses. Herbivores may also utilize symbionts to evade plant defences.
For example, some aphids use bacteria in their gut to provide essential amino acids lacking in their sap diet.
[31]
Plant modification occurs when herbivores manipulate their plant prey to increase feeding. For
example, some caterpillars roll leaves to reduce the effectiveness of plant defenses activated by sunlight.[32]
[edit] The Adaptation Dance

The back and forth relationship of plant defense and herbivore offense can be seen as a sort of
“adaptation dance” in which one partner makes a move and the other counters it.[29] This reciprocal change
drives coevolution between many plants and herbivores, resulting in what has been referred to as a
“coevolutionary arms race”.[33] The escape and radiation mechanisms for coevolution, presents the idea that
adaptations in herbivores and their host plants, has been the driving force behind speciation.[34][35]
It is important to remember that while much of the interaction of herbivory and plant defense is
negative, with one individual reducing the fitness of the other, some is actually beneficial. This beneficial
herbivory takes the form of mutualisms in which both partners benefit in some way from the interaction. Seed
dispersal by herbivores and pollination are two forms of mutualistic herbivory in which the herbivore receives
a food resource and the plant is aided in reproduction.[36]
[edit] Impacts of Herbivores
The impact of herbivory can be seen in many areas ranging from economics to ecological, and
sometimes affecting both. For example, environmental degradation from white-tailed deer (Odocoileus
virginianus) in the U.S. alone has the potential to both change vegetative communities through over-browsing
and cost forest restoration projects upwards of $750 million annually. Agricultural crop damage by the same
species totals approximately $100 million every year. Insect crop damages also contribute largely to annual
crop losses in the U.S.[37] Another area in which herbivory greatly affects economics is through the revenue
generated by recreational uses of herbivorous organisms, such as hunting and ecotourism. For example, the
hunting of herbivorous game species such as white-tailed deer, cottontail rabbits, antelope, and elk in the
U.S. contributes greatly to the billion-dollar annually hunting industry. Ecotourism is another major source of
revenue, particularly in Africa, where many large mammalian herbivores such as elephants, zebras, and
giraffes help to bring in the equivalent of millions of US dollars to various nations annually.
[edit] See also

Wikimedia Commons has media related to: Herbivory
• List of herbivorous animals

• List of food habits
• Consumer-resource systems
• Grazing
• Browsing (predation)
• Secondary production
• Plant-based diet (disambiguation)
• Pollination
• Seed dispersal
• Seed predation
[edit] References
1. ^ Campbell, N. A. (1996) Biology (4th edition) Benjamin Cummings, New York ISBN 0-8053-
1957-3
2. ^ a b c Labandeira, C.C. (1998). "Early History Of Arthropod And Vascular Plant Associations
1". Annual Reviews in Earth and Planetary Sciences 26 (1): 329–377.
doi:10.1146/annurev.earth.26.1.329.
3. ^ a b c Labandeira, C. (2007). "The origin of herbivory on land: Initial patterns of plant tissue
consumption by arthropods". Insect Science 14 (4): 259–275. doi:10.1111/j.1744-
7917.2007.00152.x.
4. ^ Sahney, S., Benton, M.J. & Falcon-Lang, H.J. (2010). "Rainforest collapse triggered
Pennsylvanian tetrapod diversification in Euramerica" (PDF). Geology 38: 1079–1082.
http://geology.geoscienceworld.org/cgi/content/abstract/38/12/1079.
5. ^ Labandeira, C.C. (2005). "The four phases of plant-arthropod associations in deep time"
(Free full text). Geologica Acta 4 (4): 409–438. http://www.geologica-
acta.com:8080/geoacta/pdf/vol0404a01.pdf. Retrieved 2008-05-15.
6. ^ Origin of dental occlusion in tetrapods: signal for terrestrial vertebrate evolution? Journal of
Experimental Zoology Part B: Molecular and Developmental Evolution. Volume 306B Issue 3, Pages
261 - 277 Special Issue: Vertebrate Dentitions: Genes, Development and Evolution Published
Online: 8 May 2006 Copyright © 2008 Wiley-Liss, Inc., A Wiley Company Robert R. Reisz *
Department of Biology, University of Toronto at Mississauga, Mississauga, Ont., Canada L5L 1C6
7. ^ Getz, W. (2011). Biomass transformation webs provide a unified approach to consumer–
resource modelling. Ecology Letters,doi: 10.1111/j.1461-0248.2010.01566.x.
8. ^ Gotelli, NJ. A Primer of Ecology. Sinauer Associates Inc., Mass. 1995
9. ^ Gotelli 1995
10.^ Smith, RL and Smith, TM. Ecology and Field Biology: Sixth Edition.Benjamin Cummings,
New York. 2001
11.^ a b c Smith and Smith, 2001
12.^ Gotelli, 1995
13.^ Nugent G, Challies CN. 1988. Diet and food preferences of white-tailed deer in north-
eastern Stewart Island. New Zealand Journal of Ecology 11: 61-73.
14.^ Nugent and Challies, 1988
15.^ Pierce, G. J. and J. G. Ollason. 1987. Eight reasons why optimal foraging theory is a
complete waste of time. Oikos 49:111-118.
16.^ Stearns, S. C. and P. Schmid-Hempel. 1987. Evolutionary insights should not be wasted.
Oikos 49:118-125
17.^ Lewis, A. C. 1986. Memory constraints and flower choice in Pieris rapae. Science 232:863-
865
18.^ Janetos, A. C. and B. J. Cole. 1981. Imperfectly optimal animals. Behav. Ecol. Sociobiol.
9:203-209
19.^ Stephens, D. W. and J. R. Krebs. 1986. Foraging theory. Princeton University Press
20.^ Charnov, E. L. 1976. Optimal foraging, the marginal value theorem. Theor. Pop. Biol.-
9:129-136.
21.^ Brown, J. S., B P. Kotler and W A. Mitchell. 1997. Competition between birds and
mammals: a comparison of giving-up densities between crested larks and gerbils. Evol. Ecol. 11:757-
771.
22.^ Breed, M. D. R. M. Bowden, M. F. Garry, and A. L. Weicker. 1996. Giving-up time variation
in response to differences in nectar volume and concentration in the giant tropical ant, Paraponera
clavata. J. Ins. behav. 9:659-672
23.^ Milchunas, D.G. and I. Noy-Meir. 2002. Grazing refuges, external avoidance of herbivory
and plant diversity. Oikos 99(1): 113-130.
24.^ Edwards P.J. and S.D. Wratten. 1985. Induced plant defences against insect grazing: fact
or artefact? Oikos 44(1):70-74.
25.^ Pillemer, E.A. and W.M. Tingey. 1976. Hooked Trichomes: A Physical Plant Barrier to a
Major Agricultural Pest. Science 193(4252): 482-484.
26.^ Langenheim, J.H. 1994. Higher plant terpenoids: a phytocentric overview of their ecological
roles. Journal of Chemical Ecology 20: 1223-1280.
27.^ Heil, M., T. Koch, A. Hilpert, B. Fiala, W. Boland, and K. Eduard Linsenmair. 2001.
Extrafloral nectar production of the ant-associated plant, Macaranga tanarius, is an induced, indirect,
defensive response elicited by jasmonic acid. Proceedings of the National Academy of Sciences
98(3): 1083-1088.
28.^ Dearing, M.D., A.M. Mangione, and W.H. Karasov. 2000. Diet breadth of mammalian
herbivores: nutrient versus detoxification constraints. Oecologia 123: 397-405.
29.^ a b Karban, R. and A.A. Agrawal. 2002. Herbivore Offense. Annual Review of Ecology and
Systematics 33:641-664.
30.^ Nishida, R. 2002. Sequestration of Defensive Substances from Plants by Lepidoptera.
Annual Review of Entomology 47:57-92.
31.^ Douglas, A.E. 1998. Nutritional Interactions in Insect-Microbial Symbioses: Aphids and
Their Symbiotic Bacteria Buchnera. Annual Review of Entomology 43:17-37.
32.^ Sagers, C.L. 1992. Manipulation of host plant quality: herbivores keep leaves in the dark.
Functional Ecology 6(6):741-743.
33.^ Mead, R.J., A.J. Oliver, D.R. King and P.H. Hubach. (1985). The Co-Evolutionary Role of
Fluoroacetate in Plant-Animal Interactions in Australia. Oikos 44(1): 55-60.
34.^ Ehrlich, P. R. and P. H. Raven. 1964. Butterflies and plants: a study of coevolution.
Evolution 18:586-608.
35.^ Thompson, J. 1999. What we know and do not know about coevolution: insect herbivores
and plants as a test case. Pages 7–30 in H. Olff, V. K. Brown, R. H. Drent, and British Ecological
Society Symposium 1997 (Corporate Author), editors. Herbivores: between plants and predators.
Blackwell Science, London, UK.
36.^ Herrera, C.M. 1985. Determinants of Plant-Animal Coevolution: The Case of Mutualistic
Dispersal of Seeds by Vertebrates. Oikos 44(1): 132-141.
37.^ AN INTEGRATED APPROACH TO DEER DAMAGE CONTROL Publication No. 809 West
Virginia Division of Natural Resources Cooperative Extension Service Wildlife Resources Section
West Virginia University Law Enforcement Section Center for Extension and Continuing Education
March 1999

• Bob Strauss, 2008, Herbivorous Dinosaurs, The New York Times
• Danell, K., R. Bergström, P. Duncan, J. Pastor (Editors)(2006) Large herbivore ecology,
ecosystem dynamics and conservation Cambridge, UK : Cambridge University Press. 506 p. ISBN
0521830052
• Crawley, M. J. (1983) Herbivory : the dynamics of animal-plant interactions Oxford :
Blackwell Scientific. 437 p. ISBN 0632008083
• Olff, H., V.K. Brown, R.H. Drent (editors) (1999) Herbivores : between plants and predators
Oxford ; Malden, Ma. : Blackwell Science. 639 p. ISBN 0632051558

• Herbivore information resource website
• The herbivore defenses of Senecio viscusus
• Herbivore defense in Lindera benzoin
• website of the herbivory lab at Cornell University
[show]v · d · eFeeding behaviours

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Others Phagocytosis · Bacterivore · Coprophagia ·

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Methods Apex predator · Bottom feeding · Browsing ·

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Predation (Carnivory • Herbivory • Parasitism • Parasitoidism • Cheating) • Symbiosis • Competition •
Mimicry
[hide] Modelling ecosystems - trophic components
Abiotic component · Abiotic stress ·

Behaviour · Biogeochemical cycle · Biomass ·
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ecology · Ecosystem model · Keystone species ·
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ratio · Feed conversion ratio · Feeding frenzy ·
Mesotrophic soil · Oligotroph · Paradox of the
plankton · Trophic cascade · Trophic level ·
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r against herbivores · Predator avoidance in
schooling fish
[hide] Modelling ecosystems - other components

Abundance · Allee effect · Depensation ·
Ecological yield · Effective population size ·
Intraspecific competition · Logistic function ·
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interaction Commensalism · Community ecology · Ecological
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Retrieved from "http://en.wikipedia.org/wiki/Herbivore"
Categories: Herbivory
W000
Evolutionism

Evolutionism refers to the biological concept of evolution,[1] specifically to a widely held 19th century
belief that organisms are intrinsically bound to improve themselves, and that changes are progressive and
arise through inheritance of acquired characters, as in Lamarckism. The belief was extended to include
cultural evolution and social evolution.[2] The term is sometimes also used to refer to acceptance of the
modern evolutionary synthesis, a scientific theory that describes how biological evolution occurs. In addition,
the term is used in a broader sense to cover a world-view on a wide variety of topics, including chemical
evolution as an alternative term for abiogenesis or for nucleosynthesis of chemical elements, galaxy
formation and evolution, stellar evolution, spiritual evolution, technological evolution and universal evolution,
which seeks to explain every aspect of the world in which we live.[3][4]
Since the overwhelming majority of scientists accepts evolution,[5] the term is seldom used in the
scientific community. In the context of modern biology, to say someone is a scientist generally implies
evolutionary views.[6] In the creation-evolution controversy, creationists often call those who accept the
validity of the modern evolutionary synthesis "evolutionists" and the theory itself as "evolutionism." Some
creationists and creationist organizations, such as the Institute of Creation Research, use these terms in an
effort to make it appear that evolutionary biology is a form of secular religion.[7][8]
Contents
[hide]
• 1 Modern use
• 2 See also
• 3 Notes
• 4 References
[edit] Modern use

In modern times, the term evolution is widely used, but the terms evolutionism and evolutionist are
seldom used in the scientific community to refer to the biological discipline as the term is considered both
redundant and anachronistic, though it has been used in discussing the creation-evolution controversy.[6]
The Institute for Creation Research, however, in order to treat evolution as a category of religions,
including atheism, fascism, humanism and occultism, commonly uses the words evolutionism and
evolutionist to describe the consensus of mainstream science and the scientists subscribing to it, thus
implying through language that the issue is a matter of religious belief.[8] The basis of this argument is to
establish that the creation-evolution controversy is essentially one of interpretation of evidence, without any
overwhelming proof (beyond current scientific theories) on either side. Creationists tend to use the term
evolutionism in an attempt to suggest that the theory of evolution and creationism are equal in a philosophical
debate.[9]
[edit] See also

• Darwinism
• Scientism
[edit] Notes
1. ^ Kirkpatrick, E. M.; Davidson, George D.; Seaton, M. A.; Simpson, J. R. (1985). Chambers
concise 20th century dictionary. Edinburgh: Chambers. ISBN 0-550-10553-0.
2. ^ Allen, R. T.; Allen, Robert W. (1994). Chambers encyclopedic English dictionary .
Edinburgh: Chambers. ISBN 0-550-11000-3.
3. ^ "Evolutionism". AllAboutGOD.com, Colorado Springs, Colorado 80949. 2002–2008.
http://www.allaboutphilosophy.org/evolutionism.htm. Retrieved 2008-12-05.
4. ^ Bitbol, Olivier; Darrigol (1992). Erwin Schrödinger—Philosophie et Naissance de la
Méchanique Quantique [Erwin Schrödinger—Philosophy and the Birth of Quantum Mechanics] .
Atlantica Séguier Frontières. p. 134. ISBN 9782863321164. http://books.google.com/books?
id=3SlJsTH1ehsC&lpg=PP1&pg=PA134.
5. ^ "Nearly all scientists (97%) say humans and other living things have evolved over time",
Public Praises Science; Scientists Fault Public, Media, Pew Research Center, 9 July 2009
6. ^ a b J. B. Gough (1983). "The Supposed Dichotomy between Creationism and Evolution".
National Center for Science Education. http://ncse.com/cej/4/2/supposed-dichotomy-between-
creationism-evolution. Retrieved 2009-09-24.
7. ^ Michael Ruse (March 2003). "Perceptions in science: Is Evolution a Secular Religion? --
Ruse". Science. pp. 299 (5612): 1523. http://www.sciencemag.org/cgi/content/full/299/5612/1523.
Retrieved 2008-12-05. "A major complaint of the Creationists, those who are committed to a
Genesis-based story of origins, is that evolution--and Darwinism in particular--is more than just a
scientific theory. They object that too often evolution operates as a kind of secular religion, pushing
norms and proposals for proper (or, in their opinion, improper) action."
8. ^ a b Steven Linke (August 28, 1992). "A Visit to the ICR Museum". TalkOrigins Archive.
http://www.talkorigins.org/faqs/icr-visit/linke.html. Retrieved 2008-12-05. "In fact, true science
supports the Biblical worldview... However, science does not support false religions (e.g. atheism,
evolutionism, pantheism, humanism, etc.)"
9. ^ Moore, John (2008). "Creationism vs. Evolutionism". Answers in Genesis.
http://www.answersingenesis.org/articles/2008/01/24/attention-to-word-meaning. Retrieved 2009-09-
19.
[edit] References
• Carneiro, Robert, Evolutionism in Cultural Anthropology: A Critical History ISBN 0-8133-
3766-6
• Korotayev, Andrey (2004). World Religions and Social Evolution of the Old World Oikumene
Civilizations: A Cross-cultural Perspective (First Edition ed.). Lewiston, New York: Edwin Mellen
Press. ISBN 0-7734-6310-0. (on the applicability of this notion to the study of social evolution)
• Review of Buckland's Bridgewater Treatise, The Times Tuesday, November 15, 1836; pg. 3;
Issue 16261; col E. ("annihilates the doctrine of spontaneous and progressive evolution of life, and its
impious corollary, chance")
• Review of Charles Darwin's The Expression of the Emotions in Man and Animals The Times
Friday, December 13, 1872; pg. 4; Issue 27559; col A. ("His [Darwin's] thorough-going 'evolutionism'
tends to eliminate...")
• Ruse, Michael. 2003. Is Evolution a Secular Religion? Science 299:1523-1524 (concluding
that evolutionary biology is not a religion in any sense but noting that several evolutionary biologists,
such as Edward O. Wilson, in their roles as citizens concerned about getting the public to deal with
reality, have made statements like "evolution is a myth that is now ready to take over Christianity").

• National Center for Science Education - The National Center for Science Education
Retrieved from "http://en.wikipedia.org/wiki/Evolutionism"
Categories: Creationism | Biological evolution | Biology theories | Empiricism

W000
Timeline of evolution

For the history of evolutionary biology, see History of evolutionary thought.
This article is about the timeline of evolution in a general aspect. See also the timeline of human
evolution.
This timeline of the evolution of life outlines the major events in the development of life on the planet
Earth (See Organism). For a thorough explanatory context, see the history of Earth, and geologic time scale.
The dates given in this article are estimates based on scientific evidence.
In biology, evolution is the process by which populations of organisms acquire and pass on novel
traits from generation to generation. Its occurrence over large stretches of time explains the origin of new
species and ultimately the vast diversity of the biological world. Contemporary species are related to each
other through common descent, products of evolution and speciation over billions of years.
Contents
[hide]
• 1 Basic timeline
• 2 Detailed timeline
• 2.1 Hadean Eon
• 2.2 Archean Eon
• 2.3 Proterozoic Eon
• 2.4 Phanerozoic Eon
• 2.4.1 Paleozoic Era
• 2.4.2 Mesozoic Era
• 2.4.3 Cenozoic Era
• 3 See also
• 5 References
[edit] Basic timeline
Life on Earth
view • discuss • edit
-4500 —
–
-4000 —
–
-3500 —
–
-3000 —
–
-2500 —
–
-2000 —
–
-1500 —
–
-1000 —
–
-500 —
–
0—
Life?
Photosynthesis?
Eukaryotes
Complex multicellular life
Animals
Land plants
"Dinosaurs"
Mammals
Flowers
←
Formation
of Earth
←
Meteorite bombardment
←
Atmospheric oxygen
←
Ediacara biota
←
Cambrian explosion
←
Modern-looking
humans
Axis scale: millions of years ago.
Dates prior to 1 billion years ago are speculative.
The basic timeline is a 4.5 billion year old Earth, with (very approximate) dates:
• 3.8 billion years of simple cells (prokaryotes),
• 3 billion years of photosynthesis,
• 2 billion years of complex cells (eukaryotes),
• 1 billion years of multicellular life,
• 600 million years of simple animals,
• 570 million years of arthropods (ancestors of insects, arachnids and crustaceans),
• 550 million years of complex animals,
• 500 million years of fish and proto-amphibians,
• 475 million years of land plants,
• 400 million years of insects and seeds,
• 360 million years of amphibians,
• 300 million years of reptiles,
• 200 million years of mammals,
• 150 million years of birds,
• 130 million years of flowers,
• 65 million years since the non-avian dinosaurs died out,
• 2.5 million years since the appearance of the genus Homo,
• 200,000 years since humans started looking like they do today,
• 25,000 years since Neanderthals died out.
[edit] Detailed timeline

Ma, ("megaannum") means "million years ago". ka means "thousand years ago" and ya
means "years ago"
[edit] Hadean Eon

3800 Ma and earlier.
Date Event
4600 Ma The planet Earth forms from the accretion disc
revolving around the young Sun.
4500 Ma According to one plausible theory, the planet Earth

and the planet Theia collide, sending a very large number
of moonlets into orbit around the young Earth. These
moonlets eventually coalesce to form the Moon.[1] The
gravitational pull of the new Moon stabilises the Earth's
fluctuating axis of rotation and sets up the conditions in
which life formed.[2]
4100 Ma The surface of the Earth cools enough for the crust
to solidify. The atmosphere and the oceans form.[3] PAH
infall,[4] and iron sulfide synthesis along deep ocean
platelet boundaries, may have led to the RNA world of
competing organic compounds.
Between 4500 and 3500 Ma The earliest life appears, possibly derived from
self-reproducing RNA molecules.[5][6] The replication of
these organisms requires resources like energy, space,
and smaller building blocks, which soon become limited,
resulting in competition, with natural selection favouring
those molecules which are more efficient at replication.
DNA molecules then take over as the main replicators and
these archaic genomes soon develop inside enclosing
membranes which provide a stable physical and chemical
environment conducive to their replication: proto-cells.[7]
[8][9]
3900 Ma Late Heavy Bombardment: peak rate of impact

events upon the inner planets by meteoroids. This
constant disturbance may have obliterated any life that
had evolved to that point, or possibly not, as some early
microbes could have survived in hydrothermal vents below
the Earth's surface;[10] or life might have been transported
to Earth by a meteoroid.[11]
Somewhere between 3900 and 2500 Ma Cells resembling prokaryotes appear.[12] These
first organisms are chemoautotrophs: they use carbon
dioxide as a carbon source and oxidize inorganic materials
to extract energy. Later, prokaryotes evolve glycolysis, a
set of chemical reactions that free the energy of organic
molecules such as glucose and store it in the chemical
bonds of ATP. Glycolysis (and ATP) continue to be used in
almost all organisms, unchanged, to this day.[13][14]
[edit] Archean Eon

3800 Ma – 2500 Ma
Date Event
3500 Ma Lifetime of the last universal ancestor;[15][16] the split between bacteria and
archaea occurs.[17]
Bacteria develop primitive forms of photosynthesis which at first do not produce
oxygen.[18] These organisms generate ATP by exploiting a proton gradient, a mechanism
still used in virtually all organisms.
3000 Ma Photosynthesizing cyanobacteria evolve; they use water as a reducing agent,

thereby producing oxygen as waste product.[19] More recent research, however, suggests
a later time of 2700 Ma. The oxygen initially oxidizes dissolved iron in the oceans, creating
iron ore. The oxygen concentration in the atmosphere subsequently rises, acting as a
poison for many bacteria. The moon is still very close to the earth and causes tides
1,000 feet (305 m) high. The earth is continually wracked by hurricane force winds. These
extreme mixing influences are thought to stimulate evolutionary processes. (See Oxygen
catastrophe)
2700 Ma Timeframe of cyanobacteria evolution suggested by more recent research.
[edit] Proterozoic Eon

2500 Ma – 542 Ma
Date Event
By 1850 Ma Eukaryotic cells appear.[20][21] Eukaryotes contain membrane-bound

organelles with diverse functions, probably derived from prokaryotes engulfing each
other via phagocytosis. (See Endosymbiosis)
By 1200 Ma Sexual reproduction first appears, increasing the rate of evolution.[22]
1200 Ma Simple multicellular organisms evolve, mostly consisting of cell colonies of

limited complexity.
850–630 Ma A global glaciation may have occurred.[23][24] Opinion is divided on whether it

increased or decreased biodiversity or the rate of evolution.[25][26][27]
580–542 Ma The Ediacaran biota represent the first large, complex multicellular organisms -
although their affinities remain a subject of debate.[28]
580–500 Ma Most modern phyla of animals begin to appear in the fossil record during the
Cambrian explosion.[29][30]
580–540 Ma The accumulation of atmospheric oxygen allows the formation of an ozone

layer.[31] This blocks ultraviolet radiation, permitting the colonisation of the land.[31]
560 Ma Earliest fungi
[edit] Phanerozoic Eon

542 Ma – present
The Phanerozoic Eon, literally the "period of well-displayed life", marks the appearance in the fossil
record of abundant, shell-forming and/or trace-making organisms. It is subdivided into three eras, the
Paleozoic, Mesozoic and Cenozoic, which are divided by major mass extinctions.
[edit] Paleozoic Era

542 Ma – 251.0 Ma
Date Event
535 Ma Major diversification of living things in the oceans: chordates, arthropods (e.g.
trilobites, crustaceans), echinoderms, mollusks, brachiopods, foraminifers and
radiolarians, etc.
530 Ma The first known footprints on land date to 530 Ma, indicating that early animal
explorations may have predated the development of terrestrial plants.[32]
525 Ma Earliest graptolites.
510 Ma First cephalopods (Nautiloids) and chitons.
505 Ma Fossilization of the Burgess Shale.
485 Ma First vertebrates with true bones (jawless fishes).
450 Ma Land arthropod burrows (millipedes) appear, along with the first complete
conodonts and echinoids.
440 Ma First agnathan fishes: Heterostraci, Galeaspida, and Pituriaspida.
434 Ma The first primitive plants move onto land,[33][citation needed] having evolved from
green algae living along the edges of lakes.[34] They are accompanied by fungi[citation
needed], which may have aided the colonization of land through symbiosis.
420 Ma Earliest ray-finned fishes, trigonotarbid arachnids, and land scorpions.
410 Ma First signs of teeth in fish. Earliest nautiid nautiloids, lycophytes, and
trimerophytes.
395 Ma First lichens, stoneworts. Earliest harvestman, mites, hexapods (springtails), and
ammonoids.
363 Ma By the start of the Carboniferous Period, the Earth begins to be recognisable.
Insects roamed the land and would soon take to the skies; sharks swam the oceans as
top predators,[35] and vegetation covered the land, with seed-bearing plants and forests
soon to flourish.
Four-limbed tetrapods gradually gain adaptations which will help them occupy a
terrestrial life-habit.
360 Ma First crabs and ferns. Land flora dominated by seed ferns.
350 Ma First large sharks, ratfishes, and hagfish.
340 Ma Diversification of amphibians.

330 Ma First amniote vertebrates (Paleothyris).
305 Ma Earliest diapsid reptiles (e.g. Petrolacosaurus).
280 Ma Earliest beetles, seed plants and conifers diversify while lepidodendrids and
sphenopsids decrease. Terrestrial temnospondyl amphibians and pelycosaurs (e.g.
Dimetrodon) diversify in species.
251.4 Ma The Permian-Triassic extinction event eliminates over 90-95% of marine species.
Terrestrial organisms were not as seriously affected as the marine biota. This "clearing of
the slate" may have led to an ensuing diversification, but life on land took 30M years to
completely recover.[36]
[edit] Mesozoic Era

Date Event
From 251.4 Ma The Mesozoic Marine Revolution begins: increasingly well-adapted and
diverse predators pressurise sessile marine groups; the "balance of power" in the
oceans shifts dramatically as some groups of prey adapt more rapidly and
effectively than others.
245 Ma Earliest ichthyosaurs.
240 Ma Increase in diversity of gomphodont cynodonts and rhynchosaurs.

225 Ma Earliest dinosaurs (prosauropods), first cardiid bivalves, diversity in cycads,
bennettitaleans, and conifers. First teleost fishes.
215 Ma First mammals (e.g. Eozostrodon), minor vertebrate extinctions occur
220 Ma
Eoraptor, among the earliest dinosaurs, appeared in the fossil record 230
million years ago.
Gymnosperm forests dominate the land; herbivores grow to huge sizes in
order to accommodate the large guts necessary to digest the nutrient-poor plants.
[citation needed], first flies and turtles (Odontochelys). First Coelophysoid dinosaurs
200 Ma The first accepted evidence for viruses (at least, the group Geminiviridae)
exists.[37] Viruses are still poorly understood and may have arisen before "life"
itself, or may be a more recent phenomenon.
Major extinctions in terrestrial vertebrates and large amphibians. Earliest
examples of Ankylosaurian dinosaurs
195 Ma First pterosaurs with specialized feeding (Dorygnathus). First sauropod

dinosaurs. Diversification in small, ornithischian dinosaurs: heterodontosaurids,
fabrosaurids, and scelidosaurids.
190 Ma Pliosaurs appear in the fossil record. First lepidopteran insects

(Archaeolepis), hermit crabs, modern starfish, irregular echinoids, corbulid bivalves,
and tubulipore bryozoans. Extensive development of sponge reefs.
176 Ma First members of the Stegosauria group of dinosaurs
170 Ma Earliest salamanders, newts, cryptoclidid & elasmosaurid plesiosaurs, and

cladotherian mammals. Cynodonts become extinct while sauropod dinosaurs
diversify.
165 Ma First rays and glycymeridid bivalves.
161 Ma Ceratopsian dinosaurs appear in the fossil record (Yinlong)
155 Ma First blood-sucking insects (ceratopogonids), rudist bivalves, and

cheilosome bryozoans. Archaeopteryx, a possible ancestor to the birds, appears in
the fossil record, along with triconodontid and symmetrodont mammals. Diversity in
stegosaurian and theropod dinosaurs.
130 Ma The rise of the Angiosperms: These flowering plants boast structures that
attract insects and other animals to spread pollen. This innovation causes a major
burst of animal evolution through co-evolution. First freshwater pelomedusid turtles.
120 Ma Oldest fossils of heterokonts, including both marine diatoms and

silicoflagellates.
115 Ma First monotreme mammals.
110 Ma First hesperornithes, toothed diving birds. Earliest limopsid, verticordiid, and
thyasirid bivalves.
106 Ma Spinosaurus, the largest theropod dinosaur, appears in the fossil record.
100 Ma Earliest bees.
90 Ma Extinction of ichthyosaurs. Earliest snakes and nuculanid bivalves. Large

diversification in angiosperms: magnoliids, rosids, hamamelidids, monocots, and
ginger. Earliest examples of ticks.
80 Ma First ants and termites.
70 Ma Multituberculate mammals increase in diversity. First yoldiid bivalves.
68 Ma Tyrannosaurus, the largest terrestrial predator of North America appears in

the fossil record. First species of Triceratops.
[edit] Cenozoic Era
65.5 Ma – present
Date Event
65.5 Ma The Cretaceous–Tertiary extinction event eradicates about half of all animal
species, including mosasaurs, pterosaurs, plesiosaurs, ammonites, belemnites,
rudist and inoceramid bivalves, most planktic foraminifers, and all of the dinosaurs
excluding their descendants the birds [38]
From 65 Ma Rapid dominance of conifers and ginkgos in high latitudes, along with
mammals becoming the dominant species. First psammobiid bivalves. Rapid
diversification in ants.
63 Ma Evolution of the creodonts, an important group of carnivorous mammals.
60 Ma Diversification of large, flightless birds. Earliest true primates, along with the
first semelid bivalves, edentates, carnivorous and lipotyphlan mammals, and owls.
The ancestors of the carnivorous mammals (miacids) were alive.
56 Ma Gastornis, a large, flightless bird appears in the fossil record, becoming an

apex predator at the time.
55 Ma Modern bird groups diversify (first song birds, parrots, loons, swifts,
woodpeckers), first whale (Himalayacetus), earliest rodents, lagomorphs, armadillos,
appearance of sirenians, proboscideans, perissodactyl and artiodactyl mammals in
the fossil record. Angiosperms diversify. The ancestor (according to theory) of the
species in Carcharodon, the early mako shark Isurus hastalis, is alive.
52 Ma First bats appear (Onychonycteris).
50 Ma Peak diversity of dinoflagellates and nanofossils, increase in diversity of

anomalodesmatan and heteroconch bivalves, brontotheres, tapirs, rhinoceroses, and
camels appear in the fossil record, diversification of primates.
40 Ma Modern type butterflies and moths appear. Extinction of Gastornis.

Basilosaurus, one of the first of the giant whales, appeared in the fossil record.
37 Ma First Nimravid carnivores ("False Saber-toothed Cats") - these species are
unrelated to modern-type felines
35 Ma Grasses evolve from among the angiosperms; grasslands begin to expand.

Slight increase in diversity of cold-tolerant ostracods and foraminifers, along with
major extinctions of gastropods, reptiles, and amphibians. Many modern mammal
groups begin to appear: first glyptodonts, ground sloths, dogs, peccaries, and the first
eagles and hawks. Diversity in toothed and baleen whales.
33 Ma Evolution of the thylacinid marsupials (Badjcinus).
30 Ma First balanids and eucalypts, extinction of embrithopod and brontothere

mammals, earliest pigs and cats.
28 Ma Paraceratherium appears in the fossil record, the largest terrestrial mammal
that ever lived.
25 Ma First deer.
20 Ma First giraffes and giant anteaters, increase in bird diversity.
15 Ma Mammut appears in the fossil record, first bovids and kangaroos, diversity in
Australian megafauna.
10 Ma Grasslands and savannas are established, diversity in insects, especially

ants and termites, horses increase in body size and develop high-crowned teeth,
major diversification in grassland mammals and snakes.
6.5 Ma First hominin (Sahelanthropus).
6 Ma Australopithecines diversify (Orrorin, Ardipithecus)
5 Ma First tree sloths and hippopotami, diversification of grazing herbivores, large

carnivorous mammals, burrowing rodents, kangaroos, birds, and small carnivores,
vultures increase in size, decrease in the number of perissodactyl mammals.
Extinction of Nimravid carnivores
4.8 Ma Mammoths appear in the fossil record.
4 Ma Evolution of Australopithecus, Stupendemys appears in the fossil record as

the largest freshwater turtle.
3 Ma The Great American Interchange, where various land and freshwater faunas
migrated between North and South America. Armadillos, opossums, hummingbirds,
and vampire bats traveled to North America while horses, tapirs, saber-toothed cats,
and deer entered South America. The first short-faced bears ( Arctodus) appear.
2.7 Ma Evolution of Paranthropus
2.5 Ma The earliest species of Smilodon evolve
2 Ma First members of the genus Homo appear in the fossil record. Diversification
of conifers in high latitudes. The eventual ancestor of cattle, Bos primigenius evolves
in India
1.7 Ma Extinction of australopithecines.
1.2 Ma Evolution of Homo antecessor. The last members of Paranthropus die out.
600 ka Evolution of Homo heidelbergensis
350 ka Evolution of Neanderthals
300 ka Gigantopithecus, a giant relative of the orangutan dies out from Asia
200 ka Anatomically modern humans appear in Africa.[39][40][41] Around 50,000
years before present they start colonising the other continents, replacing the
Neanderthals in Europe and other hominins in Asia.
40 ka The last of the giant monitor lizards ( Megalania) die out
30 ka Extinction of Neanderthals
15 ka The last Woolly rhinoceros (Coelodonta) are believed to have gone extinct
11 ka The giant short-faced bears (Arctodus) vanish from North America, with the
last Giant Ground Sloths dying out. All Equidae become extinct in North America
10 ka The Holocene Epoch starts 10,000[42] years ago after the Late Glacial
Maximum. The last mainland species of Woolly mammoth (Mammuthus primigenius)
die out, as does the last Smilodon species
6 ka Small populations of American Mastodon die off in places like Utah and
Michigan
4500 ya The last members of a dwarf race of Woolly Mammoths vanish from Wrangel
Island near Alaska
384 ya (1627) The last recorded wild Aurochs die out
75 ya (1936) The Thylacine goes extinct in a Tasmanian zoo, the last member of the family
Thylacinidae
[edit] See also
Book:Evolution

• Evolutionary history of life
• Evolutionary history of plants
• Extinction events
• Geologic time scale
• History of Earth
• Natural history
• Sociocultural evolution
• Timeline of human evolution
• Timeline of plant evolution

• The Ancestor's Tale by Richard Dawkins, for a list of ancestors common to humans and
other living species
[edit] References
1. ^ Planetary Science Institute page on the Giant Impact Hypothesis. Hartmann and Davis
belonged to the PSI. This page also contains several paintings of the impact by Hartmann himself.
2. ^ "Because the Moon helps stabilize the tilt of the Earth's rotation, it prevents the Earth from
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4. ^ *The 'PAH World'
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Geophysicist Sleep: Martian underground may have harbored early life (URL accessed on January 9,
2005)
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Proterozoic oceans". Philosophical Transactions of the Royal Society of London, Part B 361 (1470):
1023–38. doi:10.1098/rstb.2006.1843. PMID 16754612.
21.^ Fedonkin, M. A. (March 2003). "The origin of the Metazoa in the light of the Proterozoic
fossil record" (PDF). Paleontological Research 7 (1): 9–41. doi:10.2517/prpsj.7.9.
http://www.vend.paleo.ru/pub/Fedonkin_2003.pdf. Retrieved 2008-09-02.
22.^ Nicholas J. Butterfield, "Bangiomorpha pubescens n. gen., n. sp.: implications for the
evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes"
23.^ Hoffman, P.F.; Kaufman, A.J., Halverson, G.P., Schrag, D.P. (1998-08-28). "A
Neoproterozoic Snowball Earth". Science 281 (5381): 1342–6. doi:10.1126/science.281.5381.1342.
PMID 9721097. http://www.sciencemag.org/cgi/content/full/281/5381/1342?
ijkey=48d78da67bab492803c333f50c0dd84fbbef109c. Retrieved 2007-05-04. Full online article (pdf
260 Kb)
24.^ Kirschvink, J.L. (1992). "Late Proterozoic low-latitude global glaciation: The snowball
Earth". In Schopf, JW, and Klein, C. (PDF). The Proterozoic Biosphere: A Multidisciplinary Study.
Cambridge University Press, Cambridge. pp. 51–52.
http://www.gps.caltech.edu/~jkirschvink/pdfs/firstsnowball.pdf.
25.^ http://researchpages.net/media/resources/2007/06/21/richtimhywelfinal.pdf
26.^ Corsetti, F.A.; Awramik, S.M.; Pierce, D. (2003-04-15). "A complex microbiota from
snowball Earth times: Microfossils from the Neoproterozoic Kingston Peak Formation, Death Valley,
USA". Proceedings of the National Academy of Sciences 100 (8): 4399–4404.
doi:10.1073/pnas.0730560100. PMID 12682298. PMC 153566.
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27.^ Corsetti, F.A.; Olcott, A.N.; Bakermans, C. (2006). "The biotic response to Neoproterozoic
Snowball Earth". Palaeogeography, Palaeoclimatology, Palaeoecology 232 (232): 114–130.
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Geological Sciences and Geological Engineering, Queen's University.
http://geol.queensu.ca/people/narbonne/recent_pubs1.html. Retrieved 2007-03-10.
29.^ The Cambrian Period
30.^ The Cambrian Explosion – Timing
31.^ a b Formation of the Ozone Layer
32.^ "The oldest fossils of footprints ever found on land hint that animals may have beaten
plants out of the primordial seas. Lobster-sized, centipede-like or slug like animals such as
Protichnites and Climactichnites made the prints wading out of the ocean and scuttling over sand
dunes about 530 million years ago. Previous fossils indicated that animals didn't take this step until
40 million years later." Oldest fossil footprints on land
33.^ "The oldest fossils reveal evolution of non-vascular plants by the middle to late Ordovician
Period (~450–440 Ma) on the basis of fossil spores" Transition of plants to land
34.^ "The land plants evolved from the algae, more specifically green algae, as suggested by
certain common biochemical traits" The first land plants
35.^ "The ancestry of sharks dates back more than 200 million years before the earliest known
dinosaur. Introduction to shark evolution, geologic time and age determination
36.^ Sahney, S. and Benton, M.J. (2008). "Recovery from the most profound mass extinction of
all time" (PDF). Proceedings of the Royal Society: Biological 275 (1636): 759–65.
doi:10.1098/rspb.2007.1370. PMID 18198148. PMC 2596898.
37.^ "Viruses of nearly all the major classes of organisms—animals, plants, fungi and
bacteria/archaea—probably evolved with their hosts in the seas, given that most of the evolution of
life on this planet has occurred there. This means that viruses also probably emerged from the
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Review of Ecology & Systematics 33: 91–124. doi:10.1146/annurev.ecolsys.33.010802.150517.
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http://www.stratigraphy.org/cheu.pdf. Retrieved 2009-02-03. [dead link]

• Berkeley Evolution
• Tree of Life Web Project - explore complete phylogenetic tree interactively
• A more compact timeline at the TalkOrigins Archive
• Palaeos - The Trace of Life on Earth
• University of Waikato - Sequence of Plant Evolution
• University of Waikato - Sequence of Animal Evolution
• Graphical Timeline of evolution
• History of Life on Earth
• Exploring Time from Planck Time to the lifespan of the universe
• Interactive Plant Evolution Timeline - from the University of Cambridge Ensemble Project
Processes of
Population genetic
Evolutionary
developmental
concepts

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Retrieved from "http://en.wikipedia.org/wiki/Timeline_of_evolution"
Categories: Biology timelines | Evolutionary biology

W000
Objections to evolution

Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
Objections to evolution have been raised since evolutionary ideas came to prominence in the 19th
century.[1] When Charles Darwin published his 1859 book On the Origin of Species, his theory of evolution
by natural selection initially met opposition from alternate scientific theories, but came to be universally
accepted by the scientific community.[2] The observation of evolutionary processes occurring, as well as the
current theory explaining that evidence, have been uncontroversial among mainstream biologists for nearly a
century.[3]
Since then, nearly all criticisms of evolution have come from religious sources, rather than from the
scientific community.[4] Although most religions have accepted the occurrence of evolution, such as those
advocating theistic evolution, there still exist religious beliefs which reject evolutionary explanations in favor
of creationism, the belief that a deity supernaturally created the world largely in its current form.[5] The
resultant U.S.-centric creation-evolution controversy has been a focal point of recent conflict between religion
and science.
In contrast to earlier objections to evolution that were either strictly scientific or explicitly religious,
recent objections to evolution have frequently blurred the distinction between the two. Such objections have
often centered on undermining evolution's scientific basis, with the intent of combating the teaching of
evolution as fact and opposing the spread of "atheistic materialism".[6] Modern creationism is characterized
by movements such as Creation Science, neocreationism, and Intelligent Design which argue that the idea of
life being directly "designed" by a god or intelligence is at least as scientific as evolutionary theory, and
should therefore be taught in public schools. Their arguments against evolution have become widespread,
and include objections to evolution's evidence, methodology, plausibility, morality, and scientific acceptance.
The scientific community, however, does not accept such objections as having any validity, citing detractors'
misinterpretations of scientific method, evidence, and basic physical laws.[7]
While objections primarily originate from the United States, there is widespread belief in creationism
in the Muslim world,[8] South Africa and India[9] with smaller followings in Australia, New Zealand, the United
Kingdom and Canada.[10] However, in India 77% of respondents who had heard of Charles Darwin and
knew something about the theory of evolution agreed it was backed by scientific evidence.[11]
Contents
[hide]
• 1 Defining evolution
• 2 History
• 3 Scientific acceptance
• 3.1 Status as a theory
• 3.2 Degree of acceptance
• 4 Scientific status
• 4.1 Religious nature
• 4.2 Unfalsifiability
• 5 Evidence
• 5.1 Lack of observation
• 5.2 Instability of evidence
• 5.3 Unreliable or inconsistent evidence
• 6 Plausibility
• 6.1 Improbability
• 6.2 Unexplained aspects of the natural world
• 7 Impossibility
• 7.1 Creation of complex structures
• 7.2 Creation of information
• 7.3 Violation of the second law of thermodynamics
• 8 Moral implications
[edit] Defining evolution
Further information: Evolution (term)
One of the main sources of confusion and ambiguity in the creation-evolution debate is the definition
of evolution itself. In the context of biology, evolution is genetic changes in populations of organisms over
successive generations. However, the word has a number of different meanings in different fields, from
evolutionary computation to molecular evolution to sociocultural evolution to stellar and galactic evolution. It
can even refer to metaphysical evolution, spiritual evolution, or any of a number of evolutionist philosophies.
When biological evolution is conflated with other evolutionary processes, this can cause errors such as the
claim that modern evolutionary theory says anything about abiogenesis or the Big Bang.[12]
In colloquial contexts, evolution can refer to any sort of progressive development, and often bears a
connotation of gradual improvement: here evolution is understood as a process that results in greater quality
or complexity. This common definition, when misapplied to biological evolution, leads to frequent
misunderstandings. For example, the idea of devolution ("backwards" evolution) is a result of erroneously
assuming that evolution is directional or has a specific goal in mind (cf. orthogenesis). In reality, the evolution
of an organism has no "objective" other than increasing the organism's ability to survive and reproduce in its
environment; and its suitability is only defined in relation to this environment. Biologists do not consider any
one species, such as humans, to be more highly evolved or advanced than another. Certain sources have
been criticized for indicating otherwise due to a tendency to evaluate nonhuman organisms according to
anthropocentric standards rather than more objective ones.[13]
Evolution also does not require that organisms become more complex. Although the history of life
shows an apparent trend towards the evolution of complexity; there is a question if this appearance of
increased complexity is real, or if this conclusion comes from neglecting the fact that the majority of life on
earth has always consisted of prokaryotes.[14] In this view, complexity is not a necessary consequence of
evolution; rather, it is a consequence of the specific circumstances of evolution on Earth, which frequently
made greater complexity advantageous, and thus naturally selected for. Depending on the situation,
organisms' complexity can either increase, decrease, or stay the same, and all three of these trends have
been observed in evolution.[13]
Creationist sources frequently define evolution according to a colloquial, rather than scientific,
meaning.[15] As a result, many attempts to rebut evolution do not address the findings of evolutionary
biology (see straw man argument). This also means that advocates of creationism and evolutionary biologists
often simply speak past each other.[12][16]
[edit] History
Further information: History of evolutionary thought, History of creationism and Creation-evolution
controversy
Darwin's theory of evolution through common descent gained widespread acceptance, but there was
continued resistance to his views on the significance of natural selection.
Various evolutionary ideas came to prominence around the start of the nineteenth century, in
particular the transmutation of species theory put forward by Jean-Baptiste Lamarck. These were opposed
on scientific grounds, most notably by Georges Cuvier, as well as meeting political and religious objections.
[1] These ideas that natural laws controlled the development of nature and society gained vast popular
audiences with George Combe's The Constitution of Man of 1828 and the anonymous Vestiges of the
Natural History of Creation of 1844. When Charles Darwin published his 1859 book On the Origin of Species,
within fifteen to twenty years he convinced most of the scientific community that evolution through common
descent was true, but while most accepted that natural selection was a valid and empirically testable
hypothesis, his view that it was the primary mechanism of evolution was generally rejected.[2]
The earliest objections to Darwinian evolution were both scientific and religious. Darwin's
contemporaries eventually came to accept the transmutation of species based upon fossil evidence; forming
the X Club to defend it against the church and wealthy amateurs,[17] although the specific evolutionary
mechanism which Darwin provided – natural selection – was actively disputed by alternative theories such as
Lamarckism and orthogenesis. Darwin's gradualistic account was also opposed by saltationism and
catastrophism. Lord Kelvin led scientific opposition to gradualism on the basis of his thermodynamic
calculations that the Age of the Earth was between 24 and 400 million years old, an estimate strongly
disputed by geologists. These figures were corrected in 1907 when radioactive dating of rocks showed that
the Earth was billions of years old.[18][19] Kelvin's own views favoured a version of theistic evolution
accelerated by divine guidance.[20] The specific hereditary mechanism Darwin provided, pangenesis, lacked
any supporting evidence. In the early 20th century, pangenesis was replaced by Mendelian inheritance,
leading to the rise of the modern evolutionary synthesis. The modern synthesis rose to universal acceptance
among biologists with the help of new evidence, such as genetics, which confirmed Darwin's predictions and
refuted the competing theories.[21]
Protestantism, especially in America, broke out in "acrid polemics" and argument about evolution
from 1860 to the 1870s – with the turning point possibly marked with the death of Louis Agassiz in 1873 – and
by 1880 a form of "Christian evolution" was becoming the consensus.[22] In Britain while publication of The
Descent of Man by Darwin in 1871 reinvigorated debate from the previous decade, Sir Henry Chadwick notes
a steady acceptance of evolution "among more educated Christians" between 1860 and 1885. This led
evolutionary theory to be "both permissible and respectable" by 1876.[22] Frederick Temple's lectures on
Relations between Religion and Science (1884) speaking on how evolution was not "antagonistic" to religion
highlighted this trend.[23] Temple's appointment to Archbishop of Canterbury in 1896 showed the broad
acceptance of evolution within the church hierarchy.[22]
For decades Catholicism avoided official refutation of evolution. However, it would rein in Catholics
who proposed that evolution could be reconciled with the Bible, as this conflicted with First Vatican Council's
(1869–70) finding that everything was created out of nothing by God, and to question that could lead to
excommunication. In 1950, the encyclical Humani Generis of Pope Pius XII first mentioned evolution directly
and officially.[24] It allowed for inquiry into humans coming from pre-existing living matter, but to not question
Adam and Eve or the creation of the soul. In 1996, Pope John Paul II stated evolution was "more than a
hypothesis" and acknowledged the large body of work accumulated in its support, but reiterated that any
attempt to give a material explanation of the human soul was "incompatible with the truth about man."[25]
Muslim reaction covered the gamut with those believing in literal creation from the Qur'an while many
educated Muslims subscribed to a version of theistic or guided evolution where the Qur'an reinforced rather
than contradicted mainstream science. This occurred relatively quickly as medieval Madrasah's taught ideas
of Al-Jahiz, a Muslim scholar from the 9th century, who proposed concepts similar to natural selection.[8]
However, acceptance of evolution remains low in the Muslim world as prominent figures reject evolution's
underpinning philosophy of materialism as unsound to human origins and a denial of Allah.[8] Further
objections by Muslim scholars and writers largely reflect those put forward in the Western world.[26]
Regardless of acceptance from major religious hierarchies, early religious objections to Darwin's
theory are still used in opposition to evolution. The ideas that species change over time through natural
processes and that different species share common ancestors seemed to contradict the Genesis account of
Creation. Believers in Biblical infallibility attacked Darwinism as heretical. The natural theology of the early
19th century was typified by Paley's watchmaker analogy, an argument from design still used by the
creationist movement. Natural theology included a range of ideas and arguments from the outset, and when
Darwin's theory was published, ideas of theistic evolution were presented in which evolution is accepted as a
secondary cause open to scientific investigation, while still holding belief in God as a first cause with a non-
specified role in guiding evolution and creating humans.[27] This position has been adopted by
denominations of Christianity and Judaism in line with modernist theology which views the Bible and Torah
as allegorical thus removing the conflict between evolution and religion.
However, in the 1920s Christian fundamentalists in the United States developed their literalist
arguments against Modernist theology into opposition to the teaching of evolution due to fears that
‘‘Darwinism’’ had led to German militarism and was a threat to religion and morality. This opposition
developed into the creation-evolution controversy involving Christian literalists in the United States objecting
to the teaching of evolution in public schools. Although early objections dismissed evolution for contradicting
their interpretation of the Bible, this argument was invalidated when the Supreme Court ruled in Epperson v.
Arkansas that forbidding the teaching of evolution on religious grounds violated the Establishment Clause.
[28]
Since then creationists have developed more nuanced objections to evolution, alleging variously that
it is unscientific, infringes on creationists' religious freedoms or that the acceptance of evolution is a religious
stance.[29] Creationists have appealed to democratic principles of fairness, arguing that evolution is
controversial, and that science classrooms should therefore "Teach the Controversy".[30] These objections
to evolution culminated in the intelligent design movement in the early 2000s that unsuccessfully attempted
to present itself as a scientific alternative to evolution.[31][32]
[edit] Scientific acceptance

Recent objections to evolutionary theory have focused on its scientific validity,[33][34] or attempting
to come up with alternative ideas such as Creationism to debate its findings.[35] Creationists often argue, for
example, that evolution is unproven, non-factual, or controversial.[36]
[edit] Status as a theory

Further information: Evolution as theory and fact
Critics of evolution frequently assert that evolution is "just a theory", with the intent of emphasizing
evolution's allegedly unproven nature, or of characterizing it as a matter of opinion rather than of fact or
evidence. This reflects a misunderstanding of the meaning of theory in a scientific context: whereas in
colloquial speech a theory is a conjecture or guess, in science a theory is simply an explanation or model of
the world that makes testable predictions. When evolution is used to describe a theory, it refers to an
explanation for the diversity of species and their ancestry. An example of evolution as theory is the modern
synthesis of Darwinian natural selection and Mendelian inheritance. As with any scientific theory, the modern
synthesis is constantly debated, tested, and refined by scientists. There is an overwhelming consensus in the
scientific community that it remains the only robust model that accounts for the known facts concerning
evolution.[37]
Critics also state that evolution is not a fact.[38] In science, a fact is a verified empirical observation;
in colloquial contexts, however, a fact can simply refer to anything for which there is overwhelming evidence.
For example, in common usage theories such as "the Earth revolves around the Sun" and "objects fall due to
gravity" may be referred to as "facts", even though they are purely theoretical. From a scientific standpoint,
therefore, evolution may be called a "fact" for the same reason that gravity can: under the scientific definition,
evolution is an observable process that occurs whenever a population of organisms genetically changes over
time. Under the colloquial definition, the theory of evolution can also be called a fact, referring to this theory's
well-established nature. Thus, evolution is widely considered both a theory and a fact by scientists.[39][40]
[41]
Similar confusion is involved in objections that evolution is "unproven";[42] strict proof is possible
only in formal sciences such as logic and mathematics, not natural sciences (where "validated", or
"corroborated", is the proper term), so this is trivially true, and no more an indictment of evolution than calling
it a "theory". The confusion arises, however, in that the colloquial meaning of proof is simply "compelling
evidence", in which case scientists would indeed consider evolution "proven". The distinction is an important
one in philosophy of science, as it relates to the lack of absolute certainty in all empirical claims, not just
evolution.[43]
[edit] Degree of acceptance

Further information: Level of support for evolution
In 1999 a new major objection to evolution appeared in Kansas, and is in a sense self-fulfilling: it
argues that evolution is controversial or contentious.[44] Unlike past creationist arguments which sought to
abolish the teaching of evolution altogether, this argument makes the weaker claim that evolution, being
controversial, should be presented alongside other, alternative views, and students should be allowed to
evaluate and choose between the options on their own.[45] This appeal to "fairness" and a more democratic,
"balanced" approach in which conflicting views are given "equal time" appeals to American creationists, and
was endorsed by U.S. President George W. Bush.[32][42][46]
This objection forms the basis of the "Teach the Controversy" campaign, an attempt by the Discovery
Institute to promote the teaching of intelligent design in public schools. This in turn forms a major part of the
Institute's "wedge strategy", an attempt to gradually undermine evolution and ultimately to "reverse the stifling
materialist world view and replace it with a science consonant with Christian and theistic convictions".[30]
Scientists and U.S. courts have rejected this objection on the grounds that science is not based on
appeals to popularity, but on evidence. The scientific consensus of biologists, not popular opinion or fairness,
determines what is considered acceptable science, and it is argued that although evolution is clearly
controversial in the public arena, it is entirely uncontroversial among experts in the field.[47]
In response, creationists have disputed the level of scientific support for evolution. The Discovery
Institute has gathered over 600 scientists since 2001 to sign "A Scientific Dissent From Darwinism" in order
to show that there are a number of scientists who dispute what they refer to as "Darwinian evolution". This
statement did not profess outright disbelief in evolution, but expressed skepticism as to the ability of "random
mutation and natural selection to account for the complexity of life." Several counter-petitions have been
launched in turn, including A Scientific Support for Darwinism, which gathered over 7,000 signatures in four
days, and Project Steve, a tongue-in-cheek petition that has gathered 1,151 (as of January 18, 2011)
evolution-supporting scientists named "Steve".
Creationists have argued for over a century that evolution is "a theory in crisis" that will soon be
overturned,[48] based on objections that it lacks reliable evidence or violates natural laws. These objections
have been rejected by most scientists, as have claims that intelligent design, or any other creationist
explanation, meets the basic scientific standards that would be required to make them scientific alternatives
to evolution. It is also argued that even if evidence against evolution exists, it is a false dilemma to
characterize this as evidence for intelligent design.[46][49]
A similar objection to evolution is that certain scientific authorities – mainly pre-modern ones – have
doubted or rejected evolution.[50] Most commonly, it is argued that Darwin "recanted" on his deathbed, a
false anecdote originating from the Lady Hope Story.[51] These objections are generally rejected as appeals
to authority. Even if this myth were true, it would hold no bearing on the merit of the theory itself.
[edit] Scientific status

A common neo-creationist objection to evolution is that evolution does not adhere to normal scientific
standards—that it is not genuinely scientific. It is argued that evolutionary biology does not follow the scientific
method, and therefore should not be taught in science classes, or at least should be taught alongside other
views (i.e., creationism). These objections often deal with the very nature of evolutionary theory and the
scientific method.
[edit] Religious nature

Further information: Relationship between religion and science, Scientism
Creationists commonly argue against evolution on the grounds that "evolution is a religion; it is not a
science".[52] The purpose of this criticism is to undermine the higher ground biologists claim in debating
creationists, and to reframe the debate from being between science (evolution) and religion (creationism) to
being between two equally religious beliefs – or even to argue that evolution is religious while intelligent
design is not.[53][54] Those that oppose evolution frequently refer to supporters of evolution as
"evolutionists" or "Darwinists".[52]
The arguments for evolution being a religion generally amount to arguments by analogy: it is argued
that evolution and religion have one or more things in common, and that therefore evolution is a religion.
Examples of claims made in such arguments are statements that evolution is based on faith, that supporters
of evolution revere Darwin as a prophet, and that supporters of evolution dogmatically reject alternative
suggestions out-of-hand.[42][55] These claims have become more popular in recent years as the
neocreationist movement has sought to distance itself from religion, thus giving it more reason to make use
of a seemingly anti-religious analogy.[47]
In response, supporters of evolution have argued that no scientist's claims, including Darwin's, are
treated as sacrosanct, as shown by the aspects of Darwin's theory that have been rejected or revised by
scientists over the years, to form first Neo-Darwinism and later the modern evolutionary synthesis.[56][57]
The claim that evolution relies on faith, often based on the creationist belief that evolution has never been
observed, is likewise rejected on the grounds that evolution has strong supporting evidence, and therefore
does not require faith.
In general, the argument that evolution is religious has been rejected on the grounds that religion is
not defined by how dogmatic or zealous its adherents are, but by its spiritual or supernatural beliefs.
Evolutionary supporters point out evolution is neither dogmatic nor based on faith, and they accuse
creationists of equivocating between the strict definition of religion and its colloquial usage to refer to
anything that is enthusiastically or dogmatically engaged in. U.S. courts have also rejected this objection:
Assuming for the purposes of argument, however, that evolution is a religion or religious tenet,
the remedy is to stop the teaching of evolution, not establish another religion in opposition to it.
Yet it is clearly established in the case law, and perhaps also in common sense, that evolution is
not a religion and that teaching evolution does not violate the Establishment Clause.[58]
A related claim is that evolution is atheistic; creationists sometimes merge the two claims and
describe evolution as an "atheistic religion" (cf. humanism).[54] This argument against evolution is also
frequently generalized into a criticism of all science; it is argued that "science is an atheistic religion", on the
grounds that its methodological naturalism is as unproven, and thus as "faith-based", as the supernatural and
theistic beliefs of creationism.[59]
[edit] Unfalsifiability
A statement is considered falsifiable if there is an observation or a test that could be made that would
demonstrate that the statement is false. Statements that are not falsifiable cannot be examined by scientific
investigation since they permit no tests that evaluate their accuracy. Creationists such as Henry M. Morris
have claimed that evolution is unfalsifiable. They claim that any observation can be fitted into the
evolutionary framework, and that therefore it is impossible to demonstrate that evolution is wrong. As such,
they claim that evolution is non-scientific.[60][61]
Darwin and an ape, circa 1874 from Julkaistussa picture source.
However, evolution is considered falsifiable by scientists because it can make predictions that, were
they contradicted by the evidence, would falsify evolution. Several kinds of evidence have been proposed
that could falsify evolution, such as the fossil record showing no change over time, confirmation that
mutations are prevented from accumulating, or observations showing organisms being created
supernaturally or spontaneously.[60] Many of Darwin's ideas and assertions of fact have been falsified as
evolutionary science has developed and has continued to confirm his central concepts.[62] Despite this,
creationism consists largely of unsubstantiated claims that evolution has been falsified.[60] In contrast,
creationist explanations involving the direct intervention of the supernatural in the physical world are not
falsifiable, because any result of an experiment or investigation could be the unpredictable action of an
omnipotent deity.[63]
In 1976, philosopher Karl Popper said that "Darwinism is not a testable scientific theory but a
metaphysical research programme".[64] However, Popper later recanted and summarized his new view as
follows:
The theory of natural selection may so be formulated that it is far from tautological. In this case it
is not only testable, but it turns out to be not strictly universally true. There seem to be
exceptions... Thus not all phenomena of evolution are explained by natural selection alone.[65]
Darwin's own most important contribution to the theory of evolution, his theory of natural
selection, is difficult to test. There are some tests, even some experimental tests; and in some
cases, such as the famous phenomenon known as 'industrial melanism', we can observe natural
selection happening under our very eyes, as it were. Nevertheless, really severe tests of the
theory of natural selection are hard to come by, much more so than tests of otherwise
comparable theories in physics or chemistry.[66][67]
The most direct evidence that evolutionary theory is falsifiable may be the original words of Charles
Darwin who, in chapter 6 of On the Origin of Species wrote: "If it could be demonstrated that any complex
organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my
theory would absolutely break down."[68]
In response to the unfalsifiability criticism of evolutionary theory, numerous examples of potential
ways to falsify evolution have been proposed. J.B.S. Haldane, when asked what hypothetical evidence could
disprove evolution, replied "fossil rabbits in the Precambrian era".[69][70] Numerous other potential ways to
falsify evolution have also been proposed.[43] For example, the fact that humans have one fewer pair of
chromosomes than the great apes offered a testable hypotheses involving the fusion or splitting of
chromosomes from a common ancestor. The fusion hypothesis was confirmed in 2005 by discovery that
human chromosome 2 is homologous with a fusion of two chromosomes that remain separate in other
primates. Extra, inactive telomeres and centromeres remain on human chromosome 2 as a result of the
fusion.[71] The assertion of common descent could also have been disproven with the invention of DNA
analysis. If true, human DNA should be far more similar to chimpanzees and other great apes, than to other
mammals. If not, then common descent is falsified. DNA analysis has shown that humans and chimpanzees
share a large percentage of their DNA (between 95% to 99.4% depending on the measure).[72] Also, the
evolution of chimpanzees and humans from a common ancestor predicts a (geologically) recent common
ancestor. Numerous transitional fossils have since been found.[73] Hence, human evolution has passed
several falsifiable tests.
A related claim is that natural selection is tautological.[66] Specifically, it is often argued that the
phrase "survival of the fittest" is a tautology, in that fitness is defined as ability to survive and reproduce.
However, this phrase, first used by Herbert Spencer in 1864, is rarely used by biologists. Additionally, fitness
is more accurately defined as the state of possessing traits that make survival more likely; this definition,
unlike simple "survivability", avoids being trivially true.[74][75][76]
Similarly, it is argued that evolutionary theory is circular reasoning, in that evidence is interpreted as
supporting evolution, but evolution is required to interpret the evidence. An example of this is the claim that
geological strata are dated through the fossils they hold, but that fossils are in turn dated by the strata they
are in.[42] However, in most cases strata are not dated by their fossils, but by their position relative to other
strata and by radiometric dating, and most strata were dated before the theory of evolution was formulated.
[77]
In his book, Abusing Science: The Case Against Creationism, philosopher of science Philip Kitcher
specifically addresses the "falsifiability" question by taking into account notable philosophical critiques of
Popper by Carl Gustav Hempel and Willard Van Orman Quine that reject his definition of theory as a set of
falsifiable statements.[78] As Kitcher points out, if one took a strictly Popperian view of “theory,” observations
of Uranus when first discovered in 1781 would have “falsified” Newton’s celestial mechanics. Rather, people
suggested that another planet influenced Uranus’ orbit – and this prediction was indeed eventually confirmed.
Kitcher agrees with Popper that “there is surely something right in the idea that a science can succeed only if
it can fail.”[79] But he insists that we view scientific theories as consisting of an “elaborate collection of
statements,” some of which are not falsifiable, and others – what he calls “auxiliary hypotheses,” which are.
According to Kitcher, good scientific theories must have three features – unity, fecundity, and
independent testability of auxiliary hypotheses:
Unity
“A science should be unified .... Good theories consist of just one problem-solving strategy, or
a small family of problem-solving strategies, that can be applied to a wide range of problems” (1982:
47).
Fecundity
A great scientific theory, like Newton’s, opens up new areas of research... Because a
theory presents a new way of looking at the world, it can lead us to ask new questions,
and so to embark on new and fruitful lines of inquiry... Typically, a flourishing science is
incomplete. At any time, it raises more questions than it can currently answer. But
incompleteness is no vice. On the contrary, incompleteness is the mother of fecundity... A
good theory should be productive; it should raise new questions and presume that those
questions can be answered without giving up its problem-solving strategies (1982: 47–48).
Auxiliary hypotheses that are independently testable

“An auxiliary hypothesis ought to be testable independently of the particular problem it is
introduced to solve, independently of the theory it is designed to save” (1982: 46) (e.g. the evidence for
the existence of Neptune is independent of the anomalies in Uranus’s orbit).
Like other definitions of theories, including Popper’s, Kitcher makes it clear that a good theory
includes statements that have (in his terms) “observational consequences.” But, like the observation of
irregularities in Uranus’s orbit, falsification is only one possible consequence of an observation. The
production of new hypotheses is another possible – and equally important – observational consequence.
Kitcher’s account of a good theory is based not only on his understanding of how physical sciences work. He
is also taking into account the way the life sciences work.
From Kitcher’s point of view, Darwinian theory not only meets the three conditions for a good
scientific theory; it is without question an extraordinarily successful theory:
The heart of Darwinian evolutionary theory is a family of problem-solving strategies, related by
their common employment of a particular style of historical narrative. A Darwinian history is a
piece of reasoning of the following general form. The first step consists in a description of an
ancestral population of organisms. The reasoning proceeds by tracing the modification of the
population through subsequent generations, showing how characteristics were selected,
inherited, and became prevalent. Reasoning like this can be used to answer a host of biological
questions.[80]
The same kind of story can be told again and again to answer all sorts of questions about all
sorts of living things. Evolutionary theory is unified because so many diverse questions ... can
be addressed by advancing Darwinian histories. Moreover, these narratives constantly make
claims that are subject to independent check.[81]
Darwin not only provided a scheme for unifying the diversity of life. He also gave a structure to
our ignorance. After Darwin, it was important to resolve general issues about the
presuppositions of Darwinian histories. The way in which biology should proceed had been
made admirably plain, and it was clear that biologists had to tackle questions for which they had,
as yet, no answers.[82]
[edit] Evidence
Further information: Evidence of evolution
Objections to the evidence that evolution occurs tend to be more concrete and specific, often
involving direct analysis of evolutionary biology's methods and claims.
[edit] Lack of observation
Transitional species such as the Archaeopteryx have been a fixture of the creation-evolution debate
for almost 150 years.
A common claim of creationists is that evolution has never been observed.[83] Challenges to such
objections often come down to debates over how evolution is defined (see above). Under the conventional
biological definition of evolution, it is a simple matter to observe evolution occurring. Evolutionary processes,
in the form of populations changing their genetic composition from generation to generation, have been
observed in different scientific contexts, including the evolution of fruit flies, mice and bacteria in the
laboratory,[84] and of tilapia in the field. Such studies on experimental evolution, particularly those using
microorganisms, are now providing important insights into how evolution occurs.[84][85]
In response to such examples, creationists specify that they are objecting only to macroevolution, not
microevolution:[86][87] most creationist organizations do not dispute the occurrence of short-term, relatively
minor evolutionary changes, such as that observed even in dog breeding. Rather, they dispute the
occurrence of major evolutionary changes over long periods of time, which by definition cannot be directly
observed, only inferred from microevolutionary processes and the traces of macroevolutionary ones.
However, as biologists define macroevolution, both microevolution and macroevolution have been
observed. Speciations, for example, have been directly observed many times, despite popular
misconceptions to the contrary.[88] Additionally, the modern evolutionary synthesis draws no distinction
between macroevolution and microevolution, considering the former to simply be the latter on a larger scale.
[43][89] An example of this is ring species.
Additionally, past macroevolution can be inferred from historical traces. Transitional fossils, for
example, provide plausible links between several different groups of organisms, such as Archaeopteryx
linking birds and dinosaurs,[90] or the recently-discovered Tiktaalik linking fish and limbed amphibians.[91]
Creationists dispute such examples, from asserting that such fossils are hoaxes or that they belong
exclusively to one group or the other, to asserting that there should be far more evidence of obvious
transitional species.[92] Darwin himself found the paucity of transitional species to be one of the greatest
weaknesses of his theory: "Why then is not every geological formation and every stratum full of such
intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this,
perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation
lies, as I believe, in the extreme imperfection of the geological record." Darwin appealed to the limited
collections then available, the extreme lengths of time involved, and different rates of change with some living
species differing very little from fossils of the Silurian period. In later editions he added "that the periods
during which species have been undergoing modification, though very long as measured by years, have
probably been short in comparison with the periods during which these same species remained without
undergoing any change."[93] The number of clear transitional fossils has increased enormously since
Darwin's day, and this problem has been largely resolved with the advent of the theory of punctuated
equilibrium, which predicts a primarily stable fossil record broken up by occasional major speciations.[94]
Creationists counter that even observed speciations and transitional fossils are insufficient evidence
for the vast changes summarized by such phrases as "fish to philosophers" or "particles to people".[95] As
more and more compelling direct evidence for inter-species and species-to-species evolution has been
gathered, creationists have redefined their understanding of what amounts to a "created kind", and have
continued to insist that more dramatic demonstrations of evolution be experimentally produced.[96] One
version of this objection is "Were you there?", popularized by Ken Ham. It argues that because no one except
God could directly observe events in the distant past, scientific claims are just speculation or "story-telling".
[97][98] DNA sequences of the genomes of organisms allow an independent test of their predicted
relationships, since species which diverged more recently will be more closely related genetically than
species which are more distantly related; such phylogenetic trees show a hierarchical organization within the
tree of life, as predicted by common descent.[99][100]
In fields such as astrophysics or meteorology, where direct observation or laboratory experiments are
difficult or impossible, the scientific method instead relies on observation and logical inference. In such fields,
the test of falsifiability is satisfied when a theory is used to predict the results of new observations. When
such observations contradict a theory's predictions, it may be revised or discarded if an alternative better
explains the observed facts. For example, Newton's theory of gravitation was replaced by Einstein's theory of
General Relativity when the latter was observed to more precisely predict the orbit of Mercury.[101]
[edit] Instability of evidence
A related objection is that evolution is based on unreliable evidence. This objection goes further than
the less substantial "evolution isn't proven" arguments, claiming that evolution isn't even well-evidenced.
Typically, this is either based on the argument that evolution's evidence is full of frauds and hoaxes, that
current evidence for evolution is likely to be overturned because past evidence has been, or that certain
types of evidence are inconsistent and dubious.
Arguments against evolution's reliability are thus often based on analyzing the history of evolutionary
thought or the history of science in general. Creationists point out that in the past, major scientific revolutions
have overturned theories that were at the time considered near-certain. They thus claim that current
evolutionary theory is likely to undergo such a revolution in the future, on the basis that it is a "theory in crisis"
for one reason or another.[102]
Romanes's 1892 copy of Ernst Haeckel's embryo drawings, often attributed incorrectly to Haeckel.
[103]
Critics of evolution commonly appeal to past scientific hoaxes such as the Piltdown Man forgery. It is
argued that because scientists have been mistaken and deceived in the past about evidence for various
aspects of evolution the current evidence for evolution is likely to also be based on fraud and error. Much of
the evidence for evolution has been accused of being fraudulent at various times, including Archaeopteryx,
peppered moth melanism, and Darwin's finches; these claims have been subsequently refuted.[104][105]
[106]
It has also been claimed that certain former pieces of evidence for evolution which are now
considered out-of-date and erroneous, such as Ernst Haeckel's 19th-century comparative drawings of
embryos, used to illustrate his Recapitulation theory ("Ontogeny recapitulates Phylogeny"), were not merely
errors but frauds.[107] Jonathan Wells criticizes biology textbooks by alleging that they continue to reproduce
such evidence after it has been debunked.[105] In response, the National Center for Science Education
notes that none of the textbooks reviewed by Wells makes the claimed error, as Haeckel's drawings are
shown in a historical context with discussion about why they are wrong, and the accurate modern drawings
and photos used in the textbooks are misrepresented by Wells.[108]
[edit] Unreliable or inconsistent evidence

Creationists claim that evolution relies on certain types of evidence that do not give reliable
information about the past. It is argued, for example, that radiometric dating, the technique of evaluating a
material's age based on the radioactive decay rates of certain isotopes, generates inconsistent, and thus
unreliable, results. Radiocarbon dating, based on the Carbon 14 isotope, has been particularly criticized. It is
argued that radiometric decay relies on a number of unwarranted assumptions, such as the principle of
uniformitarianism, consistent decay rates, or rocks acting as closed systems. Such arguments have been
dismissed by scientists on the grounds that independent methods have confirmed the reliability of radiometric
dating as a whole; additionally, different radiometric dating methods and techniques have independently
confirmed each other's results.[109]
Another form of this objection is that fossil evidence is not reliable. This is based on a much wider
range of claims. These include that there are too many "gaps" in the fossil record,[110][111] that fossil-dating
is circular (see evolution is unfalsifiable), or that certain fossils, such as polystrate fossils, are seemingly "out
of place". Examination by geologists have found polystrate fossils to be consistent with in situ formation.[112]
It is argued that certain features of evolution support creationism's catastrophism (cf. Great Flood), rather
than evolution's gradualistic punctuated equilibrium,[113] which some assert is an "ad-hoc" theory to explain
the fossil gaps.[114]
[edit] Plausibility
Some of the oldest and most common objections to evolution dispute whether evolution can truly
account for all the apparent complexity and order in the natural world. It is argued that evolution is too
unlikely or otherwise lacking to account for various aspects of life, and therefore that an intelligence, God,
must at the very least be appealed to for those specific features.
[edit] Improbability
Further information: Teleological argument, Watchmaker analogy, Evolutionary argument against
naturalism
Because the theory of evolution is often thought of as the idea that life arose "by chance", design
arguments such as William Paley's watchmaker analogy have been popular objections to the theory since
Darwin's day.[115]
A common objection to evolution is that it is simply too unlikely for life, in its complexity and apparent
"design", to have arisen "by chance". It is argued that the odds of life having arisen without a deliberate
intelligence guiding it are so astronomically low that it is unreasonable not to infer an intelligent designer from
the natural world, and specifically from the diversity of life.[116] A more extreme version of this argument is
that evolution cannot create complex structures. The idea that it is simply too implausible for life to have
evolved is often encapsulated with a quotation that the "probability of life originating on earth is no greater
than the chance that a hurricane sweeping through a scrap-yard would have the luck to assemble a Boeing
747" (a claim attributed to astrophysicist Fred Hoyle and known as Hoyle's fallacy).[117]
This view is thus invariably justified with arguments from analogy. The basic idea of this argument for
a designer is the teleological argument, an argument for the existence of God based on the perceived order
or purposefulness of the universe. A common way of using this as an objection to evolution is by appealing to
the 18th-century philosopher William Paley's watchmaker analogy, which argues that certain natural
phenomena are analogical to a watch (in that they are ordered, or complex, or purposeful), which means that,
like a watch, they must have been designed by a "watchmaker"—an intelligent agent. This argument forms the
core of intelligent design, a neocreationist movement seeking to establish certain variants of the design
argument as legitimate science, rather than as philosophy or theology, and have them be taught alongside
evolution.[28][47]
This objection is fundamentally an argument by lack of imagination, or argument from incredulity: a
certain explanation is seen as being counter-intuitive, and therefore an alternate, more intuitive explanation is
appealed to instead. Supporters of evolution generally respond by arguing that evolution is not based on
"chance", but on predictable chemical interactions: natural processes, rather than supernatural beings, are
the "designer". Although the process involves some random elements, it is the non-random selection of
survival-enhancing genes that drives evolution along an ordered trajectory. The fact that the results are
ordered and seem "designed" is no more evidence for a supernatural intelligence than the appearance of
complex natural phenomenon (e.g. snowflakes).[118] It is also argued that there is insufficient evidence to
make statements about the plausibility or implausibility of abiogenesis, that certain structures demonstrate
poor design, and that the implausibility of life evolving exactly as it did is no more evidence for an intelligence
than the implausibility of a deck of cards being shuffled and dealt in a certain random order.[47][115]
It has also been noted that arguments against some form of life arising "by chance" are really
objections to nontheistic abiogenesis, not to evolution. Indeed, arguments against "evolution" are based on
the misconception that abiogenesis is a component of, or necessary precursor to, evolution. Similar
objections sometimes conflate the Big Bang with evolution.[12]
Christian apologist and philosopher Alvin Plantinga, a supporter of intelligent design, has formalized
and revised the improbability argument as the evolutionary argument against naturalism, which asserts that it
is irrational to reject a supernatural, intelligent creator because the apparent probability of certain faculties
evolving is so low. Specifically, Plantinga claims that evolution cannot account for the rise of reliable
reasoning faculties. Plantinga argues that whereas a God would be expected to create beings with reliable
reasoning faculties, evolution would be just as likely to lead to unreliable ones, meaning that if evolution is
true, it is irrational to trust whatever reasoning one relies on to conclude that it is true.[119] This novel
epistemological argument has been criticized similarly to other probabilistic design arguments. It has also
been argued that rationality, if conducive to survival, is more likely to be selected for than irrationality, making
the natural development of reliable cognitive faculties more likely than unreliable ones.[120][121]
[edit] Unexplained aspects of the natural world

It is frequently argued that a great weakness of evolutionary theory is that it does not, or cannot,
explain a certain aspect of the natural world. Although there is broad agreement that certain aspects of life
remain unexplained, creationists argue that evolution should be abandoned altogether because of the
phenomena it does not explain. It is argued that an alternative explanation, such as intelligent design, can
explain the things which evolution cannot. For example, Michael Behe has argued that current evolutionary
theory cannot account for certain complex structures, particularly in microbiology. On this basis, Behe argues
that such structures were "purposely arranged by an intelligent agent" (see argument from incredulity).[122]
In addition to complex structures and systems, among the phenomena that critics variously claim
evolution cannot explain are consciousness, free will, hominid intelligence, instincts, emotions,
metamorphosis, photosynthesis, homosexuality, music, language, religion, morality, and altruism (see
altruism in animals).[123] Most of these, such as homosexuality, hominid intelligence, instinct, emotion,
photosynthesis, language, and altruism, have been well-explained by evolution, while others remain
mysterious, or only have preliminary explanations. However, supporters of evolution contend that no
alternative explanation has been able to adequately explain the biological origin of these phenomena either.
[124][125]
Creationists argue against evolution on the grounds that it cannot explain certain non-evolutionary
processes, such as abiogenesis, the Big Bang, or the meaning of life. In such instances, evolution is being
redefined to refer to the entire history of the universe, and it is argued that if one aspect of the universe is
seemingly inexplicable, the entire body of scientific theories must be baseless. At this point, objections leave
the arena of evolutionary biology and become general scientific or philosophical disputes.[126]
[edit] Impossibility
This class of objections is more radical than the above, claiming that a major aspect of evolution is
not merely unscientific or implausible, but rather impossible, because it contradicts some other law of nature
or is constrained in such a way that it cannot produce the biological diversity of the world.
[edit] Creation of complex structures

Further information: Irreducible complexity
The bacterial flagellum is often invoked to illustrate the concept of irreducible complexity. Careful
analysis shows that there are no major obstacles to a gradual evolution of flagella.
"Living things have fantastically intricate features-at the anatomical, cellular, and molecular
levels-that could not function if they were any less complicated or sophisticated. The only
prudent conclusion is that they are products of Intelligent Design, not Evolution" - from Refuting
Evolution 2, Jonathan Sarfati[127]
Modern evolutionary theory posits that all biological systems must have evolved incrementally,
through a combination of natural selection and genetic drift. Both Darwin and his early detractors recognized
the potential problems that could arise for his theory of natural selection if the lineage of organs and other
biological features could not be accounted for by merely gradual, step-by-step changes over successive
generations; if all the intermediary stages between an initial organ and the organ it will become are not all
improvements upon the original, it will be impossible for the later organ to develop by the process of natural
selection alone. Anticipating early criticisms that the evolution of the eye and other complex organs seemed
impossible, Darwin noted that:
[R]eason tells me, that if numerous gradations from a perfect and complex eye to one very
imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further,
the eye does vary ever so slightly, and the variations be inherited, which is certainly the case;
and if any variation or modification in the organ be ever useful to an animal under changing
conditions of life, then the difficulty of believing that a perfect and complex eye could be formed
by natural selection, though insuperable by our imagination, can hardly be considered real.[93]
Similarly, Richard Dawkins said on the topic of the evolution of the feather in an interview for the
television program The Atheism Tapes:
There's got to be a series of advantages all the way in the feather. If you can't think of one, then
that's your problem not natural selection's problem... It's perfectly possible feathers began as
fluffy extensions of reptilian scales to act as insulators... The earliest feathers might have been a
different approach to hairiness among reptiles keeping warm.
Creationist arguments have been made such as "What use is half an eye?" and "What use is half a
wing?".[128] Research has confirmed that the natural evolution of the eye and other intricate organs is
entirely feasible.[129][130] Creationist claims have persisted that such complexity evolving without a
designer is inconceivable, however, and this objection to evolution has been refined in recent years as the
more sophisticated irreducible complexity argument of the intelligent design movement, formulated by
biochemist Michael Behe.[28]
Irreducible complexity is the idea that certain biological systems cannot be broken down into their
constituent parts and remain functional, and therefore that they could not have evolved naturally from less
complex or complete systems. Whereas past arguments of this nature generally relied on macroscopic
organs, Behe's primary examples of irreducible complexity has been cellular and biochemical in nature. He
has argued that the components of systems such as the blood clotting cascade, the immune system, and the
bacterial flagellum are so complex and interdependent that they could not have evolved from simpler
systems.[131]
"In fact, my argument for intelligent design is open to direct experimental rebuttal. Here is a
thought experiment that makes the point clear. In Darwin’s Black Box (Behe 1996) I claimed that
the bacterial flagellum was irreducibly complex and so required deliberate intelligent design.
The flip side of this claim is that the flagellum can’t be produced by natural selection acting on
random mutation, or any other unintelligent process. To falsify such a claim, a scientist could go
into the laboratory, place a bacterial species lacking a flagellum under some selective pressure
(for mobility, say), grow it for ten thousand generations, and see if a flagellum—or any equally
complex system—was produced. If that happened, my claims would be neatly disproven." -
Michael Behe[132]
In the years since Behe proposed irreducible complexity, new developments and advances in
biology, such as an improved understanding of the evolution of flagella,[133] have already undermined these
arguments.[134][135] The idea that seemingly irreducibly complex systems cannot evolve has been refuted
through evolutionary mechanisms, such as exaptation (the adaptation of organs for entirely new functions)
[136] and the use of "scaffolding", which are initially necessary features of a system that later degenerate
when they are no longer required. Potential evolutionary pathways have been provided for all of the systems
Behe used as examples of irreducible complexity.[134][137][138]
[edit] Creation of information

Further information: Physical information, Biosemiotics
Another new, and increasingly common, objection of creationists to evolution is that evolutionary
mechanisms such as mutation cannot generate new information. Creationists such as William A. Dembski,
Werner Gitt, and Lee Spetner have attempted to use information theory to dispute evolution. Dembski has
argued that life demonstrates specified complexity, and that evolution without an intelligent agent cannot
account for the generation of information that would be required to produce specified complexity. The
Christian apologetics site Answers in Genesis, for example, makes frequent appeals to concepts from
information theory in its objections to evolution and affirmations of the Genesis account of Creation; "[I]t
should be clear that a rigorous application of the science of information is devastating to materialistic
philosophy in the guise of evolution, and strongly supportive of Genesis creation."[139]
These claims have been widely rejected by the scientific community; new information is regularly
generated in evolution, whenever a novel mutation or gene duplication arises. Dramatic examples of entirely
new, unique traits arising through mutation have been observed in recent years, such as the evolution of
nylon-eating bacteria, which developed new enzymes to efficiently digest a material that never existed before
the modern era.[140][141] In fact, when an organism is considered together with the environment it evolved
in, there is no need to account for the creation of information. The information in the genome forms a record
of how it was possible to survive in a particular environment. It is not created, but rather gathered from the
environment through research—by trial and error, as mutating organisms either reproduce or fail.[142]
A related argument against evolution is that most mutations are harmful.[143] However, the vast
majority of mutations are neutral, and the minority of mutations which are beneficial or harmful are often
situational; a mutation that is harmful in one environment may be helpful in another.[144]
[edit] Violation of the second law of thermodynamics

Further information: Entropy and life
Another objection is that evolution violates the second law of thermodynamics. Though the law
applies to all systems, in the case of a closed one it states, "the entropy of an isolated system not in
equilibrium will tend to increase over time, approaching a maximum value at equilibrium". In other words, an
ideal isolated system's entropy (a measure of the dispersal of energy in a physical system so that it is not
available to do mechanical work) will tend to increase or stay the same, not decrease. Creationists argue that
evolution violates this physical law by requiring a decrease in entropy, or disorder, over time.[145]
This claim is based on a manifestation of the law only applicable to isolated systems, which do not
exchange matter or energy with their surroundings. Organisms, in contrast, are open systems, as they
constantly exchange energy and matter with their environment: for example animals eat food and excrete
waste, and radiate and absorb heat. Similarly, the Earth absorbs energy from the Sun and emits energy back
into space. The Sun-Earth-space system does not violate the second law, because the enormous increase in
entropy due to the Sun and Earth radiating into space dwarfs the local decrease in entropy caused by the
existence and evolution of self-organizing life.[39][146]
Since the second law of thermodynamics has a precise mathematical definition, this argument can
be analyzed quantitatively.[147][148] This was done by physicist Daniel Styer, who concluded: "Quantitative
estimates of the entropy involved in biological evolution demonstrate that there is no conflict between
evolution and the second law of thermodynamics."[147]
In a published letter to the editor of The Mathematical Intelligencer titled "How anti-evolutionists
abuse mathematics", mathematician Jason Rosenhouse stated:
The fact is that natural forces routinely lead to decreases in entropy. Water freezes into ice and
fertilised eggs turn into babies. Plants use sunlight to convert carbon dioxide and water into
sugar and oxygen, but [we do] not invoke divine intervention to explain the process [...]
thermodynamics offers nothing to dampen our confidence in Darwinism.[149]
[edit] Moral implications

Other common objections to evolution allege that evolution leads to objectionable results, including
bad beliefs, behaviors, and events. It is argued that the teaching of evolution degrades values, undermines
morals, and fosters irreligion or atheism. These may be considered appeals to consequences (a form of
logical fallacy), as the potential ramifications of belief in evolutionary theory have nothing to do with its
objective empirical reality.
[edit] Humans as animals
1871 caricature of Charles Darwin as an ape, accompanied by a satirical disclaimer claiming a fait
accompli for its inclusion[150]
Huxley's book Man's Place in Nature was the first devoted to human evolution and an early example
of comparative biology.
Even though biology has long shown that humans are animals, some people feel that humans should
be considered separate from, and/or superior to, animals. The mediaeval concept of a great chain of being
set out a static hierarchy in which humans are "above" animals, but below angels and God. As evolutionary
thought developed it was feared that evolution implied that there was no real separation between man and
brute, and that it undermined human social hierarchy. Assertions of ape ancestry in the 1844 publication
Vestiges of Creation gained much public acceptance but were scornfully attacked by establishment
scientists, and though Darwin avoided the subject when announcing his theory in On the Origin of Species in
1859, the issue was quickly raised. Anatomists claimed that humans had unique physical features; however,
English biologist Thomas Henry Huxley showed that they were wrong and overcame their opposition to
Darwin's ideas. Evolutionary common descent does not imply that human beings should behave like other
animals, but instead shows that animals behave in different ways, and teaches that humans behave like
humans.[151]
Traditionalists still object to the idea that diversity in life, including human beings, arose through
natural processes without a need for supernatural intervention, and they argue against evolution on the basis
that it contradicts their literal interpretation of creation myths about separate "kinds". However, most religions,
such as Catholicism, have reconciled their beliefs with evolution through theistic evolution.[152][153]
[edit] Social effects

Further information: Social effect of evolutionary theory
Some Creationists claim that perceived social ills like crime, teen pregnancies, homosexuality,
abortion, immorality, wars and genocide are caused by a belief in evolution.[154] R. Albert Mohler, Jr.,
President of Southern Baptist Theological Seminary in Louisville, Kentucky, wrote August 8, 2005, in
National Public Radio's forum, "Taking Issue", that "Debates over education, abortion, environmentalism,
homosexuality and a host of other issues are really debates about the origin—and thus the meaning—of
human life.... Evolutionary theory stands at the base of moral relativism and the rejection of traditional
morality".[155][156] Creationist Ken Ham likens evolution to a horde of termites, weakening society's
foundation. In Why Won't They Listen?, Ham suggests that "evolutionary termites" are responsible for
pornography, homosexual behavior and lawlessness. He also writes, "I'm not saying that evolution is the
cause of abortion or school violence. What I'm saying is that the more a culture abandons God's word as the
absolute authority, and the more a culture accepts an evolutionary philosophy, then the way people think,
and their attitudes, will also change."[157]
Former Texas Republican Representative Tom DeLay claimed that the Columbine school shootings
were caused by the teaching of evolution. DeLay is quoted as stating that "Our school systems teach the
children that they are nothing but glorified apes who are evolutionized [sic] out of some primordial soup."[158]
Henry M. Morris, engineering professor and founder of the Creation Research Society and the Institute of
Creation Research, claims that evolution was part of a pagan religion that emerged after the Tower of Babel,
was part of Plato's and Aristotle's philosophies, and was responsible for everything from war to pornography
to the breakup of the nuclear family.[159]
Rev. D. James Kennedy of The Center for Reclaiming America for Christ and Coral Ridge Ministries
claims that Darwin was responsible for Adolf Hitler's atrocities. In D. James Kennedy's documentary, and the
accompanying pamphlet with the same title, Darwin’s Deadly Legacy, Kennedy states that "To put it simply,
no Darwin, no Hitler." In his efforts to expose the "harmful effects that evolution is still having on our nation,
our children, and our world", Kennedy also states that, "We have had 150 years of the theory of Darwinian
evolution, and what has it brought us? Whether Darwin intended it or not, millions of deaths, the destruction
of those deemed inferior, the devaluing of human life, increasing hopelessness."[160][161][162] Discovery
Institute fellow Richard Weikart has made similar claims,[163][164] as have other creationists.[165] The claim
was central to Ben Stein's film Expelled: No Intelligence Allowed promoting intelligent design creationism.
The Anti-Defamation League describes such claims as outrageous misuse of the the Holocaust and its
imagery, and as trivializing "the many complex factors that led to the mass extermination of European Jewry.
Hitler did not need Darwin or evolution to devise his heinous plan to exterminate the Jewish people, and
Darwin and evolutionary theory cannot explain Hitler’s genocidal madness. Moreover, anti-Semitism existed
long before Darwin ever wrote a word."[162][166]
Kent Hovind of Creation Science Evangelism blames communism, socialism, World War I, World
War II, racism, the Holocaust, Stalin's war crimes, the Vietnam War and Pol Pot's Cambodian killing fields on
evolution, as well as the increase in crime, unwed mothers, and other social ills.[83] Kent Hovind's son Eric
Hovind has now taken over the family business while his father is in prison, and claims that evolution is
responsible for tattoos, body piercing, premarital sex, unwed births, sexually transmitted diseases (STDs),
divorce and child abuse.[167]
Supporters of evolution dismiss such criticisms as counterfactual, and some argue that the opposite
seems to be the case. A study published by the author and illustrator Gregory S. Paul found that religious
beliefs, including belief in creationism and disbelief in evolution, are positively correlated with social ills like
crime.[168] The Barna Group surveys find that Christians and non-Christians in the US have similar divorce
rates, and the highest divorce rates in the US are among Baptists and Pentecostals, both sects which reject
evolution and embrace creationism.[169]
Michael Shermer argued in Scientific American in October 2006 that evolution supports concepts like
family values, avoiding lies, fidelity, moral codes and the rule of law.[170] He goes on to suggest that
evolution gives more support to the notion of an omnipotent creator, rather than a tinkerer with limitations
based on a human model, the more common image subscribed to by creationists. Careful analyses of the
creationist charges that evolution has led to moral relativism and the Holocaust yields the conclusion that
these charges appear to be highly suspect.[171] Such analyses conclude that the origins of the Holocaust
are more likely to be found in historical Christian anti-semitism than in evolution.[172][173]
Evolution has been used to justify Social Darwinism, the exploitation of "lesser breeds without the
law" by "superior races," particularly in the nineteenth century.[174] Strong, typically European, nations
successfully expanded their empires, and as such, these strong nations could be said to have "survived" in
the struggle for dominance.[174] With this attitude, Europeans, with the exception of Christian missionaries,
seldom adopted the customs and languages of local people under their empires.[174]
[edit] Atheism
Another charge leveled at evolutionary theory by creationists is that belief in evolution is either
tantamount to atheism, or conducive to atheism.[175] It is commonly claimed that all proponents of
evolutionary theory are "materialistic atheists".[176] On the other hand, Davis Young argues that Creation
Science itself is harmful to Christianity because its bad science will turn more away than it recruits. Young
asks, "Can we seriously expect non-Christians to develop a respect for Christianity if we insist on teaching
the brand of science that creationism brings with it?"[177] However, evolution neither requires nor rules out
the existence of a supernatural being. Philosopher Robert Pennock makes the comparison that evolution is
no more atheistic than plumbing.[178] H. Allen Orr, professor of biology at University of Rochester, notes
that:
Of the five founding fathers of twentieth-century evolutionary biology — Ronald Fisher, Sewall
Wright, J. B. S. Haldane, Ernst Mayr, and Theodosius Dobzhansky — one was a devout Anglican
who preached sermons and published articles in church magazines, one a practicing Unitarian,
one a dabbler in Eastern mysticism, one an apparent atheist, and one a member of the Russian
Orthodox Church and the author of a book on religion and science.[179]
In addition, a wide range of religions have reconciled a belief in a supernatural being with evolution.
[180] Molleen Matsumura of the National Center for Science Education found that "of Americans in the twelve
largest Christian denominations, 89.6% belong to churches that support evolution education". These
churches include the United Methodist Church, National Baptist Convention USA, Evangelical Lutheran
Church in America, Presbyterian Church (USA), National Baptist Convention of America, African Methodist
Episcopal Church, the Roman Catholic Church, the Episcopal Church, and others.[181] A poll in 2000 done
for People for the American Way found that 70% of the American public felt that evolution was compatible
with a belief in God. Only 48% of the people polled could choose the correct definition of evolution from a list,
however.[182]
One poll reported in the journal Nature showed that among American scientists (across various
disciplines), about 40 percent believe in both evolution and an active deity (theistic evolution).[183] This is
similar to the results reported for surveys of the general American public. Also, about 40 percent of the
scientists polled believe in a God that answers prayers, and believe in immortality.[184] While about 55% of
scientists surveyed were atheists, agnostics, or nonreligious theists, atheism is far from universal among
scientists who support evolution, or among the general public that supports evolution. Very similar results
were reported from a 1997 Gallup survey of the American public and scientists.[185]
Belief in evolution
Belief in Young Belief in God-
Group[185] without God guiding the
Earth Creationism guided evolution
process
American
44% 39% 10%
public
American
5% 40% 55%
scientists
[edit] See also

Book:Evolution

• Faith and rationality
[edit] Notes
1. ^ a b Johnston, Ian C. (1999). "Section Three: The Origins of Evolutionary Theory". ... And
Still We Evolve. Liberal Studies Department, Malaspina University College.
http://records.viu.ca/~johnstoi/darwin/title.htm. Retrieved 2007-07-25.
2. ^ a b van Wyhe, John (2002-7). "Charles Darwin: gentleman naturalist: A biographical
sketch". The Complete Work of Charles Darwin Online. University of Cambridge. http://darwin-
online.org.uk/darwin.html. Retrieved 2007-07-25.
3. ^ IAP Statement on the Teaching of Evolution, Interacademy Panel
4. ^ In his comprehensive treatise on Creationism, The Creationists, historian Ronald Numbers
traces the religious motivations and scientific pretensions, of prominent creationists from George
Frederick Wright through George McCready Price, Harry Rimmer, John C. Whitcomb, Henry M.
Morris and his Institute for Creation Research (and lesser figures) to Phillip E. Johnson and the
Intelligent design movement.
Numbers, Ronald (November 30, 2006). The Creationists: From Scientific Creationism to Intelligent
Design, Expanded Edition. Harvard University Press. p. 624 pages. ISBN 0674023390.
5. ^ Godfrey, Laurie R. Scientists Confront Creationism. Pg 8. W. W. Norton & Company
(1984). ISBN 0-393-30154-0.
6. ^ Sarfati, Jonathan & Matthews, Michael (2000). Argument: Creationism is religion, not
science. Answers in Genesis.
7. ^ "Statement on the Teaching of Evolution" (PDF). American Association for the
Advancement of Science. 2006.
http://www.aaas.org/news/releases/2006/pdf/0219boardstatement.pdf. Retrieved 2007-03-20.
8. ^ a b c Abdul Majid (2002). "The Muslim Responses To Evolution". Islamic Research
Foundation International, Inc.. http://diberri.dyndns.org/cgi-bin/templatefiller/?type=&id=. Retrieved
2010-05-24.
9. ^ "Worldwide creationism, Shotgun stunner, and more". New Scientist.
http://www.newscientist.com/article/mg20327153.900-worldwide-creationism-shotgun-stunner-and-
more.html. Retrieved 2010-05-24.
10.^ "About Us". http://creation.com/about-us#who_we_are. Retrieved 2010-05-24.
11.^ "Opinions on evolution from ten countries | NCSE". National Center for Science Education.
http://ncse.com/news/2009/07/opinions-evolution-from-ten-countries-004885. Retrieved 2010-06-14.
12.^ a b c Moran, Laurence (1993). "What is Evolution?". The TalkOrigins Archive.
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165.^ This creationist claim that is part of a Discovery Institute campaign (New book by
Discovery Institute Fellow shows influence of Darwinian principles on Hitler's Nazi regime , Discovery
Institute) and is amply repeated in creationist literature. For example:
• Darwinism and the Nazi race Holocaust, Jerry Bergman, CEN Technical Journal,
13(2):101–111, 1999.
• The Holocaust and evolution, Jonathan Sarfati, Creation 22(1):4, December 1999.
• From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany,
Richard Weikart, Palgrave MacMillan, 2004.
166.^ "Anti-Evolution Film Misappropriates the Holocaust". Anti-Defamation League. April 29,
2008. http://www.adl.org/PresRele/HolNa_52/5277_52.htm. Retrieved 2009-12-07.
"Intelligent Design: It's Not Science – Religious Freedom Resources". Anti-Defamation League. 2009.
http://www.adl.org/religious_freedom/resource_kit/intelligent_design.asp. Retrieved 2009-12-07.
167.^ Creationist Links Origins to Faith, Everyday Life: Says outlook on Genesis account affects
every aspect of life , Bob Ellis, Dakota Voice, 5/7/2006
168.^ Paul, GS (2005). "Cross-National Correlations of Quantifiable Societal Health with Popular
Religiosity and Secularism in the Prosperous Democracies: A First Look". Journal of Religion &
Society 7. http://moses.creighton.edu/JRS/2005/2005-11.html. Retrieved 2007-03-24.
The paper was criticized by Moreno-Riaño, Smith, and Mach in a published article in the same
journal because "[Paul's] methodological problems do not allow for any conclusive statement to be
advanced regarding the various hypotheses Paul seeks to demonstrate or falsify." Of course,
correlation does not imply causality, and Paul does not produce any speculations about the cause of
these correlations.
169.^ "Born Again Christians Just As Likely to Divorce As Are Non-Christians". The Barna
Group. 2004. http://www.barna.org/barna-update/article/5-barna-update/194-born-again-christians-
just-as-likely-to-divorce-as-are-non-christians. Retrieved 2004-03-24.
170.^ Shermer, M (2006). "Darwin on the Right: Why Christians and conservatives should
accept evolution". Scientific American. http://www.sciam.com/article.cfm?
chanID=sa006&articleID=00068F43-E189-150E-A18983414B7F0000&colID=13. Retrieved 2007-04-
26.
171.^ Darwin and Hitler: a not-very-intelligent link, Michael Ruse, My View, Tallahassee
Democrat, February 6, 2008
172.^ Talkorigins Claim CA006.1: Adolf Hitler exploited the racist ideas of Darwinism to justify
genocide, Mark Isaak, Index to Creationist Claims, Talkorigins, created 2001-4-29, modified 2005-7-
1, © 2006
173.^ Creationists for Genocide, Hector Avalos, Talkreason
174.^ a b c Western Civilization: Ideas, Politics, and Society . Houghton Mifflin Harcourt
Publishing Company. 2008-10. ISBN 9780547147017. http://books.google.com/books?
id=kKGgoNo4un0C&pg=PA653&lpg=PA653. Retrieved 2007–03–25. "The most extreme ideological
expression of nationalism and imperialism was Social Darwinism. In the popular mind, the concepts
of evolution justified the exploitation of "lesser breeds without the law" by superior races. This
language of race and conflict, of superior and inferior people, had wide currency in the Western
states. Social Darwinists vigorously advocated the acquisition of empires, saying that strong nations-
by definition, those that were successful at expanding industry and empire-would survive and that
others would not. To these elitists, all white men were more fit than non-whites to prevail in the
struggle for dominance. Even among Europeans, some nations were deemed more fit than others for
the competition. Usually, Social Darwinists thought their own nation the best, an attitude that sparked
their competitive enthusiasm. In the nineteenth century, in contrast to the seventeenth and
eighteenth centuries, Europeans, except for missionaries, rarely adopted the customs or learned the
languages of local people. They had little sense that other cultures and other people had merit or
deserved respect. Many westerners believed that it was their duty as Christians to set an example
and to educate others. Missionaries were the first to meet and learn about many peoples and were
the first to develop writing for those without a written language. Christian missionaries were ardently
opposed to slavery."
175.^ Strobel, Lee (2004). The Case for a Creator. Zondervan. p. 32. ISBN 0310241448. "In my
quest to determine if contemporary science points toward or away from God, I knew I had to first
examine the claims of evolution in order to conclude once and for all whether Darwinism creates a
reasonable foundation for atheism. That's because if the materialism of Darwinian evolution is a fact,
then the atheist conclusions I reached as a student might still be valid."
176.^ Johnson, Phillip (1999). "The Church of Darwin". Wall Street Journal.
http://www.arn.org/docs/johnson/chofdarwin.htm. Retrieved 2010-05-23.
177.^ Young, D (1988). Christianity and the Age of the Earth . Artisan Publishers.
ISBN 093466627X.
178.^ Pennock, RT (2000). Tower of Babel: The Evidence Against the New Creationism . MIT
Press. ISBN 978-0262661652. http://ncse.com/store/title/tower-babel. Retrieved 2007-03-24.
179.^ Devolution: Why intelligent design isn’t, H. Allen Orr, Annals of Science, The New Yorker,
May 30, 2005.
180.^ "Statements from Religious Organizations". National Center for Science Education. 2002.
http://ncse.com/media/voices/religion. Retrieved 2007-03-24.
181.^ Schrock, JR (2005-05-17). "Christianity, Evolution Not in Conflict" (PDF). Wichita Eagle.
pp. 17A. http://www.emporia.edu/biosci/schrock/docs/Eagle-25.pdf. Retrieved 2007-03-24.
182.^ "Evolution and Creationism In Public Education: An In-depth Reading Of Public Opinion"
(PDF). People for the American Way. 2002. http://docs.google.com/viewer?
a=v&q=cache:UDwdl6q3IgwJ:67.192.238.59/multimedia/pdf/Reports/evolutionandcreationisminpubli
ceducation.pdf+evolutionandcreationisminpubliceducation.pdf&hl=en&gl=ca&pid=bl&srcid=ADGEES
j-27vCwtszKiottg8mjbOKovsUvtJqRXXlLit-
R3VitD5tlX4OfMPkfEEzNwQjvUSioQSua6y3LN1SR72877bW3dc6wFzFlG2pFdWl-
21CVU68FWs00NDtWslzvTBvY-TLInH7&sig=AHIEtbQjqyUehD_pbin4wiuZlHKkn--pTA. Retrieved
2007-03-24.
183.^ Larson, EJ; Witham, L (1997). "Scientists are still keeping the faith". Nature 386: 435–436.
doi:10.1038/386435a0.
184.^ Witham, L (1997). "Many scientists see God's hand in evolution". Reports of the National
Center for Science Education 17 (6): 33. http://ncse.com/rncse/17/6/many-scientists-see-gods-hand-
evolution. Retrieved 2007-03-24.
185.^ a b Robinson, BA (1995). "Public beliefs about evolution and creation".
http://www.religioustolerance.org/ev_publi.htm. Retrieved 2007-03-24.

• Philip Kitcher 1982 Abusing Science: The Case Against Creationism. Cambridge: The MIT
Press
• Jonathan Sarfati, Ph.D; 2003 Refuting Evolution 2. Master Books ISBN 0-89051-387-2
Look up evolution in Wiktionary, the free dictionary.
• Coleman, Simon; Leslie Carlin (2004). The Cultures of Creationism: Antievolution in English-
speaking Countries. Burlington, Vermont: Ashgate. p. 195. ISBN 075460912X.
• Isaak, Mark (2005). The Counter-Creationism Handbook. Westport, Connecticut: Greenwood
Press. p. 330. ISBN 031333305X.
• Rennie J (July 2002). "15 answers to creationist nonsense" (PDF). Sci. Am. 287 (1): 78–85.
doi:10.1038/scientificamerican0702-78. PMID 12085506.
http://www.swarthmore.edu/NatSci/cpurrin1/textbookdisclaimers/wackononsense.pdf.
Retrieved from "http://en.wikipedia.org/wiki/Objections_to_evolution"

Categories: Creationism | Creationist objections to evolution | Biological evolution
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Creation and evolution in public education


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The status of creation and evolution in public education has been the subject of substantial debate in
legal, political, and religious circles. Globally there is a wide range of views on this topic ranging from
countries not allowing teachers to discuss the evidence for evolution or the modern evolutionary synthesis,
which is the scientific theory that explains evolution, to mandating that only evolutionary biology is to be
taught.
While some religions do not have theological objections to the modern evolutionary synthesis as an
explanation for the present form of life on Earth, there has been much conflict over this matter within
particular (fundamentalist) branches of Christianity,[1] some adherents of which are vigorously opposed to
the consensus view of the scientific community. Conflict with evolutionary explanations is greatest in literal
interpretations of religious documents, and resistance to teaching evolution is thus related to the popularity of
these more literalist views.
Globally, evolution is taught in science courses with limited controversy, with the exception of a few
areas of the United States and several Islamic fundamentalist countries. And even there, the Supreme Court
has ruled the teaching of creationism as science in public schools to be unconstitutional. In United States,
Intelligent design has been presented as an alternative explanation to evolution in recent decades, but its
"demonstrably religious, cultural, and legal missions" have been ruled unconstitutional by a lower court.[2][3]
[4][5]
Contents
[hide]
• 1 United States
• 1.1 Early law
• 1.2 Modern legal cases
• 1.3 Movements to teach creationism in schools
• 1.4 Recent developments in state education
programs
• 1.4.1 Alabama
• 1.4.2 California
• 1.4.3 Florida
• 1.4.4 Georgia
• 1.4.5 Kansas
• 1.4.6 Kentucky
• 1.4.7 Louisiana
• 1.4.8 Ohio
• 1.4.9 Pennsylvania
• 1.4.10 Texas
• 1.4.11 Virginia
• 1.5 Recent polls
• 1.6 Consequences
• 1.7 U.S. legal quotations
[edit] United States
In the United States, creationists and proponents of evolution are engaged in a long-standing battle
over the legal status of creation and evolution in the public school science classroom.[6]
[edit] Early law

Until the late 19th century, creation was taught in nearly all schools in the United States, often from
the position that the literal interpretation of the Bible is inerrant. With the widespread acceptance of the theory
of evolution in the 1860s after being first introduced in 1859, and developments in other fields such as
geology and astronomy, public schools began to teach science that was reconciled with Christianity by most
people, but considered by a number of early fundamentalists to be directly at odds with the Bible.
In the aftermath of World War I, the Fundamentalist-Modernist Controversy brought a surge of
opposition to the idea of evolution, and following the campaigning of William Jennings Bryan several states
introduced legislation prohibiting the teaching of evolution. By 1925, such legislation was being considered in
15 states, and passed in some states, such as Tennessee. The American Civil Liberties Union offered to
defend anyone who wanted to bring a test case against one of these laws. John T. Scopes accepted, and he
taught his Tennessee class evolution in defiance of the Butler Act. The textbook in question was Hunter's
Civic Biology (1914).
The trial was widely publicized by H. L. Mencken among others, and is commonly referred to as the
Scopes Monkey Trial.
Scopes was convicted; however, the widespread publicity galvanized proponents of evolution.
When the case was appealed to the Tennessee Supreme Court, the Court overturned the decision
on a technicality (the judge had assessed the fine when the jury had been required to). Although it overturned
the conviction, the Court decided that the law was not in violation of the First Amendment. The Court held,
"We are not able to see how the prohibition of teaching the theory that man has descended from
a lower order of animals gives preference to any religious establishment or mode of worship. So
far as we know, there is no religious establishment or organized body that has in its creed or
confession of faith any article denying or affirming such a theory." Scopes v. State 289 S.W.
363, 367 (Tenn. 1927).
The interpretation of the Establishment clause up to that time was that Congress could not establish
a particular religion as the State religion. Consequently, the Court held that the ban on the teaching of
evolution did not violate the Establishment clause, because it did not establish one religion as the "State
religion." As a result of the holding, the teaching of evolution remained illegal in Tennessee, and continued
campaigning succeeded in removing evolution from school textbooks throughout the United States.[7][8][9]
[edit] Modern legal cases
The Supreme Court of the United States has made several rulings regarding evolution in public
education.
In 1967, the Tennessee public schools were threatened with another lawsuit over the Butler Act's
constitutionality, and, fearing public reprisal, Tennessee's legislature repealed the Butler Act. In the following
year, 1968, the Supreme Court of the United States ruled in Epperson v. Arkansas that Arkansas's law
prohibiting the teaching of evolution was in violation of the First Amendment. The Supreme Court held that
the Establishment Clause prohibits the state from advancing any religion, and determined that the Arkansas
law which allowed the teaching of creation while disallowing the teaching of evolution advanced a religion,
and was therefore in violation of the 1st amendment Establishment clause. This holding reflected a broader
understanding of the Establishment Clause: instead of just prohibiting laws that established a state religion,
the Clause was interpreted to prohibit laws that furthered religion. Opponents, pointing to the previous
decision, argued that this amounted to judicial activism.
In reaction to the Epperson case, creationists in Louisiana passed a law requiring that public schools
should give "equal time" to "alternative theories" of origin. The Supreme Court ruled in Edwards v. Aguillard
that the Louisiana statute, which required creation to be taught alongside evolution every time evolution was
taught, was unconstitutional.
The Court laid out its rule as follows:
"The Establishment Clause forbids the enactment of any law 'respecting an establishment of
religion.' The Court has applied a three-pronged test to determine whether legislation comports
with the Establishment Clause. First, the legislature must have adopted the law with a secular
purpose. Second, the statute's principal or primary effect must be one that neither advances nor
inhibits religion. Third, the statute must not result in an excessive entanglement of government
with religion. Lemon v. Kurtzman, 403 U.S. 602, 612-613, 91 S.Ct. 2105, 2111, 29 L.Ed.2d 745
(1971). State action violates the Establishment Clause if it fails to satisfy any of these prongs."
Edwards v. Aguillard 482 U.S. 578, *582-583, 107 S.Ct. 2573, 2577 (U.S.La.,1987).
The Court held that the law was not adopted with a secular purpose, because its purported purpose
of "protecting academic freedom" was not furthered by limiting the freedom of teachers to teach what they
thought appropriate; ruled that the act was discriminatory because it provided certain resources and
guarantees to "creation scientists" which were not provided to those who taught evolution; and ruled that the
law was intended to advance a particular religion because several state senators that had supported the bill
stated that their support for the bill stemmed from their religious beliefs.
While the Court held that creationism is an inherently religious belief, it did not hold that every
mention of creationism in a public school is unconstitutional:
"We do not imply that a legislature could never require that scientific critiques of prevailing
scientific theories be taught. Indeed, the Court acknowledged in Stone that its decision
forbidding the posting of the Ten Commandments did not mean that no use could ever be made
of the Ten Commandments, or that the Ten Commandments played an exclusively religious role
in the history of Western Civilization. 449 U.S., at 42, 101 S.Ct., at 194. In a similar way,
teaching a variety of scientific theories about the origins of humankind to schoolchildren might
be validly done with the clear secular intent of enhancing the effectiveness of science
instruction. But because the primary purpose of the Creationism Act is to endorse a particular
religious doctrine, the Act furthers religion in violation of the Establishment Clause." Edwards v.
Aguillard 482 U.S. 578, 593-594, 107 S.Ct. 2573, 2583 (U.S.La., 1987)
Just as it is permissible to discuss the crucial role of religion in medieval European history,
creationism may be discussed in a civics, current affairs, philosophy, or comparative religions class where
the intent is to factually educate students about the diverse range of human political and religious beliefs. The
line is crossed only when creationism is taught as science, just as it would be if a teacher were to proselytize
a particular religious belief.
[edit] Movements to teach creationism in schools
There continue to be numerous efforts to introduce creationism in US classrooms. One strategy is to
declare that evolution is a religion, and therefore it should not be taught in the classroom either, or that if
evolution is a religion, then surely creationism as well can be taught in the classroom.[10]
In the 1980s Phillip E. Johnson began reading the scientific literature on evolution. This led to the
writing of Darwin on Trial, which examined the evidence for evolution from religious point of view and
challenged the assumption that the only reasonable explanation for the origin of species must be a
naturalistic one, though science is defined by searching for natural explanations for phenomena. This book,
and his subsequent efforts to encourage and coordinate creationists with more credentials, was the start of
the "Intelligent design" movement. Intelligent design asserts that there is evidence that life was created by an
"intelligent designer" (mainly that the physical properties of an object are so complex that they must have
been "designed"). Proponents claim that ID takes "all available facts" into account rather than just those
available through naturalism. Opponents assert that ID is a pseudoscience because its claims cannot be
tested by experiment (see falsifiability) and do not propose any new hypotheses.
Many proponents of the ID movement support requiring that it be taught in the public schools. For
example, conservative think-tank,[11] The Discovery Institute and Phillip E. Johnson, support the policy of
"Teach the Controversy", which entails presenting to students evidence for and against evolution, and then
encouraging students to evaluate that evidence themselves.
While many proponents of ID believe that it should be taught in schools, other creationists believe
that legislation is not appropriate. Answers in Genesis has said:
"AiG is not a lobby group, and we oppose legislation for compulsion of creation teaching ... why
would we want an atheist forced to teach creation and give a distorted view? But we would like
legal protection for teachers who present scientific arguments against the sacred cow of
evolution such as staged pictures of peppered moths and forged embryo diagrams ..."[12]
Opponents point out that there is no scientific controversy, but only a political and religious one,
therefore "teaching the controversy" would only be appropriate in a social studies, religion, or philosophy
class. Many, such as Richard Dawkins, compare teaching intelligent design in schools to teaching flat
earthism, since the scientific consensus regarding these issues is identical. Dawkins has stated that teaching
creationism to children is akin to child abuse.[13]
In June 2007 the Council of Europe's "Committee on Culture, Science and Education" issued a
report, The dangers of creationism in education, which states "Creationism in any of its forms, such as
'intelligent design', is not based on facts, does not use any scientific reasoning and its contents are
pathetically inadequate for science classes."[14] In describing the dangers posed to education by teaching
creationism, it described intelligent design as "anti-science" and involving "blatant scientific fraud" and
"intellectual deception" that "blurs the nature, objectives and limits of science" and links it and other forms of
creationism to denialism.
[edit] Recent developments in state education programs

See also: Academic Freedom bills
[edit] Alabama
In 1996, the Alabama State Board of Education adopted a textbook sticker that was a disclaimer
about evolution. It has since been revised and moderated.[15][dead link]
[edit] California
In August 2008 Judge Otero ruled in favor of University of California in Association of Christian
Schools International v. Roman Stearns agreeing with the university's position that various religious books on
U.S. history and science, from A Beka Books and Bob Jones University Press, should not be used for a
college-preparatory classes.[16] The case was filed in spring 2006 by Association of Christian Schools
International against the University of California claiming religious discrimination over the rejection of five
courses as college preparatory instruction.[17] On August 8, 2008, Judge Otero entered summary judgment
against plaintiff ACSI, upholding the University of California's standards.[16] The university found the books
"didn't encourage critical thinking skills and failed to cover 'major topics, themes and components'" and were
thus, ill-suited to prepare students for college.[16]
[edit] Florida
On February 19, 2008, the Florida State Board of Education adopted new science standards in a 4-3
vote. The new science curriculum standards explicitly require the teaching of the "scientific theory of
evolution",[18] whereas the previous standards only referenced evolution using the words "change over
time."[19]
[edit] Georgia
In 2002, six parents in Cobb County, Georgia in the case Selman v. Cobb County School District
sued to have the following sticker removed from public school textbooks: "This textbook contains material on
evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be
approached with an open mind, studied carefully, and critically considered." Selman v. Cobb County School
District, No. 1:02CV2325 (N.D. Ga. filed August 21, 2002). Defense attorney Gunn said, "The only thing the
school board did is acknowledge there is a potential conflict [between evolution and creationism] and there is
a potential infringement on people's beliefs if you present it in a dogmatic way. We're going to do it in a
respectful way." Gerald R. Weber, legal director of the ACLU of Georgia, said "The progress of church-state
cases has been that the [U.S.] Supreme Court sets a line, then government entities do what they can to skirt
that line. […] Here the Supreme Court has said you can't teach creationism in the public schools. You can't
have an equal-time provision for evolution and creationism. These disclaimers are a new effort to skirt the
line." Jefferey Selman, who brought the lawsuit, claims "It singles out evolution from all the scientific theories
out there. Why single out evolution? It has to be coming from a religious basis, and that violates the
separation of church and state." The School Board said it adopted the sticker "to foster critical thinking
among students, to allow academic freedom consistent with legal requirements, to promote tolerance and
acceptance of diversity of opinion and to ensure a posture of neutrality toward religion."
On January 14, 2005, a federal judge in Atlanta ruled that the stickers should be removed as they
violated the Establishment Clause of the First Amendment.[20] The school board subsequently decided to
appeal the decision.[21][22] In comments on December 15, 2005 in advance of releasing its decision, the
appeal court panel appeared critical of the lower court ruling and a judge indicated that he did not understand
the difference between evolution and abiogenesis.[23]
On December 20, 2006, the Cobb County Board of Education abandoned all of its legal activities and
will no longer mandate that biology texts contain a sticker stating "evolution is a theory, not a fact." Their
decision was a result of compromise negotiated with a group of parents, represented by the ACLU, that were
opposed to the sticker. The parents agreed, as their part of the compromise, to withdraw their legal actions
against the board.[24]
[edit] Kansas
On August 11, 1999, by a 6–4 vote the Kansas State Board of Education changed their science
education standards to remove any mention of "biological macroevolution, the age of the Earth, or the origin
and early development of the Universe", so that evolutionary theory no longer appeared in state-wide
standardized tests and "it was left to the 305 local school districts in Kansas whether or not to teach it."[25]
This decision was hailed by creationists, and sparked a statewide and nationwide controversy with scientists
condemning the change.[26] Challengers in the state's Republican primary who made opposition to the anti-
evolution standards their focus were voted in on August 1, 2000, so on February 14, 2001, the Board voted 7–
3 to reinstate the teaching of biological evolution and the origin of the earth into the state's science education
standards.[25]
In 2004 Kansas Board of Education elections gave religious conservatives a majority and, influenced
by the Discovery Institute, they arranged the Kansas evolution hearings. On August 9, 2005, the Kansas
State Board of Education drafted new "science standards that require critical analysis of evolution – including
scientific evidence refuting the theory,"[27] which opponents analyzed as effectively stating that intelligent
design should be taught.[28] The new standards also provide a definition of science that does not preclude
supernatural explanations, and were approved by a 6–4 vote on November 8, 2005—incidentally the day of the
Dover school board election which failed to re-elect incumbent creationists (see #Pennsylvania).
In Kansas' state Republican primary elections on August 1, 2006, moderate Republicans took control
away from the anti-evolution conservatives,[29] leading to an expectation that science standards which
effectively embraced intelligent design and cast doubt on Darwinian evolution would now be changed.[30]
On February 13, 2007, the Kansas State Board of Education approved a new curriculum which
removed any reference to Intelligent Design as part of science. In the words of Dr Bill Wagnon, the board
chairman, "Today the Kansas Board of Education returned its curriculum standards to mainstream science".
The new curriculum, as well as a document outlining the differences with the previous curriculum, has been
posted on the Kansas State Department of Education's website.[31]
[edit] Kentucky
In October 1999, the Kentucky Department of Education replaced the word "evolution" with "change
over time" in state school standards.[32]
[edit] Louisiana
On 12 June 2008, bill(SB561) or the "Louisiana Academic Freedom Act" passed into law. Under the
guise of academic freedom and critical thinking, it is designed to allow teachers to introduce unqualified
references and arguments, as a way to push political agendas, and sidestep U.S. Constitutional law.
[edit] Ohio
In 2002, proponents of intelligent design asked the Ohio Board of Education to adopt intelligent
design as part of its standard biology curriculum, in line with the guidelines of the Edwards v. Aguillard
holding. In December 2002, the Board adopted a proposal that required critical analysis of evolution, but did
not specifically mention intelligent design. This decision was reversed in February 2006 following both the
conclusion of the Dover lawsuit and repeated threats of lawsuit against the Ohio Board.[33][34]
[edit] Pennsylvania
In 2004 the Dover, Pennsylvania School Board voted that a statement must be read to students of
9th grade biology mentioning Intelligent Design. This resulted in a firestorm of criticism from scientists and
science teachers and caused a group of parents to begin legal proceedings (sometimes referred to as the
Dover panda trial) to challenge the decision, based on their interpretation of the Aguillard precedent.
Supporters of the school board's position noted that the Aguillard holding explicitly allowed for a variety of
what they consider "scientific theories" of origins for the secular purpose of improving scientific education.
Others have argued that Intelligent Design should not be allowed to use this "loophole."[35] On November 8,
2005, the members of the school board in Dover were voted out and replaced by evolutionary theory
supporters. This had no bearing on the case.[36] On December 20, 2005 federal judge John E. Jones III
ruled that the Dover School Board had violated the Constitution when they set their policy on teaching
intelligent design, and stated that "In making this determination, we have addressed the seminal question of
whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its
creationist, and thus religious, antecedents."
[edit] Texas
On November 7, 2007 the Texas Education Agency director of science curriculum Christine Comer
was forced to resign over an e-mail she had sent announcing a talk given by an anti-Intelligent Design
author. In a memo obtained under the Texas Freedom of Information act, TEA officials wrote "Ms. Comer's e-
mail implies endorsement of the speaker and implies that TEA endorses the speaker's position on a subject
on which the agency must remain neutral".[37] In response over 100 biology professors from Texas
universities signed a letter to the state education commissioner denouncing the requirement to be neutral on
the subject of Intelligent Design.[38]
[edit] Virginia
Despite proponents urging that intelligent design should be included in the school system's science
curriculum the school board of Chesterfield County Public Schools in Virginia decided on May 23, 2007, to
approve science textbooks for middle and high schools which do not include the idea of intelligent design.
However, during the board meeting a statement was made that their aim was self-directed learning which
"occurs only when alternative views are explored and discussed", and directed that professionals supporting
curriculum development and implementation are to be required "to investigate and develop processes that
encompass a comprehensive approach to the teaching and learning" of the theory of evolution, "along with
all other topics that raise differences of thought and opinion." During the week before the meeting, one of the
intelligent design proponents claimed that "Students are being excluded from scientific debate. It's time to
bring this debate into the classroom", and presented "A Scientific Dissent From Darwinism".[39][40]
[edit] Recent polls

In 2000, a People for the American Way poll among Americans found that:
• 29% believe public schools should teach evolution in science class but can discuss
creationism there as a belief;
• 20% believe public schools should teach evolution only;
• 17% believe public schools should teach evolution in science class and religious theories
elsewhere;
• 16% believe public schools should teach creation only;
• 13% believe public schools should teach both evolution and creationism in science class;
• 4% believe public schools should teach both but are not sure how.
(1% had no opinion)[41]
In 2006, a poll taken over the telephone by Zogby International commissioned by the Discovery
Institute found that more than three to one of voters surveyed chose the option that biology teachers should
teach Darwin's theory of evolution, but also "the scientific evidence against it". Approximately seven in ten
(69%) sided with this view. In contrast, one in five (21%) chose the other option given, that biology teachers
should teach only Darwin's theory of evolution and the scientific evidence that supports it. One in ten was not
sure.[42] The poll's results may be called into question however, because the wording of the poll question
implies that significant scientific evidence against evolution exists to be taught.
[edit] Consequences
Over the past few years, there have been several attempts to undermine the teaching of evolution in
public schools. Tactics include claims that evolution is "merely a theory", which exploits the difference
between the general use of the word theory and the scientific usage, and thus insinuates that evolution does
not have widespread acceptance amongst scientists; promoting the teaching of alternative pseudosciences
such as intelligent design; and completely ignoring evolution in biology classes. In general, these
controversies, at the local school district level, have resulted in Federal and State court actions (usually by
parents who are opposed to teaching of religion in school). There have been a number of consequences of
these activities:
• The teaching of religious doctrines, such as Creation Science and Intelligent Design, relies
upon an understanding of and belief in the supernatural. This is in direct opposition to the principle
that science can only use natural, reproducible, testable forces to explain phenomena. This could
lead to the disabling of students' abilities to develop the critical thinking skills necessary for all
scientists.
• The costs to school districts to defend their actions in imposing religious teaching over the
science of evolution are high, diverting funds that the districts could use for the education of their
students.[43][44]
• The lack of proper science education will have a long-term effect of eroding the technological
leadership of the US.[45]
• Most biology and medical research institutions assume a well-grounded undergraduate
education in biology, which includes the study of evolution. Since modern medical research has
focused on the cellular and biochemical levels, the knowledge that all of these processes have
evolved from a common ancestor and the processes are remarkably similar between diverse species
will be critical in designing experiments to test novel treatments for disease.[46]
• Christine Comer, the Director of Science Curriculum for Texas, resigned after being placed
on administrative leave for a breach of Texas Education Agency policy, which requires a neutral
stance regarding ID and evolution. Ms. Comer had forwarded an email containing details of an
upcoming talk by Barbara Forrest, an expert on the history of the ID movement who had been an
expert witness on that subject in Kitzmiller v. Dover Area School District, and a prominent critic of ID.
Lizzette Reynolds, formerly of the U.S. Department of Education and also deputy legislative director
for former Texas Governor, George W. Bush, emailed Comer's supervisor: "This is highly
inappropriate," Reynolds said. "I believe this is an offense that calls for termination or, at the very
least, reassignment of responsibilities.[47]
[edit] U.S. legal quotations
Judge John E. Jones III made a landmark ruling in Kitzmiller v. Dover Area School District
The Supreme Court, Epperson v. Arkansas (1968):
“...the First Amendment does not permit the state to require that teaching and learning must be
tailored to the principles or prohibitions of any religious sect or dogma...the state has no
legitimate interest in protecting any or all religions from views distasteful to them.”
McLean v. Arkansas case (1982), the judge wrote that creation scientists:
“...cannot properly describe the methodology used as scientific, if they start with a conclusion
and refuse to change it regardless of the evidence developed during the course of the
investigation.”
The Supreme Court, Edwards v. Aguillard (1987):

“...Because the primary purpose of the Creationism Act is to advance a particular religious
belief, the Act endorses religion in violation of the First Amendment.”
In Webster v. New Lenox School District (1990), the Seventh Circuit Court of Appeals stated:
“If a teacher in a public school uses religion and teaches religious beliefs or espouses theories
clearly based on religious underpinnings, the principles of the separation of church and state are
violated as clearly as if a statute ordered the teacher to teach religious theories such as the
statutes in Edwards did.”
The 9th Circuit Federal Appeals Court wrote in a California case (Peloza v. Capistrano School
District, 1994):
“The Supreme Court has held unequivocally that while belief in a Divine Creator of the universe
is a religious belief, the scientific theory that higher forms of life evolved from lower ones is not.”
United States District Court Judge John E. Jones III stated thus in Kitzmiller v. Dover Area School
District, 2005:
"We have concluded that Intelligent Design is not science, and moreover that I.D. cannot
uncouple itself from its creationist, and thus religious antecedents."
From evolution.berkeley.edu[48]
[edit] Europe
[edit] Council of Europe's resolution 1580
October 4, 2007, the Council of Europe released the 'Provisional edition' of resolution 1580: The
dangers of creationism in education. The resolution rejects that creationism in any form, including "intelligent
design", can be considered scientific (Article 4), but recommends its inclusion in religion and cultural classes
(Article 16). The resolution concludes that teaching creationism in school as a scientific theory may threaten
civil rights (Articles 13 and 18). The resolution summarizes itself in Article 19:[49]
The Parliamentary Assembly therefore urges the member states, and especially their education
authorities to:
1. defend and promote scientific knowledge;

2. strengthen the teaching of the foundations of science, its history, its epistemology and
its methods alongside the teaching of objective scientific knowledge;
3. make science more comprehensible, more attractive and closer to the realities of the
contemporary world;
4. firmly oppose the teaching of creationism as a scientific discipline on an equal footing
with the theory of evolution and in general the presentation of creationist ideas in any
discipline other than religion;
5. promote the teaching of evolution as a fundamental scientific theory in the school
curricula.
[edit] Denmark
In 2007, Turkish creationist Harun Yahya sent his book The Atlas of Creation to a large number of
European, including Danish, schools.[citation needed]
On April 25, 2007, Member of Parliament Martin Henriksen (Danish People's Party) asked Minister of
Education Bertel Haarder (The Liberal Party) for information about how many educational institutions had
received The Atlas of Creation.[50] The minister responded that the Ministry of Education was not in
possession of information about the number of educational institutions that had received the book, that
choice of educational material was not up to the ministry, and that it is an objective of the discipline biology in
primary school that the education must enable the pupils to relate to values and conflicts of interest
connected with issues with a biological content.[51]
On November 11, 2007, following the October 4 release of the Council of Europe's resolution 1580,
Danish member of ISKCON and leading ID-proponent Leif Asmark Jensen published a letter on his website.
The letter is addressed to "Danish politicians" and is a clarification why Asmark and other ID-proponents
consider the resolution "so problematic that the Danish Parliament ought to ignore the resolution and
maintain the Danish tradition for openness in school education."[52]
In interview sessions during 2002, less than 10% of the interviewed Danes declared the theory of
evolution false.[53]
[edit] Netherlands
In the Netherlands some factions teach creationism in their own schools. In May 2005, a discussion
on Intelligent Design erupted when education minister Maria van der Hoeven suggested that debate about
Intelligent Design might encourage discourse between the country's various religious parties. She sought to
"stimulate an academic debate" on the subject. Following strong objection from the nation's scientists,[54]
she dropped plans of holding a conference on the matter.[55] After the 2007 elections, she was succeeded
by Ronald Plasterk, described as a "molecular geneticist, staunch atheist and opponent of intelligent design".
[56]
[edit] Norway
In 1986, the then minister of education Kjell Magne Bondevik proposed new education plans for the
elementary and middle school levels which included skepticism to the theory of evolution and would hold that
a final answer to the origin of mankind was unknown. The proposal was withdrawn after it had generated
controversy.[57]
[edit] Poland
Poland saw a major controversy over creationism in 2006 when the deputy education minister,
Mirosław Orzechowski, denounced evolution as "one of many lies" taught in Polish schools. His superior,
Minister of Education Roman Giertych, has stated that the theory of evolution would continue to be taught in
Polish schools, "as long as most scientists in our country say that it is the right theory." Giertych's father,
Member of the European Parliament Maciej Giertych, has however opposed the teaching of evolution and
has claimed that "dinosaurs and humans co-existed because Poles remember the Wawel Dragon and Scots
knows about the Loch Ness monster".[58]
[edit] Serbia
In Serbia the teaching of evolution was suspended for one week in 2004, under education minister
Ljiljana Čolić, only allowing schools to reintroduce evolution into the curriculum if they also taught
creationism.[59] "After a deluge of protest from scientists, teachers and opposition parties" says the BBC
report, Čolić's deputy made the statement, "I have come here to confirm Charles Darwin is still alive" and
announced that the decision was reversed.[60] Čolić resigned after the government said that she had caused
"problems that had started to reflect on the work of the entire government."[61]
[edit] Turkey
In Turkey, a mostly Islamic country, evolution is often a controversial subject. Evolution was added to
the school curriculum shortly after the Turkish Revolution of the 1920s and 30s.[62] There was some
resistance to this, such as that of Said Nursî and his followers, but opposition was not particularly powerful.
[62] In the 1980s, conservatives came into power, and used the ideas of scientific creationists in the US as a
method of discrediting evolution (notwithstanding material on the age of the earth, which Islamic creationism
is less specific about).
One anti-evolutionist group in Turkey is the Istanbul based Bilim Arastirma Vakfi (BAV), or "Science
Research Foundation", which was founded by Adnan Oktar. Its activities include campaigns against the
teaching of evolution. It has been described as one of the world's strongest anti-evolution movements outside
of North America.[63] US based creationist organizations such as the Institute for Creation Research have
worked alongside them. Some scientists have protested that anti-evolution books published by this group
(such as The Evolution Deceit) have become more influential than real biology textbooks. The teaching of
evolution in high schools has been fought by Ali Gören, a member of parliament and professor of medicine,
who believes such education has negative effects.
The situation is very fragile, and the status of evolution in education varies from one government to
the next. For example, in 1985 Education Minister Vehbi Dincerier had scientific creationism added to high
school texts, and also had the discredited Lamarckism presented alongside Darwinism. Only in 1998 was this
changed somewhat, with texts presenting a more balanced view, though still mentioning creationism and
Lamarckism.[63] At present the moderate Islamist Justice and Development Party, which is sympathetic to
creationist views,[62] holds power. It was elected in 2002 and again with a greater majority in 2007.
In general, material that conflicts with religious beliefs is highly controversial in Turkey. For example,
in November 2007 a prosecutor launched a probe into whether biologist Richard Dawkins' book The God
Delusion is "an attack on religious values". Its publisher could face trial and up to one year in prison if the
prosecutor concludes that the book "incites religious hatred" and insults religious values.[64]
Turkish academics who have defended evolutionary theory have received death threats, for instance
biologist Aykut Kence received an email telling him to enjoy his "final days".[63] Kence helped establish the
Evolution Group, whose aim is to improve public understanding of evolution. However, opposition to
creationism is not very powerful; Umit Sayin, a neurologist, describes academics and universities as "slow
and sluggish" in their response. Kence maintains that "if knowledgeable people keep quiet, it only helps
those who spread nonsense."[63]
[edit] United Kingdom
In each of the countries of the United Kingdom, there is an agreed syllabus for religious education
with the right of parents to withdraw their children from these lessons. The religious education syllabus does
not involve teaching creationism, but rather teaching the central tenets of major world faiths.[65] At the same
time, the teaching of evolution is compulsory in publicly funded schools. For instance, the National
Curriculum for England requires that students at Key Stage 4 (14-16) be taught:
1. that the fossil record is evidence for evolution
2. how variation and selection may lead to evolution or to extinction.
Similar requirements exist in Scotland, Wales and Northern Ireland.
In 2003 the Emmanuel Schools Foundation (previously the Vardy Foundation after its founder, Sir
Peter Vardy) sponsored a number of "faith-based" academies where evolution and creationist ideas would be
taught side-by-side in science classes. This caused a considerable amount of controversy.
The Archbishop of Canterbury Dr Rowan Williams, leader of the Church of England, has expressed
his view that creationism should not be taught in schools.[66][67]
An organisation calling itself Truth in Science has distributed teaching packs of creationist
information to schools, and claims that fifty-nine schools are using the packs as "a useful classroom
resource".[68] The government has stated that "Neither intelligent design nor creationism are recognised
scientific theories and they are not included in the science curriculum. The Truth in Science information pack
is therefore not an appropriate resource to support the science curriculum." It is arranging to communicate
this message directly to schools.[69]
The efforts to introduce creationism and intelligent design into schools in the UK is being opposed by
an organization called the British Centre for Science Education. The BCSE has been involved in government
lobbying and has a website which presents information on the relevant issues.[70][71][72]
[edit] Russia
In December 2006, a schoolgirl in St. Petersburg, Russia and her father decided to take the teaching
of evolution in Russian schools to court. The position of the Russian Ministry of Education supports the
theory of evolution. The suit has been backed by representatives of Russian Orthodox Church.[73][74]
[edit] Asia
[edit] Pakistan
As of 2005, evolution was not taught in Pakistani universities.[55] In 2006, the Pakistan Academy of
Sciences became a signatory of the InterAcademy Panel Statement on "The teaching of evolution".[75] Many
of the contemporary titles on the creation-evolution controversy, such as those by Richard Dawkins, have
been translated into Urdu.[76]
[edit] Oceania
[edit] Australia
Australia takes an aggressive stance supporting the right of teachers to teach science, including
evolution, unhindered by religions restrictions.
“ An essential element in the teaching of science is the encouragement of
students and teachers to critically appraise the evidence for notions being taught as
science. The Society states unequivocally that the dogmatic teaching of notions such as
Creationism within a science curriculum stifles the development of critical thinking
patterns in the developing mind and seriously compromises the best interests of
objective public education. This could eventually hamper the advancement of science
and technology as students take their places as leaders of future generations. ”
—Geological Society of Australia[77]
[edit] South America

[edit] Brazil
In 2004, teaching of creationism in religious education classes by Rio de Janeiro's education
department sparked protest from Brazilian scientists.[55]
[edit] See also

• A Scientific Dissent from Darwinism and A Scientific Support for Darwinism
• Clergy Letter Project, a signed statement by over 11,000 Christian clergy members rejecting
Creationism.
• Flying Spaghetti Monster
• Homeschooling
• Level of support for evolution
• "Nothing in Biology Makes Sense Except in the Light of Evolution"
• Parochial school
• Project Steve
• Religion and children
• Science, Evolution, and Creationism (book)
[edit] References
1. ^ "Beliefs of the U.S. public about evolution and creation". Ontario consultants on religious
tolerance. http://www.religioustolerance.org/ev_publi.htm. Retrieved 2010-05-05.
2. ^ Saletan, William (2005-12-21). "Is Creationism Destructible?". Slate (magazine).
http://www.slate.com/id/2132807/fr/rss/. Retrieved 2010-03-06.
3. ^ Witt, Jonathan (2006-09-29). "Science magazine reviews The Language of God". News
and Views. Seattle: Discovery Institute. http://www.evolutionnews.org/2006/09/. Retrieved 2010-03-
05.
4. ^ Lundin, Leigh (2008-05-04). "Evilution". Criminal Brief. http://www.criminalbrief.com/?
p=798. Retrieved 2010-03-05.
5. ^ Annas, J.D., M.P.H., George, J. (2006-12-30). "Intelligent Judging ― Evolution in the
Classroom and the Courtroom" (in Chinese/English). 加入收藏夹. Shouxian: ShouXi.
http://journal.shouxi.net/qikan/article.php?id=221746. Retrieved 2010-03-05.
6. ^ Battle on Teaching Evolution Sharpens
7. ^ s:Kitzmiller v. Dover Area School District/2:Context#Page 19 of 139
8. ^ Understanding the Intelligent Design Creationist Movement: Its True Nature and Goals.
(pdf) A Position Paper from the Center for Inquiry, Office of Public Policy Barbara Forrest. May, 2007.
9. ^ TalkOrigins Archive: Post of the Month: March 2006, The History of Creationism by Lenny
Flank.
10.^ Kent Hovind, a prominent creationist, who states on his web page that "Students in tax-
supported schools are being taught that evolution is a fact. We are convinced that evolution is a
religion masquerading as science and should not be part of any science curriculum. " and "It is my
contention that evolutionism is a religious world view that is not supported by science, Scripture,
popular opinion, or common sense. The exclusive teaching of this dangerous, mind-altering
philosophy in tax-supported schools, parks, museums, etc., is also a clear violation of the First
Amendment."
11.^ Wilgoren, Jodi (August 21, 2005). "Politicized Scholars Put Evolution on the Defensive".
The New York Times. http://www.nytimes.com/2005/08/21/national/21evolve.html. Retrieved April
30, 2010.
12.^ Jason Lisle vs. Eugenie Scott on CNN!
13.^ The God Delusion, Richard Dawkins, Bantam Press, 2006, ISBN 0593055489.
14.^ "The dangers of creationism in education". Council of Europe.
http://assembly.coe.int/Main.asp?link=/Documents/WorkingDocs/Doc07/EDOC11297.htm. Retrieved
2007-08-03.
15.^ Alabama Citizens for Science Education
16.^ a b c "Judge throws out religious discrimination suit". North County Times. August 8, 2008.
http://www.nctimes.com/articles/2008/08/08/news/californian/murrieta/za3f1fe48ff6b8872882574a00
00ff96d.txt. Retrieved 2008-08-24.
17.^ "Association of Christian Schools International et al. v. Roman Stearns et al. Decision"
(PDF). University of California. August 8, 2008. http://www.universityofcalifornia.edu/news/acsi-
stearns/ruling0808.pdf. Retrieved 2008-08-24.
18.^ "Evolution Wins as Creationists (Accidentally) Switch Sides in Florida". Wired.com.
http://blog.wired.com/wiredscience/2008/02/evolution-wins.html. Retrieved 2008-02-20.
19.^ News Release, Science Standards Will Call Evolution 'Scientific Theory', February 19,
2008, Retrieved 2008-02-19
20.^ Judge nixes evolution textbook stickers - Science - MSNBC.com
21.^
http://www.ajc.com/search/content/auto/epaper/editions/today/news_14ce5b3b4491d02d0025.html
22.^ The sticker didn't stick (or did it?)
23.^ THE NATION; Appeals Panel Criticizes Evolution Ruling; A federal district judge had
ordered the removal of stickers in a Georgia county's science textbooks that called evolution a
theory., Ellen Barry, Los Angeles Times, December 16, 2005
24.^ Jarvie, Jenny (December 20, 2006). "School board ends fight for ‘evolution is theory’
stickers". Los Angeles Times. http://pqasb.pqarchiver.com/latimes/access/1183217131.html?
dids=1183217131:1183217131&FMT=ABS&FMTS=ABS:FT&type=current&date=Dec+20%2C+2006
&author=Jenny+Jarvie&pub=Los+Angeles+Times&desc=The+Nation
%3B+School+board+ends+fight+for+%60evolution+is+theory%27+stickers&pqatl=google.
(subscription required)
25.^ a b "AGI Update on Challenges to the Teaching of Evolution". American Geological
Institute. 2001-03-18. http://www.agiweb.org/gap/legis106/evolution.html.
26.^ CNN.com Evolution-creation debate grows louder with Kansas controversy
27.^ News from Agape Press
28.^ The Kansas standards DO include ID
29.^ Milburn, John (2006-08-02). "Conservatives lose majority on State Board of Ed".
Associated Press.
30.^ "Nothing Wrong With Kansas: State voters move science education out of the Victorian
era". The Washington Post. August 6, 2006. http://www.washingtonpost.com/wp-
dyn/content/article/2006/08/05/AR2006080500718.html.
31.^ Kansas Curricular Standards for Science
32.^ Rivers, Margo (6 October 1999). [url=http://news.google.com/newspapers?
id=IPUaAAAAIBAJ&sjid=6kcEAAAAIBAJ&pg=5474,962749&dq=kentucky+department+of+education
+evolution+change-over-time&hl=en "State hits evolution delete key"]. Daily News (Bowling Green,
Kentucky). url=http://news.google.com/newspapers?
id=IPUaAAAAIBAJ&sjid=6kcEAAAAIBAJ&pg=5474,962749&dq=kentucky+department+of+education
+evolution+change-over-time&hl=en. Retrieved 14 November 2010.
33.^ "Ohio Education Board reverses course on promoting 'intelligent-design' creationism". The
Free Library: Americans United for Separation of Church and State. 2006.
http://www.thefreelibrary.com/Ohio+Education+Board+reverses+course+on+promoting...-
a0143580528. Retrieved 2009-09-29.
34.^ Rudoren, Jodi (15 February 2006). "Ohio Board Undoes Stand on Evolution". New York
Times. http://www.nytimes.com/2006/02/15/national/15evolution.html. Retrieved 2009-09-29.
35.^ FindLaw's Writ - Dorf: Why It's Unconstitutional to Teach "Intelligent Design" in the Public
Schools, as an Alternative to Evolution
36.^ Dover School Board Incumbents Booted - Pennsylvania News Story - WGAL Lancaster
37.^ "Texas official resigns, cites creationism conflict - USATODAY.com".
http://www.usatoday.com/news/education/2007-11-30-schools-creationism_N.htm. Retrieved 14
November 2010.
38.^ Texas biology professors voice support for evolution education, Kilgore News Herald,
December 11, 2007, Retrieved 14 November 2010
39.^ Evolution vs. Intelligent Design: Chesterfield School Board takes up debate on different
theories of life, Donna C. Gregory, Chesterfield Observer, Tuesday, June 5, 2007, Retrieved from
Richmond.com 2007-06-05
40.^ News Release, Science textbook statement from School Board Chair Thomas J. Doland,
May 23, 2007, Retrieved 2007-06-05
41.^ http://www.pfaw.org/media-center/publications/evolution-and-creationism-public-education
42.^ http://www.discovery.org/scripts/viewDB/filesDB-download.php?
command=download&id=719
43.^ What’s Wrong with ‘Theory Not Fact’ Resolutions, National Center for Science Education,
December 7, 2000, 2006)]
44.^ "'Intelligent Design' Costs Dover School District Over $1 million"
45.^ Separating Religious Fundamentalist "Science" from Science, from Evolution and the Myth
of Creationism, Tim Berra, Stanford University Press, 1990.
46.^ Teaching About Evolution and the Nature of Science
47.^ State science curriculum director resigns
48.^ Overcoming Roadblocks: Clarifying the Legalities
49.^ Provisional edition of resolution 1580, October 4 2007, Council of Europe
50.^ Question from Member of Parliament Martin Henriksen (Danish)
51.^ Response from Minister of Education Bertel Haarder (Danish)
52.^ Leif Asmark Jensen's letter to Danish politicians (Danish)
53.^ interview sessions
54.^ Martin Enserink (2005-06-03). "Evolution Politics: Is Holland Becoming the Kansas of
Europe?". Science 308 (5727): 1394. doi:10.1126/science.308.5727.1394b. PMID 15933170.
http://www.sciencemag.org/cgi/content/summary/308/5727/1394b.
55.^ a b c MacKenzie, Debora (July 2005). "A battle for science's soul". New Scientist 187
(2507): 8–9. "Eighty years after the Scopes trial drew the battle lines over evolution and creationism,
Darwin's theory is under renewed attack, this time from "intelligent design". It's an idea that is
spreading into US culture and beyond.".
56.^ "Cabinet ministers announced (update 2)". DutchNews.nl. 2007-02-13.
http://www.dutchnews.nl/news/archives/print/001501.php. Retrieved 2008-05-31.
57.^ Meldalen, Sindre Granly (February 1, 2009). "Halvparten av britene tror ikke på dette" (in
Norwegian). Dagbladet.
http://www.dagbladet.no/2009/02/01/nyheter/innnenriks/forskning/darwin/4641873/. Retrieved 2009-
09-09.
58.^ "And finally...", Warsaw Business Journal, 18 December 2006.
59.^ Darwin is off the curriculum for Serbian schools
60.^ Serbia reverses Darwin suspension
61.^ 'Anti-Darwin' Serb minister quits
62.^ a b c Edis, Taner (January 2008). "Islamic Creationism: A Short History". History of Science
Society.
http://www.hssonline.org/publications/Newsletter2008/NewsletterJanuary2008Creationism.html.
Retrieved 2008-02-24. "Islam has been the world religion that has proved most resistant to Darwinian
evolution."
63.^ a b c d Koenig, Robert (May 2001). "Creationism Takes Root Where Europe, Asia Meet".
Science 292 (5520): 1286–1287. doi:10.1126/science.292.5520.1286. PMID 11360976. "Harassed
but hard-headed, some gutsy Turkish scientists are stepping up their efforts to promote the teaching
of evolution".
64.^ "Turkey probes atheist's 'God' book". reposted at RichardDawkins.net (AP, CNN). 2007-11-
28. http://richarddawkins.net/articleComments,1917,-Turkey-probes-atheists-God-
book,CNN,page3#92514. Retrieved 2009-02-14.
65.^ International Religious Freedom Report 2002: United Kingdom
66.^ "Interview: Rowan Williams". The Guardian (London). March 21, 2006.
http://www.guardian.co.uk/religion/Story/0,,1735404,00.html. Retrieved April 30, 2010.
67.^ "Fears over teaching creationism". BBC News. March 21, 2006.
http://news.bbc.co.uk/2/hi/uk_news/education/4828238.stm. Retrieved April 30, 2010.
68.^ Revealed: rise of creationism in UK schools
69.^ Ministers to ban creationist teaching aids in science lessons
70.^ Graebsch, Almut; Schiermeier, Quirin (November 23, 2006). "Anti-evolutionists raise their
profile in Europe". Nature 444 (7118): 406–407. doi:10.1038/444406a. PMID 17122815.
71.^ The dangers of creationism in education, Report, Committee on Culture, Science and
Education, Rapporteur: Mr Guy LENGAGNE, France, Socialist Group, Parliamentary Assembly,
Council of Europe, Doc. 11297, 8 June 2007.
72.^ SCIENCE EDUCATION, Graham Stringer, Member of Parliament, Early Day Motion 2708,
11.10.2006
73.^ In Russia, a test of God vs. Darwin, Erika Niedowski, The Baltimore Sun, January 3, 2007
74.^ RIA Novosti - Russia - St. Petersburg schoolgirl sues authorities over Darwinism
75.^ IAP Statement on the teaching of evolution dated 21 June 2006. Retrieved on 17 February
2008.
76.^ Titles such as The Blind Watchmaker are also available for general readership.
77.^ Geological Society of Australia Intelligent Design Policy (PDF)
• One hundred years without Darwin are enough, Simpson, George Gaylord (1961), Teachers
College Record, 60: 617-626; Reprinted in Evolution: Oxford Readers, New York: Oxford University
Press, 1997, pp. 368–378,
• National Center for Science Education
• List of articles (mostly from Answers in Genesis) on creation education, including many on
recent American and other attempts at legislation
• Science, Evolution, and Creationism: A View from the National Academy of Sciences by the
Steering Committee on Science and Creationism, National Academy of Sciences, addressing the
issue of teaching intelligent design and creationism as science.
• Teaching About Evolution and the Nature of Science by the National Academy of Sciences.
• Kristi L. Bowman, Seeing Government Purpose through the Objective Observer's Eyes: The
Evolution-Intelligent Design Debates, 29 Harvard Journal of Law and Public Policy 417 (2006)
• Jim Chen, Legal Mythmaking in a Time of Mass Extinctions: Reconciling Stories of Origins
with Human Destiny, 29 Harvard Environmental Law Review 279 (2005)
• Wired Magazine's Article on Creationism and Intelligent Design
• Islamic Creationism in Turkey
Retrieved from "http://en.wikipedia.org/wiki/Creation_and_evolution_in_public_education"
Categories: Creationism | Religion and education | Textbook controversies | United States

creationism and evolution case law | Politics of science | Evolution and religion
W000
Evolution as theory and fact


Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
The statement "evolution is both a theory and a fact" is often seen in biological literature.[1][2][3][4][5]
[6][7] Evolution is a "theory" in the scientific sense of the term "theory"; it is an established scientific model
that explains observations and makes predictions through mechanisms such as natural selection.
When scientists say "evolution is a fact", they are using one of two meanings of the word "fact". One
meaning is empirical: evolution can be observed through changes in allele frequencies or traits of a
population over successive generations.
Another way "fact" is used is to refer to a certain kind of theory, one that has been so powerful and
productive for such a long time that it is universally accepted by scientists. When scientists say evolution is a
fact in this sense, they mean it is a fact that all living organisms have descended from a common ancestor (or
ancestral gene pool) [8] even though this cannot be directly observed. This implies more tangibly that it is a
fact that humans share a common ancestor with other primates.
Contents
[hide]
• 1 Evolution, fact and theory
• 1.1 Evolution
• 1.2 Fact
• 1.3 Theory
• 2 Evolution compared with gravity
• 3 Evolution as theory and fact in the literature
• 3.1 Evolution as fact and theory
• 3.2 Evolution as fact not theory
• 4 Predictive power
• 5 Related concepts and terminology
• 6 See also
• 7 Notes
• 8 References
[edit] Evolution, fact and theory
Evolution has been described as "fact and theory", "fact not theory", and "only a theory, not a fact".
This illustrates a confusion in terminology that hampers discussion.[9][10] The meanings of the terms
"evolution", "fact", and "theory" are described below.
[edit] Evolution
Main articles: Introduction to evolution and Evolution
Evolution is usually defined simply as changes in trait or gene frequency in a population of organisms
from one generation to the next. However, "evolution" is often used to include the following additional claims:
1. Differences in trait composition between isolated populations over many generations may
result in the origin of new species.
2. All living organisms alive today have descended from a common ancestor (or ancestral gene
pool).
According to Douglas Futuyma:
Biological evolution may be slight or substantial; it embraces everything from slight changes in
the proportion of different alleles within a population (such as those determining blood types) to
the successive alterations that led from the earliest proto-organism to snails, bees, giraffes, and
dandelions.[11]
The term "evolution", especially when referred to as a "theory", is also used more broadly to
incorporate processes such as natural selection and genetic drift.
[edit] Fact
Main article: Scientific fact
Fact is often used by scientists to refer to experimental or empirical data or objective verifiable
observations.[12][13][14][15] "Fact" is also used in a wider sense to mean any theory for which there is
overwhelming evidence.
A fact is a hypothesis that is so firmly supported by evidence that we assume it is true, and act
as if it were true. —Douglas Futyuma[16]
Evolution is a fact in the sense that it is overwhelmingly validated by the evidence. Frequently,
evolution is said to be a fact in the same way as the Earth revolving around the Sun is a fact.[16][17] The
following quotation from H. J. Muller, "One Hundred Years Without Darwin Are Enough" explains the point.
There is no sharp line between speculation, hypothesis, theory, principle, and fact, but only a
difference along a sliding scale, in the degree of probability of the idea. When we say a thing is a fact,
then, we only mean that its probability is an extremely high one: so high that we are not bothered by
doubt about it and are ready to act accordingly. Now in this use of the term fact, the only proper one,
evolution is a fact.[3]
The National Academy of Science (U.S.) makes a similar point:
Scientists most often use the word "fact" to describe an observation. But scientists can also
use fact to mean something that has been tested or observed so many times that there is no longer a
compelling reason to keep testing or looking for examples. The occurrence of evolution in this sense is
fact. Scientists no longer question whether descent with modification occurred because the evidence
is so strong.[18]
Philosophers of science argue that we do not know mind-independent empirical truths with absolute
certainty: even direct observations may be "theory laden" and depend on assumptions about our senses and
the measuring instruments used. In this sense all facts are provisional.[1][19]
[edit] Theory
Main article: Scientific theory
A scientific theory is a well-supported body of interconnected statements that explains observations
and can be used to make testable predictions. Scientific theories describe the coherent framework into which
observable data fit. The "theory of evolution" is the framework that best explains observed changes of
species over time and best predicts the new observations that continue to be made in evolutionary biology
and related sciences.
The scientific definition of the word "theory" is different from the colloquial sense of the word.
Colloquially, "theory" can mean a hypothesis, a conjecture, an opinion, or a speculation that does not have to
be based on facts or make testable predictions. However, In science, the meaning of theory is more rigorous.
A theory is hypothesis corroborated by observation of facts and make testable predictions. In science, a
current theory is a theory that has no equally acceptable or more acceptable alternative theory.
[edit] Evolution compared with gravity

See also: Gravity and History of gravitational theory
The application of the terms "fact" and "theory" to evolution is similar to their use in describing
gravity.[20]
The most obvious fact of gravity is that objects in our everyday experience tend to fall downwards
when not otherwise prevented from doing so. People throughout history have wondered what causes this
effect. Many explanations have been proposed over the centuries. Aristotle, Galileo, Newton, and Einstein
have all developed useful models of gravity, each of which constitutes a theory of gravity. (Newton, for
example, realized that the fact of gravity can be extended to the tendency of any two masses to attract one
another.) The word "gravity", therefore, can be used to refer to the observed facts (i.e., that masses attract
one another) and the theory used to explain the facts (the reason why masses attract one another). In this
way, gravity is both a theory and a fact.
In the study of biological species, the facts include the existence of many different species in
existence today, some very similar to each other and some very dissimilar, the remains of extinct species in
the fossil record, and so forth. In species that rapidly reproduce, for example fruit flies, the process of change
from generation to generation — that is, evolutionary change — has been observed in the laboratory.[21] The
observation of fruit fly populations changing over time is also an example of a fact. So evolution is a fact just
as the observations of gravity are a fact.
There have been many attempts to explain these biological observations over the years.
Lamarckism, transmutationism and orthogenesis were all non-Darwinian theories that attempted to explain
the observations of species and fossils, as well as other evidence. However, the modern theory of evolution
is the explanation for all relevant observations regarding the development of life, based on a model that
explains all the available data and observations (and provides testable predictions). Thus, evolution is not
only a fact but also a theory, just as gravity is both a fact and a theory.
[edit] Evolution as theory and fact in the literature
The confusion over the word evolution and the distinction between "fact" and "theory" is largely due
to authors using evolution to refer to three related yet distinct ideas: first, the changes that occur within
species over generations; second, the mechanism thought to drive change; and third, the concept of
common descent. However, among biologists there is a consensus that evolution is a fact:
• American zoologist and paleontologist George Simpson stated that "Darwin... finally and
definitely established evolution as a fact."[22]
• H. J. Muller wrote, "If you like, then, I will grant you that in an absolute sense evolution is not
a fact, or rather, that it is no more a fact than that you are hearing or reading these words." [3]
• Kenneth R. Miller writes, "evolution is as much a fact as anything we know in science." [23]
• Ernst Mayr observed, "The basic theory of evolution has been confirmed so completely that
most modern biologists consider evolution simply a fact. How else except by the word evolution can
we designate the sequence of faunas and floras in precisely dated geological strata? And
evolutionary change is also simply a fact owing to the changes in the content of gene pools from
generation to generation."[7]
[edit] Evolution as fact and theory

Commonly "fact" is used to refer to the observable changes in organisms' traits over generations
while the word "theory" is reserved for the mechanisms that cause these changes:
• Paleontologist Stephen Jay Gould writes, "Evolution is a theory. It is also a fact. And facts
and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the
world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away
when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced
Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans
evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some
other yet to be discovered."[2]
• Similarly, biologist Richard Lenski says, "Scientific understanding requires both facts and
theories that can explain those facts in a coherent manner. Evolution, in this context, is both a fact
and a theory. It is an incontrovertible fact that organisms have changed, or evolved, during the
history of life on Earth. And biologists have identified and investigated mechanisms that can explain
the major patterns of change."[6]
• Biologist T. Ryan Gregory says, "biologists rarely make reference to 'the theory of evolution,'
referring instead simply to 'evolution' (i.e., the fact of descent with modification) or 'evolutionary
theory' (i.e., the increasingly sophisticated body of explanations for the fact of evolution). That
evolution is a theory in the proper scientific sense means that there is both a fact of evolution to be
explained and a well-supported mechanistic framework to account for it." [20]
[edit] Evolution as fact not theory

Other commentators, focusing on the changes in species over generations and in some cases
common ancestry have stressed that evolution is a fact to emphasize the weight of supporting evidence while
denying it is helpful to use the term "theory":
• R. C. Lewontin wrote, "It is time for students of the evolutionary process, especially those
who have been misquoted and used by the creationists, to state clearly that evolution is a fact, not
theory."[24]
• Douglas Futuyma writes in his Evolutionary Biology book, "The statement that organisms
have descended with modifications from common ancestors—the historical reality of evolution—is not
a theory. It is a fact, as fully as the fact of the earth's revolution about the sun." [11]
• Richard Dawkins says, "One thing all real scientists agree upon is the fact of evolution itself.
It is a fact that we are cousins of gorillas, kangaroos, starfish, and bacteria. Evolution is as much a
fact as the heat of the sun. It is not a theory, and for pity's sake, let's stop confusing the
philosophically naive by calling it so. Evolution is a fact." [25]
• Neil Campbell wrote in his 1990 biology textbook, "Today, nearly all biologists acknowledge
that evolution is a fact. The term theory is no longer appropriate except when referring to the various
models that attempt to explain how life evolves... it is important to understand that the current
questions about how life evolves in no way implies any disagreement over the fact of evolution." [4]
[edit] Predictive power

A central tenet in science is that a scientific theory is supposed to have predictive power, and
verification of predictions are seen as an important and necessary support for the theory. The theory of
evolution has provided such predictions. Four examples are:
• Genetic information must be transmitted in a molecular way that will be almost exact but
permit slight changes. Since this prediction was made, biologists have discovered the existence of
DNA, which has a mutation rate of roughly 10−9 per nucleotide per cell division; this provides just
such a mechanism.[26]
• Some DNA sequences are shared by very different organisms. It has been predicted by the
theory of evolution that the differences in such DNA sequences between two organisms should
roughly resemble both the biological difference between them according to their anatomy and the
time that had passed since these two organisms have separated in the course of evolution, as seen
in fossil evidence. The rate of accumulating such changes should be low for some sequences,
namely those that code for critical RNA or proteins, and high for others that code for less critical RNA
or proteins; but for every specific sequence, the rate of change should be roughly constant over time.
These results have been experimentally confirmed. Two examples are DNA sequences coding for
rRNA, which is highly conserved, and DNA sequences coding for fibrinopeptides (amino acid chains
that are discarded during the formation of fibrin), which are highly non-conserved.[26]
• Prior to 2004, paleontologists had found fossils of amphibians with necks, ears, and four
legs, in rock no older than 365 million years old. In rocks more than 385 million years old they could
only find fish, without these amphibian characteristics. Evolutionary theory predicted that since
amphibians evolved from fish, an intermediate form should be found in rock dated between 365 and
385 million years ago. Such an intermediate form should have many fish-like characteristics,
conserved from 385 million years ago or more, but also have many amphibian characteristics as well.
In 2004, an expedition to islands in the Canadian arctic searching specifically for this fossil form in
rocks that were 375 million years old discovered fossils of Tiktaalik.[27]
• Evolutionary theory predicts that novel inventions can arise, while creationists predict that
new "information" cannot arise, and that the Second Law of Thermodynamics only allows for
"information" to be lost.[28] In an ongoing experiment, Richard Lenski observed that E. coli evolved
the ability to metabolize citrate, which constitutes a novel invention, and an increase in the
information of the DNA of the E. coli.[29]
[edit] Related concepts and terminology

• Speculative or conjectural explanations are called hypotheses. Well-tested and corroborated
(or validated) explanations are called theories.
• "Fact" does not mean "absolute certainty". In the words of Stephen J. Gould: In science,
"fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional
assent."[2]
• "Proof" of a theory does not exist in natural sciences. Proof only exists in formal sciences,
such as mathematics. Experimental observation of the predictions made by a hypothesis or theory is
called validation.
• A scientific law is a concept related to a scientific theory. Very well-established "theories" that
rely on a simple principle are often called scientific "laws". For example, it is common to encounter
reference to "the law of gravity", "the law of natural selection", or the "laws of evolution."
[edit] See also

Book:Evolution

• Epistemology
• Evidence of common descent
• Evolution is just a theory, not a fact (in objections to evolution)
• Misconceptions about evolution (in List of misconceptions)
• Theory vs. Fact (in Creation-evolution controversy)
[edit] Notes
1. ^ a b Moran, Laurence (1993-01-22). "Evolution is a Fact and a Theory". Talk.origins.
http://www.talkorigins.org/faqs/evolution-fact.html. Retrieved 2007-10-18.
2. ^ a b c Gould, Stephen Jay (1981-05-01). "Evolution as Fact and Theory". Discover 2 (5): 34–
37. http://www.stephenjaygould.org/library/gould_fact-and-theory.html. Reprinted in:
• Vetter, Herbert F. (ed.) (1982). Speak Out Against The New Right. Beacon Press.
ISBN 0807004863.
• Gould, Stephen Jay (1994-04-01). Hen's Teeth and Horse's Toes. New York: Norton.
ISBN 0393017168.
3. ^ a b c Muller, H. J. (1959). "One hundred years without Darwin are enough". School Science
and Mathematics 59: 304–305. doi:10.1111/j.1949-8594.1959.tb08235.x.
http://www.skepticfiles.org/evolut/100pcnts.htm. Reprinted in:
• Zetterberg, Peter (ed.) (1983-05-01). Evolution Versus Creationism: The Public
Education Controversy. Phoenix AZ: ORYX Press. ISBN 0897740610.
4. ^ a b Campbell, Neil A.; Reece, Jane B. (2002-02-05). Biology 6th ed.. Benjamin Cummings.
p. 1175. ISBN 0805366245.
5. ^ Dobzhansky, Theodosius (1973-03-01). "Nothing in biology makes sense except in the light
of evolution". American Biology Teacher 35. http://people.delphiforums.com/lordorman/light.htm.
Reprinted in:
• Zetterberg, Peter (ed.) (1983-05-01). Evolution Versus Creationism: The Public
Education Controversy. Phoenix AZ: ORYX Press. ISBN 0897740610.
6. ^ a b Lenski, Richard E. (2000). "Evolution: Fact and Theory". American Institute of Biological
Sciences. http://www.actionbioscience.org/evolution/lenski.html. Retrieved 2007-10-18.
7. ^ a b Mayr, Ernst (1988). Toward a New Philosophy of Biology: Observations of an
Evolutionist. Cambridge: Harvard University Press. ISBN 0-674-89666-1.
8. ^ Cavalier-Smith T (2006). "Cell evolution and Earth history: stasis and revolution". Philos
Trans R Soc Lond B Biol Sci 361 (1470): 969–1006. doi:10.1098/rstb.2006.1842. PMID 16754610.
9. ^ Is "Evolution" a "Theory" or "Fact" or Is This Just a Trivial Game of Semantics? by Casey
Luskin
10.^ Committee for Skeptical Inquiry — Evolution & Creationism: Terminology in Conflict by
Richard Joltes
11.^ a b Futuyma, Douglas J. (1997). , Evolutionary Biology, 3rd ed.. Sinauer Associates. p. 751.
ISBN 0878931899.
12.^ Wordnet entry for phrase "scientific fact"
13.^ United States National Park Service Glossary
14.^ Webster's New Millennium Dictionary of English, Preview Edition (v 0.9.6) , Copyright ©
2003–2006 Lexico Publishing Group, LLC
15.^ Webster's Encyclopedic Unabridged Dictionary of the English Language (1996) gives a
third meaning of the word "fact" as (3) A truth known by actual experience or observation; something
known to be true: 'Scientists gather facts about plant growth.'
16.^ a b Hypotheses, Facts, and the Nature of Science, —Douglas Futyuma
17.^ Guardian article by Richard Dawkins, Jerry Coyne
18.^ Science and Creationism: A View from the National Academy of Sciences, Second Edition
(1999), National Academy of Sciences (NAS), National Academy Press, Washington DC, 2006.
19.^ Wilkins, JS (1997). "Evolution and Philosophy:Is Evolution Science, and What Does
'Science' Mean?". The TalkOrigins Archive. http://www.talkorigins.org/faqs/evolphil/falsify.html.
20.^ a b Gregory, T. Ryan (2007). "Evolution as Fact, Theory, and Path". Evolution: Education
and Outreach 1 (1): 46–52. doi:10.1007/s12052-007-0001-z.
21.^ Dobzhansky T, Pavlovsky O (1971). "Experimentally created incipient species of
Drosophila". Nature 230 (5292): 289–92. doi:10.1038/230289a0. PMID 5549403.
22.^ Robinson, B.A. (2005-08-30). "Is the theory of evolution merely a "theory"?".
http://www.religioustolerance.org/ev_stat.htm. Retrieved 2007-10-18.
23.^ "Miller, Kenneth S. (2007). Finding Darwin's God: A Scientist's Search for Common Ground
Between God and Evolution (P.S.). New York, N.Y: Harper Perennial. ISBN 0061233501.
24.^ Lewontin, R. C. (1981). "Evolution/Creation Debate: a time for truth". Bioscience 31: 559.
Reprinted in:
• Zetterberg, Peter, ed. (1983-05-01). Evolution Versus Creationism: the public
education controversy. Phoenix AZ: Oryx Press. ISBN 0897740610.
25.^ Natural History article : The Illusion of Design by Richard Dawkins
26.^ a b Bruce Alberts; Alexander Johnson; Julian Lewis; Martin Raff; Keith Roberts; Peter
Walter (March, 2002). Molecular Biology of the Cell (4th ed.). Routledge. ISBN 0-8153-3218-1.
27.^ "Shubin, Neil. (2008). Your Inner Fish. Pantheon. ISBN 9780375424472.
28.^ TalkOrigins.org
29.^ NS:bacteria make major evolutionary shift in the lab
[edit] References
• J.P. Franck, et al., "Evolution of a satellite DNA family in tilapia." Annual Meeting Canadian
Federation of Biological Societies. Halifax, (1990).
• M. Losseau-Hoebeke, "The biology of four haplochromine species of Lake Kivu (Zaire) with
evolutionary implications." Thesis, Dept. Ichthyology, Rhodes University, Grahamstown, (1992).
• Not Just a Theory Discredits the assertion that evolution is "just a theory", with an
explanation of the meaning of the word 'theory' in a scientific context.
• Talk Origins Response to the claim that no examples of speciation have been observed.
• Glenn Branch; Louise S. Mead (2008-06-06). "“Theory” in Theory and Practice" (pdf). Evo
Edu Outreach (2008) 1:287–289. Springer Science + Business Media.
http://www.springerlink.com/content/fr258627q2x3t378/fulltext.pdf. Retrieved 2008-07-21.
Retrieved from "http://en.wikipedia.org/wiki/Evolution_as_theory_and_fact"
Categories: Creationist objections to evolution | Biology theories | Evolutionary biology

W000
Life

For other uses, see Life (disambiguation).
Life
Life
Domains and Kingdoms
Life on Earth:
• Non-cellular life (viruses) [note 1]
• Cellular life
• Bacteria
• Archaea
• Eukarya
• Protista
• Fungi
• Plantae
• Animalia
Life (cf. biota) is a characteristic that distinguishes objects that have signaling and self-sustaining
processes (biology) from those that do not,[1][2] either because such functions have ceased (death), or else
because they lack such functions and are classified as inanimate.[3]
In biology, the science of living organisms, life is the condition which distinguishes active organisms
from inorganic matter.[4] Living organisms undergo metabolism, maintain homeostasis, possess a capacity
to grow, respond to stimuli, reproduce and, through natural selection, adapt to their environment in
successive generations. More complex living organisms can communicate through various means.[1][5] A
diverse array of living organisms (life forms) can be found in the biosphere on Earth, and the properties
common to these organisms—plants, animals, fungi, protists, archaea, and bacteria—are a carbon- and water-
based cellular form with complex organization and heritable genetic information.
In philosophy and religion, the conception of life and its nature varies. Both offer interpretations as to
how life relates to existence and consciousness, and both touch on many related issues, including life
stance, purpose, conception of a god or gods, a soul or an afterlife.
Contents
[hide]
• 1 Early theories about life
• 1.1 Materialism
• 1.2 Hylomorphism
• 1.3 Vitalism
• 2 Definitions
• 2.1 Biology
• 2.1.1 Proposed
• 2.1.2 Viruses
• 2.2 Biophysics
• 2.3 Living systems theories
• 2.3.1 Gaia hypothesis
• 2.3.2 Nonfractionability
• 2.3.3 Life as a property of ecosystems
• 3 Origin
• 4 Conditions for life
• 4.1 Range of tolerance
• 4.2 Extremophiles
• 4.3 Chemical element requirements
• 5 Classification of life
• 6 Extraterrestrial life
[edit] Early theories about life
[edit] Materialism
Plant life
Herds of zebra and impala gathering on the Masai Mara plain
An aerial photo of microbial mats around the Grand Prismatic Spring of Yellowstone National Park.
Some of the earliest theories of life were materialist, holding that all that exists is matter, and that all
life is merely a complex form or arrangement of matter. Empedocles (430 BC) argued that every thing in the
universe is made up of a combination of four eternal "elements" or "roots of all": earth, water, air, and fire. All
change is explained by the arrangement and rearrangement of these four elements. The various forms of life
are caused by an appropriate mixture of elements. For example, growth in plants is explained by the natural
downward movement of earth and the natural upward movement of fire.[6]
Democritus (460 BC), the disciple of Leucippus, thought that the essential characteristic of life is
having a soul (psyche). In common with other ancient writers, he used the term to mean the principle of living
things that causes them to function as a living thing. He thought the soul was composed of fire atoms,
because of the apparent connection between life and heat, and because fire moves.[7] He also suggested
that humans originally lived like animals, gradually developing communities to help one another, originating
language, and developing crafts and agriculture.[8]
In the scientific revolution of the 17th century, mechanistic ideas were revived by philosophers like
Descartes.
[edit] Hylomorphism
Hylomorphism is the theory (originating with Aristotle (322 BC)) that all things are a combination of
matter and form. Aristotle was one of the first ancient writers to approach the subject of life in a scientific way.
Biology was one of his main interests, and there is extensive biological material in his extant writings.
According to him, all things in the material universe have both matter and form. The form of a living thing is its
soul (Greek psyche, Latin anima). There are three kinds of souls: the "vegetative soul" of plants, which
causes them to grow and decay and nourish themselves, but does not cause motion and sensation; the
"animal soul" which causes animals to move and feel; and the rational soul which is the source of
consciousness and reasoning which (Aristotle believed) is found only in man.[9] Each higher soul has all the
attributes of the lower one. Aristotle believed that while matter can exist without form, form cannot exist
without matter, and therefore the soul cannot exist without the body.[10]
Consistent with this account is a teleological explanation of life. A teleological explanation accounts
for phenomena in terms of their purpose or goal-directedness. Thus, the whiteness of the polar bear's coat is
explained by its purpose of camouflage. The direction of causality is the other way round from materialistic
science, which explains the consequence in terms of a prior cause. Modern biologists now reject this
functional view in terms of a material and causal one: biological features are to be explained not by looking
forward to future optimal results, but by looking backwards to the past evolutionary history of a species,
which led to the natural selection of the features in question.
[edit] Vitalism
Vitalism is the belief that the life-principle is essentially immaterial. This originated with Stahl (17th
century), and held sway until the middle of the 19th century. It appealed to philosophers such as Henri
Bergson, Nietzsche, Wilhelm Dilthey, anatomists like Bichat, and chemists like Liebig.
Vitalism underpinned the idea of a fundamental separation of organic and inorganic material, and the
belief that organic material can only be derived from living things. This was disproved in 1828 when Friedrich
Wöhler prepared urea from inorganic materials. This so-called Wöhler synthesis is considered the starting
point of modern organic chemistry. It is of great historical significance because for the first time an organic
compound was produced from inorganic reactants.
Later, Helmholtz, anticipated by Mayer, demonstrated that no energy is lost in muscle movement,
suggesting that there were no vital forces necessary to move a muscle. These empirical results led to the
abandonment of scientific interest in vitalistic theories, although the belief lingered on in non-scientific
theories such as homeopathy, which interprets diseases and sickness as caused by disturbances in a
hypothetical vital force or life force.
[edit] Definitions
It is still a challenge for scientists and philosophers to define life in unequivocal terms.[11][12][13]
Defining life is difficult—in part—because life is a process, not a pure substance.[14] Any definition must be
sufficiently broad to encompass all life with which we are familiar, and it should be sufficiently general that,
with it, scientists would not miss life that may be fundamentally different from life on Earth.[15]
[edit] Biology
Since there is no unequivocal definition of life, the current understanding is descriptive, where life is a
characteristic of organisms that exhibit all or most of the following phenomena:[14][16]
1. Homeostasis: Regulation of the internal environment to maintain a constant state; for
example, electrolyte concentration or sweating to reduce temperature.
2. Organization: Being structurally composed of one or more cells, which are the basic units of
life.
3. Metabolism: Transformation of energy by converting chemicals and energy into cellular
components (anabolism) and decomposing organic matter (catabolism). Living things require energy
to maintain internal organization (homeostasis) and to produce the other phenomena associated with
life.
4. Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism
increases in size in all of its parts, rather than simply accumulating matter.
5. Adaptation: The ability to change over a period of time in response to the environment. This
ability is fundamental to the process of evolution and is determined by the organism's heredity as well
as the composition of metabolized substances, and external factors present.
6. Response to stimuli: A response can take many forms, from the contraction of a unicellular
organism to external chemicals, to complex reactions involving all the senses of multicellular
organisms. A response is often expressed by motion, for example, the leaves of a plant turning
toward the sun (phototropism) and by chemotaxis.
7. Reproduction: The ability to produce new individual organisms, either asexually from a single
parent organism, or sexually from two parent organisms.
[edit] Proposed
To reflect the minimum phenomena required, some have proposed other biological definitions of life:
• Living things are systems that tend to respond to changes in their environment, and inside
themselves, in such a way as to promote their own continuation.[ citation needed]
• A network of inferior negative feedbacks (regulatory mechanisms) subordinated to a superior
positive feedback (potential of expansion, reproduction).[17]
• A systemic definition of life is that living things are self-organizing and autopoietic (self-
producing). Variations of this definition include Stuart Kauffman's definition as an autonomous agent
or a multi-agent system capable of reproducing itself or themselves, and of completing at least one
thermodynamic work cycle.[18]
• Life is a self-sustained chemical system capable of undergoing Darwinian evolution.[19]
• Things with the capacity for metabolism and motion.[14]
• Life is a delay of the spontaneous diffusion or dispersion of the internal energy of the
biomolecules towards more potential microstates.[20]
• Living beings are thermodynamic systems that have an organized molecular structure.[20]
[edit] Viruses
Viruses are most often considered replicators rather than forms of life. They have been described as
"organisms at the edge of life,"[21] since they possess genes, evolve by natural selection,[22] and replicate
by creating multiple copies of themselves through self-assembly. However, viruses do not metabolize and
require a host cell to make new products. Virus self-assembly within host cells has implications for the study
of the origin of life, as it may support the hypothesis that life could have started as self-assembling organic
molecules.[23][24]
[edit] Biophysics
Biophysicists have also commented on the nature and qualities of life forms—notably that they
function on negative entropy.[25][26] In more detail, according to physicists such as John Bernal, Erwin
Schrödinger, Eugene Wigner, and John Avery, life is a member of the class of phenomena which are open or
continuous systems able to decrease their internal entropy at the expense of substances or free energy taken
in from the environment and subsequently rejected in a degraded form (see: entropy and life).[27][28][29]
[edit] Living systems theories

Some scientists have proposed in the last few decades that a general living systems theory is
required to explain the nature of life.[30] Such a general theory, arising out of the ecological and biological
sciences, attempts to map general principles for how all living systems work. Instead of examining
phenomena by attempting to break things down into component parts, a general living systems theory
explores phenomena in terms of dynamic patterns of the relationships of organisms with their environment.
[31]
[edit] Gaia hypothesis

The idea that the Earth is alive is probably as old as humankind, but the first public expression of it as
a fact of science was by a Scottish scientist, James Hutton. In 1785 he stated that the Earth was a
superorganism and that its proper study should be physiology. Hutton is rightly remembered as the father of
geology, but his idea of a living Earth was forgotten in the intense reductionism of the 19th century.[32] The
Gaia hypothesis, originally proposed in the 1960s by scientist James Lovelock,[33][34] explores the idea that
the life on Earth functions as a single organism which actually defines and maintains environmental
conditions necessary for its survival.[35]
[edit] Nonfractionability
Robert Rosen (1991) built on the assumption that the explanatory powers of the mechanistic
worldview cannot help understand the realm of living systems. One of several important clarifications he
made was to define a system component as "a unit of organization; a part with a function, i.e., a definite
relation between part and whole." From this and other starting concepts, he developed a "relational theory of
systems" that attempts to explain the special properties of life. Specifically, he identified the
"nonfractionability of components in an organism" as the fundamental difference between living systems and
"biological machines."[36]
[edit] Life as a property of ecosystems
A systems view of life treats environmental fluxes and biological fluxes together as a "reciprocity of
influence",[37] and a reciprocal relation with environment is arguably as important for understanding life as it
is for understanding ecosystems. As Harold J. Morowitz (1992) explains it, life is a property of an ecological
system rather than a single organism or species.[38] He argues that an ecosystemic definition of life is
preferable to a strictly biochemical or physical one. Robert Ulanowicz (2009) also highlights mutualism as the
key to understand the systemic, order-generating behavior of life and ecosystems.[39]
[edit] Origin
Main article: Origin of life
For religious beliefs about the creation of life, see Creation myth.
Evidence suggests that life on Earth has existed for about 3.7 billion years.[40] All known life forms
share fundamental molecular mechanisms, and based on these observations, theories on the origin of life
attempt to find a mechanism explaining the formation of a primordial single cell organism from which all life
originates. There are many different hypotheses regarding the path that might have been taken from simple
organic molecules via pre-cellular life to protocells and metabolism. Many models fall into the "genes-first"
category or the "metabolism-first" category, but a recent trend is the emergence of hybrid models that
combine both categories.[41]
There is no scientific consensus as to how life originated and all proposed theories are highly
speculative. However, most currently accepted scientific models build in one way or another on the following
hypotheses:
• The Miller-Urey experiment, and the work of Sidney Fox, suggest that conditions on the
primitive Earth may have favored chemical reactions that synthesized some amino acids and other
organic compounds from inorganic precursors.
• Phospholipids spontaneously form lipid bilayers, the basic structure of a cell membrane.
Life as we know it today synthesizes proteins, which are polymers of amino acids using instructions
encoded by cellular genes—which are polymers of deoxyribonucleic acid (DNA). Protein synthesis also
entails intermediary ribonucleic acid (RNA) polymers. One possibility is that genes came first[42] and then
proteins. Another possibility is that proteins came first[43] and then genes. However, because genes are
required to make proteins, and proteins are required to make genes, the problem of considering which came
first is like that of the chicken or the egg. Most scientists have adopted the hypothesis that because DNA and
proteins function together so intimately, it's unlikely that they arose independently.[44] Therefore, many
scientists consider the possibility, apparently first suggested by Francis Crick,[45] that the first life was based
on the DNA-protein intermediary: RNA.[44] In fact, RNA has the DNA-like properties of information storage
and replication and the catalytic properties of some proteins. Crick and others actually favored the RNA-first
hypothesis[46] even before the catalytic properties of RNA had been demonstrated by Thomas Cech.[47]
A significant issue with the RNA-first hypothesis is that experiments designed to synthesize RNA
from simple precursors have not been nearly as successful as the Miller-Urey experiments that synthesized
other organic molecules from inorganic precursors. One reason for the failure to create RNA in the laboratory
is that RNA precursors are very stable and do not react with each other under ambient conditions. However,
the successful synthesis of certain RNA molecules under conditions hypothesized to exist prior to life on
Earth has been achieved by adding alternative precursors in a specified order with the precursor phosphate
present throughout the reaction.[48] This study makes the RNA-first hypothesis more plausible to many
scientists.[49]
Recent experiments have demonstrated true Darwinian evolution of unique RNA enzymes
(ribozymes) made up of two separate catalytic components that replicate each other in vitro.[50] In describing
this work from his laboratory, Gerald Joyce stated: "This is the first example, outside of biology, of
evolutionary adaptation in a molecular genetic system."[51] Such experiments make the possibility of a
primordial RNA World even more attractive to many scientists.
[edit] Conditions for life

The diversity of life on Earth today is a result of the dynamic interplay between genetic opportunity,
metabolic capability, environmental challenges,[52] and symbiosis.[53][54][55] For most of its existence,
Earth's habitable environment has been dominated by microorganisms and subjected to their metabolism
and evolution. As a consequence of such microbial activities on a geologic time scale, the physical-chemical
environment on Earth has been changing, thereby determining the path of evolution of subsequent life.[52]
For example, the release of molecular oxygen by cyanobacteria as a by-product of photosynthesis induced
fundamental, global changes in the Earth's environment. The altered environment, in turn, posed novel
evolutionary challenges to the organisms present, which ultimately resulted in the formation of our planet's
major animal and plant species. Therefore this "co-evolution" between organisms and their environment is
apparently an inherent feature of living systems.[52]
[edit] Range of tolerance

The inert components of an ecosystem are the physical and chemical factors necessary for life—
energy (sunlight or chemical energy), water, temperature, atmosphere, gravity, nutrients, and ultraviolet solar
radiation protection.[56] In most ecosystems the conditions vary during the day and often shift from one
season to the next. To live in most ecosystems, then, organisms must be able to survive a range of
conditions, called "range of tolerance."[57] Outside of that are the "zones of physiological stress," where the
survival and reproduction are possible but not optimal. Outside of these zones are the "zones of intolerance,"
where life for that organism is implausible. It has been determined that organisms that have a wide range of
tolerance are more widely distributed than organisms with a narrow range of tolerance.[57]
[edit] Extremophiles
Deinococcus radiodurans can resist radiation exposure.

Main article: Extremophile
To survive, some microorganisms can assume forms that enable them to withstand freezing,
complete desiccation, starvation, high-levels of radiation exposure, and other physical or chemical
challenges. Furthermore, some microorganisms can survive exposure to such conditions for weeks, months,
years, or even centuries.[52] Extremophiles are microbial life forms that thrive outside the ranges life is
commonly found in. They also excel at exploiting uncommon sources of energy. While all organisms are
composed of nearly identical molecules, evolution has enabled such microbes to cope with this wide range of
physical and chemical conditions. Characterization of the structure and metabolic diversity of microbial
communities in such extreme environments is ongoing. An understanding of the tenacity and versatility of life
on Earth, as well as an understanding of the molecular systems that some organisms utilize to survive such
extremes, will provide a critical foundation for the search for life beyond Earth.[52]
[edit] Chemical element requirements

All life forms require certain core chemical elements needed for biochemical functioning. This list of
core life elements usually includes carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—the "Big Six"
elemental macronutrients for all organisms[58] —often represented by the acronym CHNOPS. Together these
make up nucleic acids, proteins and lipids, the bulk of living matter.
However, alternative hypothetical types of biochemistry have been proposed which eliminate one or
more of these elements, swap out an element for one not on the list, or change required chiralities or other
chemical properties. For example, the recently discovered GFAJ-1 bacteria in Mono Lake, California may be
able to partially substitute phosphorus with arsenic, which is toxic to most forms of life.[59][60]
[edit] Classification of life

Main article: Biological classification
The hierarchy of biological classification's eight major taxonomic ranks, which is an example of
definition by genus and differentia. Life is divided into domains, which are subdivided into further groups.
Intermediate minor rankings are not shown.
Traditionally, people have divided organisms into the classes of plants and animals, based mainly on
their ability of movement. The first known attempt to classify organisms was conducted by the Greek
philosopher Aristotle (384–322 BC). He classified all living organisms known at that time as either a plant or
an animal. Aristotle distinguished animals with blood from animals without blood (or at least without red
blood), which can be compared with the concepts of vertebrates and invertebrates respectively. He divided
the blooded animals into five groups: viviparous quadrupeds (mammals), birds, oviparous quadrupeds
(reptiles and amphibians), fishes and whales. The bloodless animals were also divided into five groups:
cephalopods, crustaceans, insects (which also included the spiders, scorpions, and centipedes, in addition to
what we now define as insects), shelled animals (such as most molluscs and echinoderms) and "zoophytes."
Though Aristotle's work in zoology was not without errors, it was the grandest biological synthesis of the time
and remained the ultimate authority for many centuries after his death.[61]
The exploration of the American continent revealed large numbers of new plants and animals that
needed descriptions and classification. In the latter part of the 16th century and the beginning of the 17th,
careful study of animals commenced and was gradually extended until it formed a sufficient body of
knowledge to serve as an anatomical basis for classification.
In the late 1740s, Carolus Linnaeus introduced his method, still used, to formulate the scientific name
of every species.[62] Linnaeus took every effort to improve the composition and reduce the length of the
many-worded names by abolishing unnecessary rhetoric, introducing new descriptive terms and defining
their meaning with an unprecedented precision. By consistently using his system, Linnaeus separated
nomenclature from taxonomy. This convention for naming species is referred to as binomial nomenclature.
The fungi were originally treated as plants. For a short period Linnaeus had placed them in the taxon
Vermes in Animalia. He later placed them back in Plantae. Copeland classified the Fungi in his Protoctista,
thus partially avoiding the problem but acknowledged their special status.[63] The problem was eventually
solved by Whittaker, when he gave them their own kingdom in his five-kingdom system. As it turned out, the
fungi are more closely related to animals than to plants.[64]
As new discoveries enabled us to study cells and microorganisms, new groups of life were revealed,
and the fields of cell biology and microbiology were created. These new organisms were originally described
separately in protozoa as animals and protophyta/thallophyta as plants, but were united by Haeckel in his
kingdom protista, later the group of prokaryotes were split off in the kingdom Monera, eventually this kingdom
would be divided in two separate groups, the Bacteria and the Archaea, leading to the six-kingdom system
and eventually to the current three-domain system.[65] The classification of eukaryotes is still controversial,
with protist taxonomy especially problematic.[66]
As microbiology, molecular biology and virology developed, non-cellular reproducing agents were
discovered, such as viruses and viroids. Sometimes these entities are considered to be alive but others
argue that viruses are not living organisms since they lack characteristics such as cell membrane,
metabolism and do not grow or respond to their environments. Viruses can however be classed into
"species" based on their biology and genetics but many aspects of such a classification remain controversial.
[67]
Since the 1960s a trend called cladistics has emerged, arranging taxa in an evolutionary or
phylogenetic tree. It is unclear, should this be implemented, how the different codes will coexist.[68]
Linnaeus Haeckel Chatton Copeland Whittaker Woese et al.
1735[69] 1866[70] 1925[71][72] 1938[63][73] 1969[74] 1977[75][76]
2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 6 kingdoms
Eubacteria
Prokaryota Mychota Monera
(not Archaebacteria
Protista
treated)
Protoctista Protista Protista
Eukaryota Plantae Plantae Plantae

Vegetabilia Plantae
Protoctista Fungi Fungi
Animalia Animalia Animalia Animalia Animalia
[edit] Extraterrestrial life

Main articles: Extraterrestrial life and astrobiology
Panspermia hypothesis
Earth is the only planet in the universe known to harbor life. The Drake equation, which relates the
number of extraterrestrial civilizations in our galaxy with which we might come in contact, has been used to
discuss the probability of life elsewhere, but scientists disagree on many of the values of variables in this
equation. Depending on those values, the equation may either suggest that life arises frequently or
infrequently.
The region around a main sequence star that could support Earth-like life on an Earth-like planet is
known as the habitable zone. The inner and outer radii of this zone vary with the luminosity of the star, as
does the time interval during which the zone will survive. Stars more massive than the Sun have a larger
habitable zone, but will remain on the main sequence for a shorter time interval during which life can evolve.
Small red dwarf stars have the opposite problem, compounded with higher levels of magnetic activity and the
effects of tidal locking from close orbits. Hence, stars in the intermediate mass range such as the Sun may
possess the optimal conditions for Earth-like life to develop. The location of the star within a galaxy may also
have an impact on the likelihood of life forming.
Panspermia, also called exogenesis, is a hypothesis proposing that life originated elsewhere in the
universe and was subsequently transferred to Earth in the form of spores perhaps via meteorites, comets or
cosmic dust. However, this hypothesis does not help explain the ultimate origin of life.
[edit] Death
Main article: Death
Death is the permanent termination of all vital functions or life processes in an organism or cell.[78]
[79] After death, the remains of an organism become part of the biogeochemical cycle. Organisms may be
consumed by a predator or a scavenger and leftover organic material may then be further decomposed by
detritivores, organisms which recycle detritus, returning it to the environment for reuse in the food chain.
One of the challenges in defining death is in distinguishing it from life. Death would seem to refer to
either the moment at which life ends, or when the state that follows life begins.[80] However, determining
when death has occurred requires drawing precise conceptual boundaries between life and death. This is
problematic, however, because there is little consensus over how to define life. The nature of death has for
millennia been a central concern of the world's religious traditions and of philosophical inquiry. Many religions
maintain faith in either some kind of afterlife, reincarnation, or resurrection.
[edit] Extinction
Main article: Extinction
Extinction is the gradual process by which a group of taxa or species dies out, reducing biodiversity.
[81] The moment of extinction is generally considered to be the death of the last individual of that species.
Because a species' potential range may be very large, determining this moment is difficult, and is usually
done retrospectively after a period of apparent absence. Species become extinct when they are no longer
able to survive in changing habitat or against superior competition. Over the history of the Earth, over 99% of
all the species that have ever lived have gone extinct;[82] however, mass extinctions may have accelerated
evolution by providing opportunities for new groups of organisms to diversify.[83]
[edit] Fossils
Main article: Fossil
Fossils are the preserved remains or traces of animals, plants, and other organisms from the remote
past. The totality of fossils, both discovered and undiscovered, and their placement in fossil-containing rock
formations and sedimentary layers (strata) is known as the fossil record. Such a preserved specimen is
called a "fossil" if it is older than the arbitrary date of 10,000 years ago.[84] Hence, fossils range in age from
the youngest at the start of the Holocene Epoch to the oldest from the Archaean Eon, a few billion years old.
[edit] See also

• Alpha taxonomy • Life form
• Artificial life • Life on Mars
• Biological • Meaning of life
immortality • Nature
• Biology—the study • Non-cellular life
of life • Organic life
• Carbon-based life • Organism
• Cell • Origin of life
• Conway's Game • Personal life
of Life • Phylogenetics
• Entropy and life • Prehistoric life
• Evolutionary • Prion
history of life • Quality of life
• Extraterrestrial life • Silicon-based life
• Extremophile • Synthetic life
• Gaia hypothesis
• Genetics
• Genetic
engineering
• Hierarchy of life
• Kingdom (biology)
[edit] Notes
1. ^ The 'evolution' of viruses and other similar forms is still uncertain. Therefore, this
classification may be paraphyletic because cellular life might have evolved from non-cellular life, or
polyphyletic because the most recent common ancestor might not be included.
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http://www.webcitation.org/5kwsdvU8f.
79.^ Defining of death.
80.^ Encyclopedia of Death and Dying
81.^ "Extinction - definition". Archived from the original on 2009-10-31.
http://www.webcitation.org/5kwseRB80.
82.^ What is an extinction?
84.^ FAQs - San Diego Natural History Museum

• Kauffman, Stuart. The Adjacent Possible: A Talk with Stuart Kauffman
• Nealson KH, Conrad PG (December 1999). "Life: past, present and future". Philos. Trans. R.
Soc. Lond., B, Biol. Sci. 354 (1392): 1923–39. doi:10.1098/rstb.1999.0532. PMID 10670014.
PMC 1692713. http://journals.royalsociety.org/content/7r10hqn3rp1g1vag/.
• Walker, Martin G. LIFE! Why We Exist...And What We Must Do to Survive Dog Ear
Publishing, 2006, ISBN 1-59858-243-7

Wikimedia Commons has media related to: Tree of life
Wikiquote has a collection of quotations related to: Life
Look up life or living in Wiktionary, the free dictionary.
Wikispecies has information related to: The Taxonomy of Life
• Wikispecies - a free directory of life

• "The Adjacent Possible: A Talk with Stuart Kauffman"
• Stanford Encyclopedia of Philosophy entry
• Life under extreme conditions An in depth look at how life can form under the most extreme
conditions and circumstaces.

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Magnorder
Domain/Super Superphylum/
Superclass Superorder Superfam
kingdom Superdivision
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Domain (biology)

This article is about the "domain" rank in biological classification. For other uses, see Domain
(disambiguation).
It has been suggested that Three-domain system be merged into this article or
section. (Discuss)
definition by genus and differentia. Life is divided into domains, which are subdivided into further groups.
Intermediate minor rankings are not shown.
In biological taxonomy, a domain (also superregnum, superkingdom, or empire) is the highest
taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese,
introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya.[1] The
arrangement of taxa reflects the fundamental differences in the genomes. There are some alternative
classifications of life:[citation needed]
• The two-empire system or superdomain system, with top-level groupings of Prokaryota (or
Monera) and Eukaryota.
• The six-kingdom system with top-level groupings of Eubacteria, Archaebacteria, Protista,
Fungi, Plantae, and Animalia.[citation needed]
• The three-empire system (Eubacteria, Archaea, Eukarya) with five Supergroups in the
Eukarya[2]
None of the three systems currently include non-cellular life.[citation needed]
[edit] See also

• Phylogenetics
• Systematics
[edit] References
1. ^ Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal
for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci USA 87 (12): 4576–9.
doi:10.1073/pnas.87.12.4576. PMID 2112744. http://www.pnas.org/cgi/reprint/87/12/4576. Retrieved
11 February 2010.
2. ^ Holt, Jack R. and Carlos A. Iudica, 2010, Taxa of Life..
Magnorder
Phylum/Divisi
on
Infrakingdom/B
ranch

Retrieved from "http://en.wikipedia.org/wiki/Domain_(biology)"
Categories: Scientific classification

W000
Kingdom (biology)

definition by genus and differentia. A domain contains one or more kingdoms. Intermediate minor rankings
are not shown.
In biology, kingdom (Latin: regnum, pl. regna) is a taxonomic rank, which is either the highest rank or
in the more recent three-domain system, the rank below domain. Kingdoms are divided into smaller groups
called phyla (in zoology) or divisions in botany. The complete sequence of ranks is life, domain, kingdom,
phylum, class, order, family, genus, and species.
Currently, textbooks from the United States use a system of six kingdoms (Animalia, Plantae, Fungi,
Protista, Archaea, Bacteria) while British, Australian and Latin American textbooks may describe five
kingdoms (Animalia, Plantae, Fungi, Protista, and Prokaryota or Monera).
Historically, the number of kingdoms in widely accepted classifications has grown from two to six.
However, phylogenetic research from about 2000 onwards does not support any of the traditional systems.
Contents
[hide]
• 1 Two kingdoms
• 2 Three kingdoms
• 3 Four kingdoms
• 4 Five kingdoms
• 5 Six kingdoms
• 6 Cavalier-Smith's six kingdoms
• 7 International Society of Protistologists Classification 2005
• 8 Summary
• 9 See also
• 10 References
[edit] Two kingdoms

The classification of living things into animals and plants is an ancient one. Aristotle (384 BC–322 BC)
classified animal species in his work the History of Animals, and his pupil Theophrastus (c. 371–c. 287 BC)
wrote a parallel work on plants (the History of Plants).[1]
Carolus Linnaeus (1707–1778) laid the foundations for modern biological nomenclature, now
regulated by the Nomenclature Codes. He distinguished two kingdoms of living things: Regnum Animale
('animal kingdom') for animals and Regnum Vegetabile ('vegetable kingdom') for plants. (Linnaeus also
included minerals, placing them in a third kingdom, Regnum Lapideum.) Linnaeus divided each kingdom into
classes, later grouped into phyla for animals and divisions for plants.
life
Regnum Vegetabile
Regnum Animale
[edit] Three kingdoms

In 1674, Antonie van Leeuwenhoek, often called the "father of microscopy", sent the Royal Society of
London a copy of his first observations of microscopic single-celled organisms. Up to the last few decades,
the existence of such microscopic organisms was entirely unknown. At first these organisms were divided
into animals and plants and placed in the appropriate Kingdom. However, by the mid-19th century it had
become clear that "the existing dichotomy of the plant and animal kingdoms [had become] rapidly blurred at
its boundaries and outmoded".[2] In 1866, following earlier proposals by Richard Owen and John Hogg, Ernst
Haeckel proposed a third kingdom of life. Haeckel revised the content of this kingdom a number of times
before settling on a division based on whether organisms were unicellular (Protista) or multicellular (animals
and plants).[2]
life
Kingdom Protista
Kingdom Plantae
Kingdom Animalia
[edit] Four kingdoms
The development of microscopy, and the electron microscope in particular, revealed an important
distinction between those unicellular organisms whose cells do not have a distinct nucleus, prokaryotes, and
those unicellular and multicellular organisms whose cells do have a distinct nucleus, eukaryotes. In 1938,
Herbert F. Copeland proposed a four-kingdom classification, moving the two prokaryotic groups, bacteria and
"blue-green algae", into a separate Kingdom Monera.[2]
life
Kingdom Monera (prokaryotes, i.e. bacteria and "blue-green
algae")
Kingdom Protista (single-celled eukaryotes)
Kingdom Plantae
Kingdom Animalia
It gradually became apparent how important the prokaryote/eukaryote distinction is, and Stanier and
van Niel popularized Édouard Chatton's proposal in the 1960s to recognize this division in a formal
classification. This required the creation, for the first time, of a rank above kingdom, a superkingdom or
empire, also called a domain.[3]
life
Empire Prokaryota
Kingdom Protista
Kingdom Plantae
Kingdom Animalia
[edit] Five kingdoms
The differences between fungi and other organisms regarded as plants had long been recognized.
For example, at one point Haeckel moved the fungi out of Plantae into Protista, before changing his mind.[2]
Robert Whittaker recognized an additional kingdom for the Fungi. The resulting five-kingdom system,
proposed in 1969 by Whittaker, has become a popular standard and with some refinement is still used in
many works and forms the basis for new multi-kingdom systems. It is based mainly on differences in
nutrition; his Plantae were mostly multicellular autotrophs, his Animalia multicellular heterotrophs, and his
Fungi multicellular saprotrophs. The remaining two kingdoms, Protista and Monera, included unicellular and
simple cellular colonies.[4] The five kingdom system may be combined with the two empire system.
life
Empire Prokaryota
Kingdom Monera
Empire Eukaryota
Kingdom Protista
Kingdom Plantae
Kingdom Fungi
Kingdom Animalia
[edit] Six kingdoms
From around the mid-1970s onwards, there was an increasing emphasis on molecular level
comparisons of genes (initially ribosomal RNA genes) as the primary factor in classification; genetic similarity
was stressed over outward appearances and behavior. Taxonomic ranks, including kingdoms, were to be
groups of organisms with a common ancestor, whether monophyletic (all descendants of a common
ancestor) or paraphyletic (only some descendants of a common ancestor). Based on such RNA studies, Carl
Woese divided the prokaryotes (Kingdom Monera) into two groups, called Eubacteria and Archaebacteria,
stressing that there was as much genetic difference between these two groups as between either of them
and all eukaryotes. Eukaryote groups, such as plants, fungi and animals may look different, but are more
similar to each other in their genetic makeup at the molecular level than they are to either the Eubacteria or
Archaebacteria. (It was also found that the eukaryotes are more closely related, genetically, to the
Archaebacteria than they are to the Eubacteria.) Although the primacy of the eubacteria-archaebacteria
divide has been questioned, it has also been upheld by subsequent research.[5]
Woese attempted to establish a "three primary kingdom" or "urkingdom" system.[6] In 1990, the
name "domain" was proposed for the highest rank.[7] The six-kingdom system shown below represents a
blending of the classic five-kingdom system and Woese's three-domain system. Such six-kingdom systems
have become standard in many works.
life
Domain Bacteria
Kingdom Bacteria
Domain Archaea
Kingdom Archaea
Domain Eukarya
Kingdom Protista
Kingdom Plantae
Kingdom Fungi
Kingdom Animalia
Woese also recognized that the Protista kingdom was not a monophyletic group and might be further
divided at the level of kingdom.
[edit] Cavalier-Smith's six kingdoms

Thomas Cavalier-Smith has published extensively on the evolution and classification of life,
particularly protists. His views have been influential but controversial, and not always widely accepted.[8] In
1998, he published a six-kingdom model,[9] which has been revised in subsequent papers. The version
published in 2009 is shown below.[10] (Compared to the version he published in 2004,[11] the alveolates and
the rhizarians have been moved from Kingdom Protozoa to Kingdom Chromista.) Cavalier-Smith does not
accept the importance of the fundamental eubacteria–archaebacteria divide put forward by Woese and others
and supported by recent research.[5] His Kingdom Bacteria includes the Archaebacteria as part of a
subkingdom along with a group of eubacteria (Posibacteria). Nor does he accept the requirement for groups
to be monophyletic. His Kingdom Protozoa includes the ancestors of Animalia and Fungi. Thus the diagram
below does not represent an evolutionary tree.
life
Empire Prokaryota
Kingdom Bacteria — includes Archaebacteria as part of a
subkingdom
Empire Eukaryota
Kingdom Protozoa — e.g. Amoebozoa, Choanozoa,
Excavata
Kingdom Chromista — e.g. Alveolata, cryptophytes,
Heterokonta (stramenopiles), Haptophyta, Rhizaria
Kingdom Plantae — e.g. glaucophytes, red and green algae,

land plants
Kingdom Fungi
Kingdom Animalia
See also: Thomas Cavalier-Smith

[edit] International Society of Protistologists Classification 2005
One hypothesis of eukaryotic relationships, modified from Simpson and Roger (2004).
The "classic" six-kingdom system is still recognizably a modification of the original two-kingdom
system: Animalia remains; the original category of plants has been split into Plantae and Fungi; and single-
celled organisms have been introduced and split into Bacteria, Archaea and Protista.
Research published in the 21st century has produced a rather different picture. In 2004, a review
article by Simpson and Roger noted that the Protista were "a grab-bag for all eukaryotes that are not animals,
plants or fungi". They argued that only monophyletic groups–an ancestor and all of its descendents — should
be accepted as formal ranks in a classification. On this basis, the diagram opposite (redrawn from their
article) showed the real "kingdoms" (their quotation marks) of the eukaryotes.[12] A classification produced in
2005 for the International Society of Protistologists, which reflected the consensus of the time[ citation
needed], followed this approach, dividing the eukaryotes into the same six "supergroups".[13] Although the
published classification deliberately did not use formal taxonomic ranks, other sources[ citation needed] have
treated each of the six as a separate Kingdom.
life
Domain Bacteria
Bacteria
Domain Archaea
Archaea
Domain Eukarya
Excavata — Various flagellate protozoa
Amoebozoa — most lobose amoeboids and slime moulds
Opisthokonta — animals, fungi, choanoflagellates, etc.
Rhizaria — Foraminifera, Radiolaria, and various other

amoeboid protozoa
Chromalveolata — Stramenopiles (or Heterokonta),

Haptophyta, Cryptophyta (or cryptomonads), and Alveolata
Archaeplastida (or Primoplantae) — Land plants, green

algae, red algae, and glaucophytes
In this system, the traditional kingdoms have vanished. For example, research shows that the
multicellular animals (Metazoa) are descended from the same ancestor as the unicellular choanoflagellates
and the fungi. A classification system which places these three groups into different kingdoms (with
multicellular animals forming Animalia, choanoflagellates part of Protista and Fungi a separate kingdom) is
not monophyletic. The monophyletic group is the Opisthokonta, made up of all those organisms believed to
have descended from a common ancestor, some of which are unicellular (choanoflagellates), some of which
are multicellular but not closely related to animals (some fungi), and others of which are traditional
multicellular animals.[13]
However, in the same year as the International Society of Protistologists' classification was published
(2005), doubts were being expressed as to whether some of these supergroups were monophyletic,
particularly the Chromalveolata,[14] and a review in 2006 noted the lack of evidence for several of the
supposed six supergroups.[15]
As of 2010[update], there is widespread agreement that the Rhizaria belong with the Stramenopiles
and the Alveolata, in a clade dubbed the SAR supergroup[citation needed], so that Rhizara is not one of the
main eukaryote groups.[10][16][17][18][19] Beyond this, there does not appear to be a consensus. Rogozin
et al. in 2009 noted that "The deep phylogeny of eukaryotes is an extremely difficult and controversial
problem."[20] As of December 2010[update], there appears to be a consensus that the 2005 six supergroup
model does not reflect the true phylogeny of the eukaryotes and hence how they should be classified,
although there is no agreement as to the model which should replace it.[17][21][22]
[edit] Summary
The sequence from the two-kingdom system up to Cavalier-Smith's six-kingdom system can be
summarized in the table below.
Linnaeus Haeckel Chatton Copeland Whittaker Woese et al.

1735[23] 1866[24] 1925[25][26] 1938[27][28] 1969[4] 1977[6][29]
2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 6 kingdoms
(not Protista Eubacteria

treated) Prokaryota Mychota Monera
Archaebacteria
Eukaryota Protoctista Protista Protista

Plantae Plantae Plantae
Vegetabilia Plantae
Protoctista Fungi Fungi
Animalia Animalia Animalia Animalia Animalia

Note that the equivalences in this table are not perfect. For example, Haeckel placed the red algae
(his Florideae, modern Florideophyceae) and blue-green algae (his Archephyta, modern Cyanobacteria) in
his Plantae.
One or other of the kingdom-level classifications of life is still widely employed as a useful way of
grouping organisms, notwithstanding the problems with this approach:
• Kingdoms such as Bacteria represent grades rather than clades, and so are rejected by
phylogenetic classification systems.
• Research in the 21st century does not support the classification of the eukaryotes into any of
the standard systems. As of April 2010[update], the situation appears to be that there is no set of
kingdoms sufficiently supported by current research to gain widespread acceptance; as Roger &
Simpson say: "with the current pace of change in our understanding of the eukaryote tree of life, we
should proceed with caution."[31]
[edit] See also

• Cladistics
• Systematics
[edit] References
1. ^ Singer, Charles J. (1931), A short history of biology, a general introduction to the study of
living things, Oxford: Clarendon Press, OCLC 1197036
2. ^ a b c d Scamardella, Joseph M. (1999), "Not plants or animals: a brief history of the origin of
Kingdoms Protozoa, Protista and Protoctista", International Microbiology 2 (4): 207–16,
PMID 10943416
3. ^ Stanier, R.Y. & Van Neil, C.B. (1962), "The concept of a bacterium", Archiv Für
Mikrobiologie 42: 17–35, doi:10.1007/BF00425185, PMID 13916221
4. ^ a b Whittaker, R.H. (January 1969), "New concepts of kingdoms or organisms. Evolutionary
relations are better represented by new classifications than by the traditional two kingdoms", Science
163 (863): 150–60, PMID 5762760, http://www.sciencemag.org/cgi/pmidlookup?
view=long&pmid=5762760
5. ^ a b Dagan, T.; Roettger, M.; Bryant, D & Martin, W. (2010), "Genome Networks Root the
Tree of Life between Prokaryotic Domains", Genome Biology and Evolution 2:: 379–92,
doi:doi:10.1093/gbe/evq025
6. ^ a b Balch, W.E.; Magrum, L.J.; Fox, G.E.; Wolfe, C.R.; & Woese, C.R. (August 1977), "An
ancient divergence among the bacteria", J. Mol. Evol. 9 (4): 305–11, doi:10.1007/BF01796092,
PMID 408502
7. ^ Woese, C.R.; Kandler, O. & Wheelis, M. (1990), "Towards a natural system of organisms:
proposal for the domains Archaea, Bacteria, and Eucarya", Proc Natl Acad Sci U S A 87 (12): 4576–
9, doi:10.1073/pnas.87.12.4576, PMID 2112744
8. ^ Palaeos.com, Origins of the Eukarya, archived from the original on 2010-04-29,
http://www.webcitation.org/5pLfYf6U7, retrieved 2010-04-29
9. ^ Cavalier-Smith, T. (1998), "A revised six-kingdom system of life", Biological Reviews 73
(03): 203–66, doi:10.1017/S0006323198005167,
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=685
10.^ a b Cavalier-Smith, Thomas (2009), "Kingdoms Protozoa and Chromista and the eozoan
root of the eukaryotic tree", Biology Letters 6: 342–5, doi:10.1098/rsbl.2009.0948
11.^ a b Cavalier-Smith, T. (2004), "Only six kingdoms of life", Proc. R. Soc. Lond. B 271 (1545):
1251–62, doi:10.1098/rspb.2004.2705, PMID 15306349, PMC 1691724,
http://www.cladocera.de/protozoa/cavalier-smith_2004_prs.pdf, retrieved 2010-04-29
12.^ Simpson, Alastair G.B. & Roger, Andrew J. (2004), "The real ‘kingdoms’ of eukaryotes",
Current Biology 14 (17): R693–6, doi:10.1016/j.cub.2004.08.038, PMID 15341755
13.^ a b Adl, Sina M.; et al. (2005), "The New Higher Level Classification of Eukaryotes with
Emphasis on the Taxonomy of Protists", Journal of Eukaryotic Microbiology 52 (5): 399,
doi:10.1111/j.1550-7408.2005.00053.x, http://www.blackwell-synergy.com/doi/abs/10.1111/j.1550-
7408.2005.00053.x
14.^ Harper, J.T.; Waanders, E. & Keeling, P. J. (2005), "On the monophyly of chromalveolates
using a six-protein phylogeny of eukaryotes", Nt. J. System. Evol. Microbiol. 55 (Pt 1): 487–496,
doi:10.1099/ijs.0.63216-0, PMID 15653923,
http://www.botany.ubc.ca/keeling/PDF/05chromalvJSEM.pdf
15.^ Parfrey, Laura W.; Barbero, Erika; Lasser, Elyse; Dunthorn, Micah; Bhattacharya,
Debashish; Patterson, David J. & Katz, Laura A. (2006), "Evaluating Support for the Current
Classification of Eukaryotic Diversity", PLoS Genet. 2 (12): e220, doi:10.1371/journal.pgen.0020220,
PMID 17194223, PMC 1713255, http://www.pubmedcentral.nih.gov/articlerender.fcgi?
tool=pmcentrez&artid=1713255
16.^ Fabien Burki, Kamran Shalchian-Tabrizi, Marianne Minge, Åsmund Skjæveland, Sergey I.
Nikolaev, Kjetill S. Jakobsen, Jan Pawlowski (2007). "Phylogenomics Reshuffles the Eukaryotic
Supergroups". PLoS ONE 2 (8): e790. doi:10.1371/journal.pone.0000790. PMID 17726520.
PMC 1949142. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000790.
17.^ a b Burki, Fabien; Shalchian-Tabrizi, Kamran; Pawlowski, Jan (2008). "Phylogenomics
reveals a new 'megagroup' including most photosynthetic eukaryotes". Biology Letters 4 (4): 366–
369. doi:10.1098/rsbl.2008.0224. PMID 18522922.
18.^ Burki, F. et al. (2009), "Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic
Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates",
Genome Biology and Evolution 1: 231–8, doi:10.1093/gbe/evp022
19.^ Hackett, J.D.; Yoon, H.S.; Li, S.; Reyes-Prieto, A.; Rummele, S.E. & Bhattacharya, D.
(2007), "Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the
association of Rhizaria with chromalveolates", Mol. Biol. Evol. 24: 1702–13,
doi:10.1093/molbev/msm089
20.^ Rogozin, I.B.; Basu, M.K.; Csürös, M. & Koonin, E.V. (2009), "Analysis of Rare Genomic
Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis
as the Point of Primary Radiation of Eukaryotes", Genome Biology and Evolution 1: 99–113,
doi:10.1093/gbe/evp011
21.^ Burki, Fabien; Shalchian-Tabrizi, Kamran; Minge, Marianne; Skjæveland, Åsmund;
Nikolaev, Sergey I.; Jakobsen, Kjetill S. & Pawlowski, Jan (2007), "Phylogenomics Reshuffles the
Eukaryotic Supergroups", PLoS ONE 2 (8): e790, doi:10.1371/journal.pone.0000790,
PMID 17726520, PMC 1949142, http://www.plosone.org/article/info%3Adoi
%2F10.1371%2Fjournal.pone.0000790
22.^ Kim, E.; Graham, L.E. & Redfield, Rosemary Jeanne (2008), "EEF2 analysis challenges the
monophyly of Archaeplastida and Chromalveolata", PLoS ONE 3 (7): e2621,
doi:10.1371/journal.pone.0002621, PMID 18612431
23.^ C. Linnaeus (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per
classes, ordines, genera & species.
24.^ E. Haeckel (1866). Generelle Morphologie der Organismen. Reimer, Berlin.
25.^ É. Chatton (1925). "Pansporella perplexa. Réflexions sur la biologie et la phylogénie des
protozoaires". Ann. Sci. Nat. Zool 10-VII: 1–84.
26.^ É. Chatton (1937). Titres et Travaux Scientifiques (1906–1937). Sette, Sottano, Italy.
27.^ H. Copeland (1938). "The kingdoms of organisms". Quarterly review of biology 13: 383–
420. doi:10.1086/394568.
28.^ H. F. Copeland (1956). The Classification of Lower Organisms . Palo Alto: Pacific Books.
29.^ Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain:
the primary kingdoms". Proc. Natl. Acad. Sci. U.S.A. 74 (11): 5088–90. PMID 270744.
30.^ Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal
for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci U S A 87 (12): 4576–9.
doi:10.1073/pnas.87.12.4576. PMID 2112744. PMC 54159.
31.^ Roger, A.J. & Simpson, A.G.B. (2009), "Evolution: Revisiting the Root of the Eukaryote
Tree", Current Biology 19 (4): R165–7, doi:10.1016/j.cub.2008.12.032, PMID 19243692

• The five kingdom concept
• Whittaker's classification

Magnorder
Phylum/Divisi
on
Infrakingdom/B
ranch
Retrieved from "http://en.wikipedia.org/wiki/Kingdom_(biology)"
Categories: Scientific classification | Botanical nomenclature | Zoological nomenclature

W000
Phylum

For other uses, see Phyla.
definition by genus and differentia. A kingdom contains one or more phyla. Intermediate minor rankings are
not shown.
In biology, a phylum ( /ˈfaɪləm/; plural: phyla)[note 1] is a taxonomic rank below Kingdom and above
Class. "Phylum" is equivalent to the botanical term division.[1] The Kingdom Animalia contains approximately
forty phyla. The relationships among phyla are becoming increasingly well known, and larger clades can be
found to contain many of the phyla.
Contents
[hide]
• 1 General description and familiar examples
• 2 Defining a phylum
• 2.1 Definition based on genetic relation
• 2.2 Definition based on body plan
• 3 Lists
• 3.1 Animal phyla
• 3.2 Groups formerly ranked as phyla
• 3.3 Plant divisions
• 3.4 Fungal divisions
• 3.5 Bacterial Phyla/Divisions
• 3.6 Archaeal Phyla/Division
• 4 See also
• 5 Notes
• 6 References
[edit] General description and familiar examples
Informally, phyla can be thought of as grouping organisms based on general body plan,[2] as well as
developmental or internal organizations.[3] For example, though seemingly divergent, spiders and crabs both
belong to Arthropoda, whereas earthworms and tapeworms, similar in shape, are from Annelida and
Platyhelminthes, respectively. Although the International Code of Botanical Nomenclature allows the use of
the term "phylum" in reference to plants, the term "Division" is almost always used by botanists.
The best known animal phyla are the Mollusca, Porifera, Cnidaria, Platyhelminthes, Nematoda,
Annelida, Arthropoda, Echinodermata, and Chordata, the phylum to which humans belong, along with all
other vertebrate species, as well as some invertebrates such as the lamprey. Although there are 36 animal
phyla, these nine include over 96% of animal species. Many phyla are exclusively marine, and only one
phylum, the Onychophora (velvet worms) is entirely absent from the world's oceans—although ancestral
onycophorans were marine.[4]
[edit] Defining a phylum

At the most basic level, a phylum can be defined in two ways: as a group of organisms with a certain
degree of morphological or developmental similarity (the phenetic definition), or a group of organisms with a
certain degree of evolutionary relatedness (the phylogenetic definition).[5] Attempting to define a level of the
Linnean hierarchy without referring to (evolutionary) relatedness is an unsatisfactory approach, but the
phenetic definition is more useful when addressing questions of a morphological nature—such as how
successful different body plans were.
[edit] Definition based on genetic relation
The largest objective measure in the above definitions is the "certain degree"—how unrelated do
organisms need to be to be members of different phyla? The minimal requirement is that all organisms in a
phylum should be related closely enough for them to be clearly more closely related to one another than to
any other group.[5] However, even this is problematic, as the requirement depends on our current knowledge
about organisms' relationships: As more data becomes available, particularly from molecular studies, we are
better able to judge the relationships between groups. So phyla can be merged or split if it becomes apparent
that they are related to one another or not; for example, since the onychophora and the tardigrada have now
been accepted as stem groups of the arthropods, these three phyla should be combined.
This changeability of phyla has led some biologists to call for the concept of a phylum to be
abandoned in favour of cladistics, a method in which groups are placed on a "family tree" without any formal
ranking of group size.[5] So as to provide a handle on the size and significance of groups, a "body-plan"
based definition of a phylum has been proposed by paleontologists Graham Budd and Sören Jensen. The
definition was posited by paleontologists because it is extinct organisms that are typically hardest to classify,
because they can be extinct off-shoots that diverged from a phylum's history before the characters that define
the modern phylum were all acquired.
[edit] Definition based on body plan

By Budd and Jensen's definition, phyla are defined by a set of characters shared by all their living
representatives. This has a couple of small problems—for instance, characters common to most members of
a phylum may be secondarily lost by some members. It is also defined based on an arbitrary point of time
(the present). However, as it is character based, it is easy to apply to the fossil record. A more major problem
is that it relies on an objective decision of which group of organisms should be considered a phylum.
Its utility is that it makes it easy to classify extinct organisms as "stem groups" to the phyla with which
they bear the most resemblance, based only on the taxonomically important similarities.[5] However, proving
that a fossil belongs to the crown group of a phylum is difficult, as it must display a character unique to a sub-
set of the crown group.[5] Further, organisms in the stem group to a phylum can bear all the aspects of the
"body plan" of the phylum without all the characters necessary to fall within it. This weakens the idea that
each of the phyla represents a distinct body plan.[6]
Based upon this definition, which some say is unreasonably affected by the chance survival of rare
groups, which vastly increase the size of phyla, representatives of many modern phyla did not appear until
long after the Cambrian.[7]
[edit] Lists
[edit] Animal phyla
Distinguishing Species
Phylum Meaning Common Name
characteristic described
Thorny Thorny-headed Reversible

Acanthocephala about 756
headed worms worms spiny proboscis
Acoelomorpha Without Acoels No mouth or

gut alimentary canal
(alimentary canal =
digestive tract in
digestive system)
Segmented Multiple about

Annelida Little ring
worms circular segment 16,300 modern
Jointed Chitin 1,134,000

Arthropoda Arthropods
foot exoskeleton +
between
Lophophore
Brachiopoda Arm foot Lamp shells 300 and 500
and pedicle
extant
Lophophore, about
Moss Moss animals,
Bryozoa no pedicle, ciliated 5,000 living
animals sea mats
tentacles species
Chitinous
Longhair about 100
Chaetognatha Arrow worms spines either side of
jaw modern species
head, fins
Hollow dorsal
nerve cord, notochord,
about
Chordata Cord Chordates pharyngeal slits,
100,000+
endostyle, post-anal
tail
Stinging Nematocysts about
Cnidaria Coelenterates
nettle (stinging cells) 11,000
Comb Eight "comb about 100

Ctenophora Comb jellies
bearer rows" of fused cilia modern species
Circular mouth
Wheel
Cycliophora Symbion surrounded by small at least 3
carrying
cilia
Fivefold radial about

Spiny symmetry in living 7,000 extant and
Echinodermata Echinoderms
skin forms, mesodermal 13,000 extinct
calcified spines species
Set of hooks
Echiura Spine tail Spoon worms about 140
at posterior end
Inside Anus inside

Entoprocta Goblet worm about 150
anus ring of cilia
Hair Two terminal

Gastrotricha Meiofauna about 690
stomach adhesive tubes
Jaw
Gnathostomulida Jaw worms about 100
orifice
Acorn worms, Stomochord in about 100
Hemichordata Half cord
pterobranchs collar, pharyngeal slits living species
Eleven
Motion
Kinorhyncha Mud dragons segments, each with a about 150
snout
dorsal plate
Corset Umbrella-like
Loricifera Brush heads about 122
bearer scales at each end
Tiny jaw Accordion like

Micrognathozoa — 1
animals extensible thorax
Thin Mollusks / Muscular foot

Mollusca 112,000[8]
shell molluscs and mantle round shell
Thread Round cross 80,000–

Nematoda Round worms
like section, keratin cuticle 1,000,000
Thread Horsehair
Nematomorpha about 320
form worms
A sea about
Nemertea Ribbon worms
nymph 1,200
Onychophora Claw Velvet worms Legs tipped by about 200

bearer chitinous claws modern
Single layer of
Straight ciliated cells
Orthonectida about 20
swim surrounding a mass of
sex cells
Zeus's Horseshoe
Phoronida U-shaped gut 20
mistress worms
Plate
Placozoa 1
animals
Flat about
Platyhelminthes Flat worms
worms 25,000[9]
Pore Perforated over 5,000

Porifera Sponges
bearer interior wall modern
Little
Priapulida 16
Priapus
Single axial
Lozenge
Rhombozoa — cell surrounded by 75
animal
ciliated cells
Rotifera Wheel Rotifers Anterior crown about

bearer of cilia 2,000
Mouth
Small
Sipuncula Peanut worms surrounded by 144–320
tube
invertible tentacles
Four
Slow
Tardigrada Water bears segmented body and 1,000+
step
head
Strange Ciliated
Xenoturbellida — 2
flatworm deuterostome
Total: 36 2,000,000-
Protostome
Deuterostome Bilateria
Basal/disputed
Other
[edit] Groups formerly ranked as phyla

Name as phylum Common name Current consensus
Divided into several pseudocoelomate
Aschelminthes Pseudocoelomates
phyla.
Subgroup of phylum Chordata; perhaps

Craniata —
synonymous with Vertebrata.
Cephalochordata Lancelets Subphylum of phylum Chordata.
Cephalorhyncha — Superphylum Scalidophora.
Enterepneusta Acorn worms Class of phylum Hemichordata.
Peanut worms and Divided into phyla Sipuncula and

Gephyra
spoon worms Echiura.
Divided into phyla Orthonectida and

Mesozoa Mesozoans
Rhombozoa.
Myxozoa Severely modified Cnidarians.
Subclass of Maxillopoda of phylum

Pentastomida Tongue worms
Arthropoda.
Part of family Siboglinidae of phylum

Pogonophora Beard worms
Annelida.
Pterobranchia — Class of phylum Hemichordata.

Class Hexactinellida of phylum
Symplasma Glass sponges
Porifera.
Urochordata Tunicates Subphylum of phylum Chordata.
Part of family Siboglinidae of phylum

Vestimentifera Vent worms
Annelida.
[edit] Plant divisions

Distinguishing
Division Meaning Common name
characteristics
Horn-shaped
Flower-horn
Anthocerotophyta Hornworts sporophytes, no vascular
plants
system
Persistent
Bryophyta Moss plants Mosses unbranched sporophytes,
no vascular system
Ephemeral
Marchantia
Marchantiophyta Liverworts unbranched sporophytes,
plants
no vascular system
Lycopodiophyta Wolf foot Clubmosses & Microphyll leaves,

plants Spikemosses vascular system
Prothallus
Ferns &
Pteridophyta Fern plants gametophytes, vascular
Horsetails
system
Only known from

Fern with
Pteridospermatophyta Seed ferns fossils, mostly Devonian,
seeds plant
ranking in dispute[10]
Cones containing
Sap/pitch
Coniferophyta Conifers seeds and wood composed
plants
of tracheids
Seeds, crown of
Cycadophyta Palm plants Cycads
compound leaves
Seeds not
Ginkgo Ginkgo,
Ginkgophyta protected by fruit (single
plants Maidenhair
species)
Seeds and woody

Gnetophyta Gnetophytes vascular system with
vessels
Anthophyta (or Flower plant Flowering plants Flowers and fruit,

vascular system with
Magnoliophyta)
vessels
[edit] Fungal divisions

Common Distinguishing
Phylum Meaning
name characteristics
Little pot Cellulose in cell walls,

Chytridiomycota Chytrids
mushroom flagellated gametes
Second Imperfect Unclassified fungi; only

Deuteromycota
mushroom fungi asexual reproduction observed
Yolk Blend gametangia to form

Zygomycota Zygomycetes
mushroom a zygosporangium
Ball Form arbuscular

Glomeromycota None
mushroom mycorrhizae with plants
Bag/Wineskin Produce spores in an

Ascomycota Sac fungi
Mushroom 'ascus'
Basidium Produce spores from a

Basidiomycota Club Fungi
Mushroom 'basidium'
[edit] Bacterial Phyla/Divisions
Main article: Bacterial phyla
Currently there are 29 phyla accepted by LPSN[11]
1. Acidobacteria, phenotipically diverse and mostly uncultured
2. Actinobacteria, High-G+C Gram positive species
3. Aquificae, only 14 thermophilic genera, deep branching
4. Bacteroidetes
5. Caldiserica, formerly candidate division OP5, Caldisericum exile is the sole representative
6. Chlamydiae, only 6 genera
7. Chlorobi, only 7 genera
8. Chloroflexi,
9. Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila,
Desulfurispirillum alkaliphilum)
10.Cyanobacteria, also known as the blue-green algae
11.Deferribacteres
12.Deinococcus-Thermus, Deinococcus radiodurans and Thermus aquaticus are "commonly
known" species of this phyla
13.Dictyoglomi
14.Elusimicrobia, formerly candidate division Thermite Group 1
15.Fibrobacteres
16.Firmicutes, Low-G+C Gram positive species, such as the spore-formers Bacilli (aerobic) and
Clostridia (anaerobic)
17.Fusobacteria
18.Gemmatimonadetes
19.Lentisphaerae, formerly clade VadinBE97
20.Nitrospira
21.Planctomycetes
22.Proteobacteria, the most know phyla, containing most of the "commonly known" species,
such as Escherichia coli or Pseudomonas aeruginosa
23.Spirochaetes, species include Borrelia burgdorferi, which causes Lyme disease
24.Synergistetes
25.Tenericutes, alternatively class Mollicutes in phylum Firmicutes (notable genus:
Mycoplasma)
26.Thermodesulfobacteria
27.Thermomicrobia
28.Thermotogae, deep branching
29.Verrucomicrobia
[edit] Archaeal Phyla/Division

1. Crenarchaeota, Second most common archaeal phylum
2. Euryarchaeota, most common archaeal phylum
3. Korarchaeota
4. Nanoarchaeota, ultra-small symbiotes
5. Thaumarchaeota
[edit] See also
Biology portal
• Cladistics
• Phylogenetics
• Systematics
• Taxonomy
[edit] Notes
1. ^ The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to
φυλή phyle, "tribe, clan."
[edit] References
1. ^ "Life sciences". The American Heritage New Dictionary of Cultural Literacy (third ed.).
Houghton Mifflin Company. 2005. http://dictionary.reference.com/browse/phylum. Retrieved 2008-10-
04. "Phyla in the plant kingdom are frequently called divisions."
2. ^ Valentine, James W. (2004). On the Origin of Phyla. Chicago: University Of Chicago Press.
pp. 7. ISBN 0226845486. "Classifications of organisms in hierarchical systems were in use by the
seventeenth and eighteenth centuries. Usually organisms were grouped according to their what?
morphological similarities as perceived by those early workers, and those groups were then grouped
according to their similarities, and so on, to form a hierarchy."
3. ^ Parker, Andrew (2003). In the blink of an eye: How vision kick-started the big bang of
evolution. Sydney: Free Press. pp. 1–4. ISBN 0743257332. "The job of an evolutionary biologist is to
create dinosaurs for the devil to consume, make sense of the conflicting diversity of form — there is
not always a relationship between internal and external parts. Early in the history of the subject, it
became obvious that internal organisations were generally more important to the higher classification
of animals than are external shapes. The internal organisation puts general restrictions on how an
animal can exchange gases, obtain nutrients and reproduce."
4. ^ Davidson, E. H; Erwin, D. H (2006). "Gene Regulatory Networks and the Evolution of
Animal Body Plans". Science (American Association for the Advancement of Science) 311 (5762):
796–800. doi:10.1126/science.1113832. PMID 16469913.
http://www.sciencemag.org/cgi/content/abstract/311/5762/796.
5. ^ a b c d e Budd, G.E.; Jensen, S. (2000). "A critical reappraisal of the fossil record of the
bilaterian phyla". Biological Reviews 75 (02): 253–295. doi:10.1017/S000632310000548X.
PMID 10881389. http://www.journals.cambridge.org/abstract_S000632310000548X. Retrieved 2007-
05-26.
6. ^ Budd, G.E. (1998). "Arthropod body-plan evolution in the Cambrian with an example from
anomalocaridid muscle". Lethaia (Blackwell Synergy) 31 (3): 197–210. doi:10.1111/j.1502-
3931.1998.tb00508.x. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1502-
3931.1998.tb00508.x.
7. ^ Briggs, D. E. G; Fortey, R. A (2005). "Wonderful strife: systematics, stem groups, and the
phylogenetic signal of the Cambrian radiation". Paleobiology 31 (2 (Suppl)): 94–112.
doi:10.1666/0094-8373(2005)031[0094:WSSSGA]2.0.CO;2.
8. ^ Feldkamp, S. (2002) Modern Biology. Holt, Rinehart, and Winston, USA. (pp. 725)
9. ^ Species Register. "Flatworms — Phylum Platyhelminthes". Marine Discovery Centres.
http://www.woodbridge.tased.edu.au/mdc/Species%20Register/phylum_platyhelminthes.htm.
10.^ ""Kingdom Plantae Tree of Life"".
http://www.fossilmuseum.net/Tree_of_Life/KingdomPlantae.htm.
11.^ J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: Phyla".
http://www.bacterio.cict.fr/classifphyla.html. Retrieved 30 December 2010.

• Are phyla "real"? Is there really a well-defined "number of animal phyla" extant and in the
fossil record?
• Major Phyla Of Animals
Look up Phylum in Wiktionary, the free dictionary.
Magnorder
Kingdom Phylum/Divisi Class Legion Order Family

on
Infrakingdom/B
ranch
Retrieved from "http://en.wikipedia.org/wiki/Phylum"
Categories: Scientific classification | Phyla | Botanical nomenclature | Greek loanwords

W000
Class (biology)

definition by genus and differentia. Intermediate minor rankings are not shown.
In biological classification, class (Latin: classis) is
• a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, order, family,
genus, and species, with class fitting between phylum and order. As for the other well-known ranks,
there is the option of an immediately lower rank, indicated by the prefix sub-: subclass (Latin:
subclassis).
• a taxonomic unit, a taxon, in that rank. In that case the plural is classes (Latin classes)
The composition of each class is determined by a taxonomist. Often there is no exact agreement,
with different taxonomists taking different positions. There are no hard rules that a taxonomist needs to follow
in describing a class, but for well-known animals there is likely to be consensus. For example, dogs are
usually assigned to the phylum Chordata (animals with notochords); in the class Mammalia; in the order
Carnivora (mammals that eat meat).
Contents
[hide]
• 1 Hierarchy of ranks
• 2 History of the concept
• 3 See also
• 4 References
[edit] Hierarchy of ranks

For some clades, a number of additional classifications are used. The different classes are used
relatively rarely.
Meaning of
Name Example 1 Example 2 Example 3[1]
prefix
Superclass super: above Tetrapoda
Class Mammalia Maxillopoda Sauropsida
Subclass sub: under Thecostraca Avialae
Infraclass infra: below Cirripedia Aves

parvus: small,
Parvclass Neornithes
unimportant
[edit] History of the concept

The class as a distinct rank of biological classification having its own distinctive name (and not just
called a top-level genus (genus summum) was first introduced by a French botanist Joseph Pitton de
Tournefort in his classification of plants (appeared in his 1694 Eléments de botanique). Carolus Linnaeus
was the first to use it consistently, in dividing of all three of his kingdoms of Nature (minerals, plants, and
animals) in his Systema Naturae (1735, 1st ed.).[2] Since then class had been considered the highest level of
the taxonomic hierarchy until the embranchements, now called phyla, and divisions were introduced in the
nineteenth century.
[edit] See also

• Systematics
• Cladistics
• Phylogenetics
• Taxonomy
[edit] References
1. ^ Classification according to Systema Naturae 2000, which conflicts with Wikipedia's
classification. "The Taxonomicon: Neornithes". http://taxonomicon.taxonomy.nl/TaxonTree.aspx?
id=1014031. Retrieved 3 December 2010.
2. ^ Mayr E. (1982). The Growth of Biological Thought . Cambridge: The Belknap Press of
Harvard University Press. ISBN 0-674-36446-5
Magnorder
Phylum/Divisi
on
Infrakingdom/B
ranch

This biology article is a stub. You can help Wikipedia by expanding it.v · d · e
Retrieved from "http://en.wikipedia.org/wiki/Class_(biology)"
Categories: Botanical nomenclature | Scientific classification | Biology stubs

W000
Order (biology)

This article is about the taxonomic rank. For the sequence of species in a taxonomic list, see
taxonomic order.
challenged and removed. (May 2008)
definition by genus and differentia. A class contains one or more orders. Intermediate minor rankings are not
shown.
In scientific classification used in biology, the order (Latin: ordo) is
1. a taxonomic rank used in the classification of organisms. Other well-known ranks are life,
domain, kingdom, phylum, class, family, genus, and species, with order fitting in between class and
family. An immediately higher rank, superorder, may be added directly above order, while suborder
would be a lower rank.
2. a taxonomic unit, a taxon, in that rank. In that case the plural is orders (Latin ordines).
Example: Walnuts and hickories belong to the family Juglandaceae (or walnut family),
which is placed in the order Fagales.
What does and does not belong to each order is determined by a taxonomist. Similarly for the
question if a particular order should be recognized at all. Often there is no exact agreement, with different
taxonomists each taking a different position. There are no hard rules that a taxonomist needs to follow in
describing or recognizing an order. Some taxa are accepted almost universally, while others are recognised
only rarely.
For some groups of organisms, consistent suffixes are used to denote that the rank is an order. The
Latin suffix -(i)formes meaning "having the form of" is used for the scientific name of orders of birds and
fishes, but not for those of mammals and invertebrates. The suffix -ales is for the name of orders of vascular
plants.
Contents
[hide]
• 1 Hierarchy of ranks
• 2.1 Botany
• 2.2 Zoology
• 3 See also
[edit] Hierarchy of ranks

For some clades, a number of additional classifications are used.
Name Meaning of prefix Example
Magnorder magnus: large, great, important Epitheria
Superorder super: above Euarchontoglires
Order Primates
Suborder sub: under Haplorrhini
Infraorder infra: below Simiiformes

Parvorder parvus: small, unimportant Catarrhini

The order as a distinct rank of biological classification having its own distinctive name (and not just
called a higher genus (genus summum)) was first introduced by a German botanist Augustus Quirinus
Rivinus in his classification of plants (appeared in a series of treatises in the 1690s). Carolus Linnaeus was
the first to apply it consistently to the division of all three kingdoms of Nature (minerals, plants, and animals)
in his Systema Naturae (1735, 1st. Ed.).
[edit] Botany
For plants the Linnaean orders, in the Systema Naturae and the Species Plantarum, were strictly
artificial, introduced to subdivide the artificial classes into more comprehensible smaller groups. When the
word ordo was first consistently used for natural units of plants, in nineteenth century works such as the
Prodromus of de Candolle and the Genera Plantarum of Bentham & Hooker, it indicated taxa that are now
given the rank of family (see ordo naturalis).
In French botanical publications, from Michel Adanson's Familles naturelles des plantes (1763) and
until the end of the 19th century, the word famille (plural: familles) was used as a French equivalent for this
Latin ordo. This equivalence was explicitly stated in the Alphonse De Candolle's Lois de la nomenclature
botanique (1868), the precursor of the currently used International Code of Botanical Nomenclature .
In the first international Rules of botanical nomenclature of 1906 the word family (familia) was
assigned to the rank indicated by the French "famille", while order ( ordo) was reserved for a higher rank, for
what in the nineteenth century had often been named a cohors (plural cohortes).
Some of the plant families still retain the names of Linnaean "natural orders" or even the names of
pre-Linnaean natural groups recognised by Linnaeus as orders in his natural classification (e.g. Palmae or
Labiatae). Such names are known as descriptive family names.
[edit] Zoology
In zoology, the Linnaean orders were used more consistently. That is, the orders in the zoology part
of the Systema Naturae refer to natural groups. Some of his ordinal names are still in use (e.g. Lepidoptera
for the order of moths and butterflies, or Diptera for the order of flies, mosquitoes, midges, and gnats).
[edit] See also

Biology portal
• Cladistics
• Phylogenetics
• Rank (botany)
• Rank (zoology)
• Biological classification
• Systematics
• Taxonomy
• Virus classification
Magnorder
Phylum/Divisi
on
Infrakingdom/B
ranch
Retrieved from "http://en.wikipedia.org/wiki/Order_(biology)"
Categories: Scientific classification | Zoological nomenclature

W000
Family (biology)

"Subfamily" redirects here. For the protein classification, see Protein subfamily.
definition by genus and differentia. An order contains one or more families. Intermediate minor rankings are
not shown.
In biological classification, family (Latin: familia) is
• a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, class, order,
genus, and species, with family fitting between order and genus. As for the other well-known ranks,
there is the option of an immediately lower rank, indicated by the prefix sub-: subfamily (Latin:
subfamilia).
• a taxonomic unit, a taxon, in that rank. In that case the plural is families (Latin familiae)
Example: Walnuts and hickories belong to the Juglandaceae, or walnut family.
What does and does not belong to each family is determined by a taxonomist. Similarly for the
question if a particular family should be recognized at all. Often there is no exact agreement, with different
taxonomists each taking a different position. There are no hard rules that a taxonomist needs to follow in
describing or recognizing a family. Some taxa are accepted almost universally, while others are recognised
only rarely.
Contents
[hide]
• 2 Uses
• 3 See also
• 4 References

The taxonomic term familia was first used by French botanist Pierre Magnol in his Prodromus
historiae generalis plantarum, in quo familiae plantarum per tabulas disponuntur (1689) where he called the
seventy-six groups of plants he recognised in his tables families ( familiae). The concept of rank at that time
was not yet settled, and in the preface to the Prodromus Magnol spoke of uniting his families into larger
genera, which is far from how the term is used today.
Carolus Linnaeus used the word familia in his Philosophia botanica (1751) to denote major groups of
plants: trees, herbs, ferns, palms, and so on. He used this term only in the morphological section of the book,
discussing the vegetative and generative organs of plants. Subsequently, in French botanical publications,
from Michel Adanson's Familles naturelles des plantes (1763) and until the end of the 19th century, the word
famille was used as a French equivalent of the Latin ordo (or ordo naturalis). In nineteenth century works
such as the Prodromus of Augustin Pyramus de Candolle and the Genera Plantarum of George Bentham
and Joseph Dalton Hooker this word ordo was used for what now is given the rank of family.
In zoology, the family as a rank intermediate between order and genus was introduced by Pierre
André Latreille in his Précis des caractères génériques des insectes, disposés dans un ordre naturel (1796).
He used families (some of them not named) in some but not in all his orders of "insects" (which then included
all arthropods).
Since the beginning of the 20th century, however, the term has been consistently used in its modern
sense. Its usage and characteristic ending of the names belonging to this category are governed by the
various nomenclature codes. These are "-idae" in the zoological code,[1] and "-aceae" in the botanical[2] and
bacteriological codes.[3]
[edit] Uses
Families may be used for evolutionary, palaeontological and generic studies because they are more
stable than lower taxonomic levels such as genera and species.[4][5]
[edit] See also

• Systematics, the study of the diversity of life
• Cladistics, the classification of organisms by their order of branching in an evolutionary tree
• Phylogenetics, the study of evolutionary relatedness among various groups of organisms
• Taxonomy
• Virus classification
• List of Anuran families
• List of Testudines families
• List of fish families
• List of families of spiders
Compare:
• family
• protein family
• gene family
[edit] References
1. ^ International Commission on Zoological Nomenclature (1999). "Article 29. Family-group
names". International Code of Zoological Nomenclature (4th ed.). ISBN 0-85301-006-4.
http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?nfv=&article=29.
2. ^ J. McNeill, F. R. Barrie, H. M. Burdet, V. Demoulin, D. L. Hawksworth, K. Marhold, D. H.
Nicholson, J. Prado, P. C. Silva, J. E. Skog, J. H. Wiersema & N. J. Turland, ed (2005). "Article 18".
International Code of Botanical Nomenclature (Vienna Code) . Regnum Vegetabile 146. Ruggell,
Liechtenstein: A.R.G. Gantner Verlag KG. ISBN 3-906166-48-1.
http://ibot.sav.sk/icbn/frameset/0022Ch3Sec2a018.htm.
3. ^ S. P. Lapage, P. H. A. Sneath, E. F. Lessel, V. B. D. Skerman, H. P. R. Seeliger & W. A.
Clark, ed (1992). "Rules of Nomenclature with Recommendations". International Code of
Nomenclature of Bacteria (1990 revision ed.). ASM Press. ISBN 1-55581-039-X.
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=icnb&part=A185.
4. ^ Sarda Sahney, Michael J. Benton & Paul A. Ferry (2010). "Links between global taxonomic
diversity, ecological diversity and the expansion of vertebrates on land" (PDF). Biology Letters 6 (4):
544–547. doi:10.1098/rsbl.2009.1024.
http://rsbl.royalsocietypublishing.org/content/6/4/544.full.pdf+html.
5. ^ Sarda Sahney & Michael J. Benton (2008). "Recovery from the most profound mass
extinction of all time" (PDF). Proceedings of the Royal Society B: Biological Sciences 275 (1636):
759–765. doi:10.1098/rspb.2007.1370. PMID 18198148. PMC 2596898.
Retrieved from "http://en.wikipedia.org/wiki/Family_(biology)"
Categories: Scientific classification | Zoological nomenclature | Botanical nomenclature

W000
Genus

"Genera" redirects here. For the operating system, see Genera (operating system).
For other uses, see Genus (disambiguation).
challenged and removed. (August 2006)
In biology, a genus (plural: genera) is a low-level taxonomic rank (a taxon) used in the classification
of living and fossil organisms, which is an example of definition by genus and differentia. The term comes
from Latin genus "descent, family, type, gender",[1] cognate with Greek: γένος – genos, "race, stock, kin".[2]
definition by genus and differentia. A family contains one or more genera. Intermediate minor rankings are
not shown.
The composition of a genus is determined by a taxonomist. The standards for genus classification
are not strictly codified, and hence different authorities often produce different classifications for genera. In
the hierarchy of the binomial classification system, genus comes above species and below family.
Contents
[hide]
• 1 Generic name
• 1.1 Binomial nomenclature
• 1.2 Pivotal in binomial nomenclature
• 1.3 The problem of identical names used for
different genera
• 1.4 Types and genera
• 2 Guidelines
• 2.1 Nomenclature
• 3 See also
• 4 References
[edit] Generic name

The scientific name of a genus may be called the generic name or generic epithet: it is always
capitalized. It plays a pivotal role in binomial nomenclature, the system of biological nomenclature.
[edit] Binomial nomenclature
The rules for scientific names are laid down in the Nomenclature Codes; depending on the kind of
organism and the Kingdom it belongs to, a different Code may apply, with different rules, laid down in a
different terminology. The advantages of scientific over common names are that they are accepted by
speakers of all languages, and that each species has only one name. This reduces the confusion that may
arise from the use of a common name to designate different things in different places (example elk), or from
the existence of several common names for a single species.
It is possible for a genus to be assigned to a kingdom governed by one particular Nomenclature
Code by one taxonomist, while other taxonomists assign it to a kingdom governed by a different Code, but
this is the exception, not the rule.
[edit] Pivotal in binomial nomenclature

The generic name often is a component of the names of taxa of lower rank. For example, Canis
lupus is the scientific name of the Gray wolf, a species, with Canis the generic name for the dog and its close
relatives, and with lupus particular (specific) for the wolf (lupus is written in lower case). Similarly, Canis
lupus familiaris is the scientific name for the domestic dog.
Taxonomic units in higher ranks often have a name that is based on a generic name, such as the
family name Canidae, which is based on Canis. However, not all names in higher ranks are necessarily
based on the name of a genus: for example, Carnivora is the name for the order to which the dog belongs.
[edit] The problem of identical names used for different genera
A genus in one kingdom is allowed to bear a scientific name that is in use as a generic name (or the
name of a taxon in another rank) in a kingdom that is governed by a different Nomenclature Code. Although
this is discouraged by both the International Code of Zoological Nomenclature and the International Code of
Botanical Nomenclature, there are some five thousand such names that are in use in more than one
kingdom. For instance, Anura is the name of the order of frogs but also is the name of a genus of plants
(although not current: it is a synonym); Aotus is the genus of golden peas and night monkeys; Oenanthe is
the genus of wheatears and water dropworts, Prunella is the genus of accentors and self-heal, and
Proboscidea is the order of elephants and the genus of devil's claws.
Within the same kingdom one generic name can apply to only one genus. This explains why the
platypus genus is named Ornithorhynchus—George Shaw named it Platypus in 1799, but the name Platypus
had already been given to a group of ambrosia beetles by Johann Friedrich Wilhelm Herbst in 1793. Names
with the same form but applying to different taxa are called homonyms. Since beetles and platypuses are
both members of the kingdom Animalia, the name Platypus could not be used for both. Johann Friedrich
Blumenbach published the replacement name Ornithorhynchus in 1800.
[edit] Types and genera

Because of the rules of scientific naming, or "binomial nomenclature", each genus should have a
designated type, although in practice there is a backlog of older names that may not yet have a type. In
zoology this is the type species (see Type (zoology)); the generic name is permanently associated with the
type specimen of its type species. Should this specimen turn out to be assignable to another genus, the
generic name linked to it becomes a junior synonym, and the remaining taxa in the former genus need to be
reassessed.
See scientific classification and Nomenclature Codes for more details of this system. Also see type
genus.
[edit] Guidelines
There are no hard and fast rules that a taxonomist has to follow in deciding what does and what does
not belong in a particular genus. This does not mean that there is no common ground among taxonomists in
what constitutes a "good" genus. For instance, some rules-of-thumb for delimiting a genus are outlined in
Gill.[3] According to these, a genus should fulfill three criteria to be descriptively useful:
1. monophyly – all descendants of an ancestral taxon are grouped together;
2. reasonable compactness – a genus should not be expanded needlessly; and
3. distinctness – in regards of evolutionarily relevant criteria, i.e. ecology, morphology, or
biogeography; note that DNA sequences are a consequence rather than a condition of diverging
evolutionary lineages except in cases where they directly inhibit gene flow (e.g. postzygotic barriers).
[edit] Nomenclature
None of the Nomenclature Codes require such criteria for ...difficulties occurring in
defining a genus, because these are concerned with the generic nomenclature: similar cases
nomenclature rules, not with taxonomy. These regulate formal abound, and become complicated by
nomenclature, aiming for universal and stable scientific names. the different views taken of the matter
by the various taxonomists.
Prof. C. S. Rafinesque.
1836[4]
[edit] See also
• Andrew Delmar Hopkins
[edit] References
1. ^ Merriam Webster Dictionary
2. ^ Genos, Henry George Liddell, Robert Scott, 'A Greek-English Lexicon , at Perseus
3. ^ Gill, F. B., B. Slikas, and F. H. Sheldon. “Phylogeny of titmice (Paridae): II. Species
relationships based on sequences of the mitochondrial cytochrome-b gene.” Auk 122(1): 121-143,
2005. (Google Scholar)
4. ^ Rafinesque, Prof. C. S. (1836). "Generic Rules". Flora telluriana Pars Prima First Part of
the Synoptical Flora Telluriana, Centuries I, II, III, IV. With new Natural Classes, Orders and families:
containing the 2000 New or revised Genera and Species of Trees, Palms, Shrubs, Vines, Plants,
Lilies, Grasses, Ferns, Algas, Fungi, & c. from North and South America, Polynesia, Australia, Asia
Europe and Africa, omitted or mistaken by the authors, that were observed or ascertained, described
or revised, collected or figured, between 1796 and 1836. . 1. Philadelphia: H. Probasco.
http://www.us.archive.org/GnuBook/?id=floratelluriana00rafi#99. Retrieved 2009-04-02. "...difficulties
occurring in generic nomenclature: similar cases abound, and become complicated by the different
views taken of the matter by the various botanists."

• Nomenclator Zoologicus: Index of all genus and subgenus names in zoological nomenclature
from 1758 to 2004.
• Fauna Europaea Database for Taxonomy
Magnorder
Phylum/Divisi
on
Infrakingdom/B
ranch
Retrieved from "http://en.wikipedia.org/wiki/Genus"

Categories: Scientific classification | Botanical nomenclature | Zoological nomenclature | Genera
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Species

For other uses, see Species (disambiguation).
definition by genus and differentia. A genus contains one or more species. Intermediate minor rankings are
not shown.
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A
species is often defined as a group of organisms capable of interbreeding and producing fertile offspring.
While in many cases this definition is adequate, more precise or differing measures are often used, such as
similarity of DNA, morphology or ecological niche. Presence of specific locally adapted traits may further
subdivide species into subspecies.
The commonly used names for plant and animal taxa sometimes correspond to species: for example,
"lion," "walrus," and "Camphor tree" – each refers to a species. In other cases common names do not: for
example, "deer" refers to a family of 34 species, including Eld's Deer, Red Deer and Elk (Wapiti). The last
two species were once considered a single species, illustrating how species boundaries may change with
increased scientific knowledge.
Species that are believed to have the same ancestors are grouped together, and this group is called
a genus. A species can only belong to one genus that it was grouped into. The belief is best checked by a
similarity of their DNA, but for practical reasons, other similar properties are used. For plants similarities of
flowers are used. All species are given a two part name (called a "binomial name" - "bi" for two, "nomial" for
name). The first part of a binomial name is the generic name, the genus of the species. The second part is
the specific name (or specific epithet). For example, Boa constrictor, which is commonly called by its
bionomial name, and is one of five species of the Boa genus. The first part of the name is capitalized, and the
second part has a lower case. The two part name is written in itallics.
A usable definition of the word "species" and reliable methods of identifying particular species are
essential for stating and testing biological theories and for measuring biodiversity. Traditionally, multiple
examples of a proposed species must be studied for unifying characters before it can be regarded as a
species. Extinct species known only from fossils are generally difficult to assign precise taxonomic rankings.
Because of the difficulties with both defining and tallying the total numbers of different species in the
world, it is estimated that there are anywhere between 2 and 100 million different species.[1]
Contents
[hide]
• 1 Biologists' working definition
• 1.1 Common names and species
• 1.2 Placement within genera
• 1.3 Abbreviated names
• 2 Difficulty of defining "species" and identifying particular
species
• 3 Definitions of species
• 4 Numbers of species
• 5 Importance in biological classification
• 6 Implications of assignment of species status
• 7 Historical development of the species concept
• 8 Species as taxa
• 9 See also
[edit] Biologists' working definition
A usable definition of the word "species" and reliable methods of identifying particular species is
essential for stating and testing biological theories and for measuring biodiversity. Traditionally, multiple
examples of a proposed species must be studied for unifying characters before it can be regarded as a
species. It is generally difficult to give precise taxonomic rankings to extinct species known only from fossils.
Some biologists may view species as statistical phenomena, as opposed to the traditional idea, with
a species seen as a class of organisms. In that case, a species is defined as a separately evolving lineage
that forms a single gene pool. Although properties such as DNA-sequences and morphology are used to help
separate closely related lineages,[2] this definition has fuzzy boundaries.[3] However, the exact definition of
the term "species" is still controversial, particularly in prokaryotes,[4] and this is called the species problem.
[5] Biologists have proposed a range of more precise definitions, but the definition used is a pragmatic choice
that depends on the particularities of the species of concern.[5]
[edit] Common names and species

The commonly used names for plant and animal taxa sometimes correspond to species: for example,
"lion", "walrus", and "Camphor tree" – each refers to a species. In other cases common names do not: for
example, "deer" refers to a family of 34 species, including Eld's Deer, Red Deer and Elk (Wapiti). The last
two species were once considered a single species, illustrating how species boundaries may change with
increased scientific knowledge.
Because of the difficulties with both defining and tallying the total numbers of different species in the
world, it is estimated that there are anywhere between 2 and 100 million different species.[1]
[edit] Placement within genera
Ideally, a species is given a formal, scientific name, although in practice there are very many
unnamed species (which have only been described, not named). When a species is named, it is placed
within a genus. From a scientific point of view this can be regarded as a hypothesis that the species is more
closely related to other species within its genus (if any) than to species of other genera. Species and genus
are usually defined as part of a larger taxonomic hierarchy. The best-known taxonomic ranks are, in order:
life, domain, kingdom, phylum, class, order, family, genus, and species. This assignment to a genus is not
immutable; later a different (or the same) taxonomist may assign it to a different genus, in which case the
name will also change.
In biological nomenclature, the name for a species is a two-part name (a binomial name), treated as
Latin, although roots from any language can be used as well as names of locales or individuals. The generic
name is listed first (with its leading letter capitalized), followed by a second term, the specific name (or
specific epithet). For example, the species commonly known as the Longleaf Pine is Pinus palustris; gray
wolves belong to the species Canis lupus, coyotes to Canis latrans, golden jackals to Canis aureus, etc., and
all of those belong to the genus Canis (which also contains many other species). The name of the species is
the whole binomial, not just the second term (which may be called the specific name for animals).
This binomial naming convention, later formalized in the biological codes of nomenclature, was first
used by Leonhart Fuchs and introduced as the standard by Carolus Linnaeus in his 1753, Species Plantarum
(followed by his, 1758 Systema Naturae, 10th edition). At that time, the chief biological theory was that
species represented independent acts of creation by God and were therefore considered objectively real and
immutable, so the hypothesis of common descent did not apply.
[edit] Abbreviated names
Books and articles sometimes intentionally do not identify species fully and use the abbreviation "sp."
in the singular or "spp." in the plural in place of the specific epithet: for example, Canis sp. This commonly
occurs in the following types of situations:
• The authors are confident that some individuals belong to a particular genus but are not sure
to which exact species they belong. This is particularly common in paleontology.
• The authors use "spp." as a short way of saying that something applies to many species
within a genus, but do not wish to say that it applies to all species within that genus. If scientists
mean that something applies to all species within a genus, they use the genus name without the
specific epithet.
In books and articles, genus and species names are usually printed in italics. If using "sp." and
"spp.", these should not be italicized.
[edit] Difficulty of defining "species" and identifying particular species

Main article: Species problem
The Greenish Warbler demonstrates the concept of a ring species.
It is surprisingly difficult to define the word "species" in a way that applies to all naturally occurring
organisms, and the debate among biologists about how to define "species" and how to identify actual species
is called the species problem. Over two dozen distinct definitions of "species" are in use amongst biologists.
[6]
Most textbooks follow Ernst Mayr's definition of a species as "groups of actually or potentially
interbreeding natural populations, which are reproductively isolated from other such groups".[5]
Various parts of this definition serve to exclude some unusual or artificial matings:
• Those that occur only in captivity (when the animal's normal mating partners may not be
available) or as a result of deliberate human action
• Animals that may be physically and physiologically capable of mating but, for various
reasons, do not normally do so in the wild
The typical textbook definition above works well for most multi-celled organisms, but there are
several types of situations in which it breaks down:
• By definition it applies only to organisms that reproduce sexually. So it does not work for
asexually reproducing single-celled organisms and for the relatively few parthenogenetic multi-celled
organisms. The term "phylotype" is often applied to such organisms.
• Biologists frequently do not know whether two morphologically similar groups of organisms
are "potentially" capable of interbreeding.
• There is considerable variation in the degree to which hybridization may succeed under
natural conditions, or even in the degree to which some organisms use sexual reproduction between
individuals to breed.
• In ring species, members of adjacent populations interbreed successfully but members of
some non-adjacent populations do not.
• In a few cases it may be physically impossible for animals that are members of the same
species to mate. However, these are cases in which human intervention has caused gross
morphological changes, and are therefore excluded by the biological species concept.
Horizontal gene transfer makes it even more difficult to define the word "species". There is strong
evidence of horizontal gene transfer between very dissimilar groups of prokaryotes, and at least occasionally
between dissimilar groups of eukaryotes; and Williamson[7] argues that there is evidence for it in some
crustaceans and echinoderms. All definitions of the word "species" assume that an organism gets all its
genes from one or two parents that are very like that organism, but horizontal gene transfer makes that
assumption false.
[edit] Definitions of species
See also: Species problem
The question of how best to define "species" is one that has occupied biologists for centuries, and
the debate itself has become known as the species problem. Darwin wrote in chapter II of On the Origin of
Species:
No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he
means when he speaks of a species. Generally the term includes the unknown element of a distinct
act of creation.[8]
But later, in The Descent of Man, when addressing "The question whether mankind consists of one
or several species", Darwin revised his opinion to say:
it is a hopeless endeavour to decide this point on sound grounds, until some definition of the
term "species" is generally accepted; and the definition must not include an element that cannot
possibly be ascertained, such as an act of creation.[9]
The modern theory of evolution depends on a fundamental redefinition of "species". Prior to Darwin,
naturalists viewed species as ideal or general types, which could be exemplified by an ideal specimen
bearing all the traits general to the species. Darwin's theories shifted attention from uniformity to variation
and from the general to the particular. According to intellectual historian Louis Menand,
Once our attention is redirected to the individual, we need another way of making
generalizations. We are no longer interested in the conformity of an individual to an ideal type; we are
now interested in the relation of an individual to the other individuals with which it interacts. To
generalize about groups of interacting individuals, we need to drop the language of types and
essences, which is prescriptive (telling us what finches should be), and adopt the language of statistics
and probability, which is predictive (telling us what the average finch, under specified conditions, is
likely to do). Relations will be more important than categories; functions, which are variable, will be
more important than purposes; transitions will be more important than boundaries; sequences will be
more important than hierarchies.
This shift results in a new approach to "species"; Darwin
concluded that species are what they appear to be: ideas, which are provisionally useful for
naming groups of interacting individuals. "I look at the term species", he wrote, "as one arbitrarily given
for the sake of convenience to a set of individuals closely resembling each other ... It does not
essentially differ from the word variety, which is given to less distinct and more fluctuating forms. The
term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for
convenience sake." [10]
Practically, biologists define species as populations of organisms that have a high level of genetic
similarity. This may reflect an adaptation to the same niche, and the transfer of genetic material from one
individual to others, through a variety of possible means. The exact level of similarity used in such a definition
is arbitrary, but this is the most common definition used for organisms that reproduce asexually (asexual
reproduction), such as some plants and microorganisms.
This lack of any clear species concept in microbiology has led to some authors arguing that the term
"species" is not useful when studying bacterial evolution. Instead they see genes as moving freely between
even distantly related bacteria, with the entire bacterial domain being a single gene pool. Nevertheless, a
kind of rule of thumb has been established, saying that species of Bacteria or Archaea with 16S rRNA gene
sequences more similar than 97% to each other need to be checked by DNA-DNA Hybridization if they
belong to the same species or not.[11] This concept has been updated recently, saying that the border of
97% was too low and can be raised to 98.7%.[12]
In the study of sexually reproducing organisms, where genetic material is shared through the process
of reproduction, the ability of two organisms to interbreed and produce fertile offspring of both sexes is
generally accepted as a simple indicator that the organisms share enough genes to be considered members
of the same species. Thus a "species" is a group of interbreeding organisms.
This definition can be extended to say that a species is a group of organisms that could potentially
interbreed – fish could still be classed as the same species even if they live in different lakes, as long as they
could still interbreed were they ever to come into contact with each other. On the other hand, there are many
examples of series of three or more distinct populations, where individuals of the population in the middle can
interbreed with the populations to either side, but individuals of the populations on either side cannot
interbreed. Thus, one could argue that these populations constitute a single species, or two distinct species.
This is not a paradox; it is evidence that species are defined by gene frequencies, and thus have fuzzy
boundaries.
Consequently, any single, universal definition of "species" is necessarily arbitrary. Instead, biologists
have proposed a range of definitions; which definition a biologists uses is a pragmatic choice, depending on
the particularities of that biologist's research.
Typological species
A group of organisms in which individuals are members of the species if they sufficiently
conform to certain fixed properties or "rights of passage". The clusters of variations or phenotypes
within specimens (i.e. longer or shorter tails) would differentiate the species. This method was used as
a "classical" method of determining species, such as with Linnaeus early in evolutionary theory.
However, we now know that different phenotypes do not always constitute different species (e.g.: a 4-
winged Drosophila born to a 2-winged mother is not a different species). Species named in this
manner are called morphospecies.[13]
Morphological species
A population or group of populations that differs morphologically from other populations. For
example, we can distinguish between a chicken and a duck because they have different shaped bills
and the duck has webbed feet. Species have been defined in this way since well before the beginning
of recorded history. This species concept is highly criticized because more recent genetic data reveal
that genetically distinct populations may look very similar and, contrarily, large morphological
differences sometimes exist between very closely related populations. Nonetheless, most species
known have been described solely from morphology.
Biological / Isolation species
A set of actually or potentially interbreeding populations. This is generally a useful formulation
for scientists working with living examples of the higher taxa like mammals, fish, and birds, but more
problematic for organisms that do not reproduce sexually. The results of breeding experiments done in
artificial conditions may or may not reflect what would happen if the same organisms encountered
each other in the wild, making it difficult to gauge whether or not the results of such experiments are
meaningful in reference to natural populations.
Biological / reproductive species
Two organisms that are able to reproduce naturally to produce fertile offspring of both sexes.
Organisms that can reproduce but almost always make infertile hybrids of at least one sex, such as a
mule, hinny or F1 male cattalo are not considered to be the same species.
Recognition species
Based on shared reproductive systems, including mating behavior. The Recognition concept
of species has been introduced by Hugh E. H. Paterson, after earlier work by Wilhelm Petersen.
Mate-recognition species
A group of organisms that are known to recognize one another as potential mates. Like the
isolation species concept above, it applies only to organisms that reproduce sexually. Unlike the
isolation species concept, it focuses specifically on pre-mating reproductive isolation.
Evolutionary / Darwinian species
A group of organisms that shares an ancestor; a lineage that maintains its integrity with
respect to other lineages through both time and space. At some point in the progress of such a group,
some members may diverge from the main population and evolve into a subspecies, a process that
eventually will lead to the formation of a new full species if isolation (geographical or ecological) is
maintained.
Phylogenetic (Cladistic)[verification needed]
A group of organisms that shares an ancestor; a lineage that maintains its integrity with
respect to other lineages through both time and space. At some point in the progress of such a group,
members may diverge from one another: when such a divergence becomes sufficiently clear, the two
populations are regarded as separate species. This differs from evolutionary species in that the parent
species goes extinct taxonomically when a new species evolve, the mother and daughter populations
now forming two new species. Subspecies as such are not recognized under this approach; either a
population is a phylogenetic species or it is not taxonomically distinguishable.
Ecological species
A set of organisms adapted to a particular set of resources, called a niche, in the environment.
According to this concept, populations form the discrete phonetic clusters that we recognize as species
because the ecological and evolutionary processes controlling how resources are divided up tend to
produce those clusters.
Genetic species
Based on similarity of DNA of individuals or populations. Techniques to compare similarity of
DNA include DNA-DNA hybridization, and genetic fingerprinting (or DNA barcoding).
Phenetic species
Based on phenotypes.[verification needed]
Microspecies
Species that reproduce without meiosis or fertilization so that each generation is genetically
identical to the previous generation. See also apomixis.
Cohesion species
Most inclusive population of individuals having the potential for phenotypic cohesion through
intrinsic cohesion mechanisms. This is an expansion of the mate-recognition species concept to allow
for post-mating isolation mechanisms; no matter whether populations can hybridize successfully, they
are still distinct cohesion species if the amount of hybridization is insufficient to completely mix their
respective gene pools.
Evolutionarily Significant Unit (ESU)
An evolutionarily significant unit is a population of organisms that is considered distinct for
purposes of conservation. Often referred to as a species or a wildlife species, an ESU also has several
possible definitions, which coincide with definitions of species.
In practice, these definitions often coincide, and the differences between them are more a matter of
emphasis than of outright contradiction. Nevertheless, no species concept yet proposed is entirely objective,
or can be applied in all cases without resorting to judgment. Given the complexity of life, some have argued
that such an objective definition is in all likelihood impossible, and biologists should settle for the most
practical definition.
For most vertebrates, this is the biological species concept (BSC), and to a lesser extent (or for
different purposes) the phylogenetic species concept (PSC). Many BSC subspecies are considered species
under the PSC; the difference between the BSC and the PSC can be summed up insofar as that the BSC
defines a species as a consequence of manifest evolutionary history, while the PSC defines a species as a
consequence of manifest evolutionary potential. Thus, a PSC species is "made" as soon as an evolutionary
lineage has started to separate, while a BSC species starts to exist only when the lineage separation is
complete. Accordingly, there can be considerable conflict between alternative classifications based upon the
PSC versus BSC, as they differ completely in their treatment of taxa that would be considered subspecies
under the latter model (e.g., the numerous subspecies of honey bees).
[edit] Numbers of species
Undiscovered and discovered species[verification needed][citation needed]

Bearing in mind the aforementioned problems with categorising species, the following numbers are
only a soft guide. In 2007, they broke down as follows:[14]
Total number of species (estimated): 7–100 millions (identified and unidentified), including:
• 5–10 million bacteria;[15]
• 74,000–120,000 fungi;[16]
Of the identified eukaryote species we have:[14]
• 1.6 million, including:
• 297,326 plants, including:
• 15,000 mosses,
• 13,025 Ferns and horsetails,
• 980 gymnosperms,
• 258,650 angiosperms,
• 199,350 dicotyledons,
• 59,300 monocotyledons,
• 9,671 Red and green algae,
• 28,849 fungi & other non-animals, including:
• 10,000 lichens,
• 16,000 mushrooms,
• 2,849 brown algae,
• 1,250,000 animals, including:
• 1,203,375 invertebrates:
• 950,000 insects,
• 81,000 mollusks,
• 40,000 crustaceans,
• 2,175 corals,
• 130,200 others;
• 59,811 vertebrates:
• 29,300 fish,
• 6,199 amphibians,
• 8,240 reptiles,
• 9,956 birds,
• 5,416 mammals
At present, organisations such as the Global Taxonomy Initiative, the European Distributed Institute
of Taxonomy and the Census of Marine Life[17] (the latter only for marine organisms) are trying to improve
taxonomy and implement previously undiscovered species to the taxonomy system. Because we know but a
portion of the organisms in the biosphere, we do not have a complete understanding of the workings of our
environment. To make matters worse, despite the discovery of new species, according to professor James
Mallet, we are wiping out these species at an unprecedented rate.[18] This means that even before a new
species has had the chance of being studied and classified, it may already be extinct.
[edit] Importance in biological classification

The idea of species has a long history. It is one of the most important levels of classification, for
several reasons:
• It often corresponds to what lay people treat as the different basic kinds of organism – dogs
are one species, cats another.
• It is the standard binomial nomenclature (or trinomial nomenclature) by which scientists
typically refer to organisms.
• It is the highest taxonomic level that cannot be made more or less inclusionary.
After years of use, the concept remains central to biology and a host of related fields, and yet also
remains at times ill-defined.
[edit] Implications of assignment of species status

The naming of a particular species may be regarded as a hypothesis about the evolutionary
relationships and distinguishability of that group of organisms. As further information comes to hand, the
hypothesis may be confirmed or refuted. Sometimes, especially in the past when communication was more
difficult, taxonomists working in isolation have given two distinct names to individual organisms later
identified as the same species. When two named species are discovered to be of the same species, the older
species name is usually retained, and the newer species name dropped, a process called synonymization, or
colloquially, as lumping. Dividing a taxon into multiple, often new, taxons is called splitting. Taxonomists are
often referred to as "lumpers" or "splitters" by their colleagues, depending on their personal approach to
recognizing differences or commonalities between organisms (see lumpers and splitters).
Traditionally, researchers relied on observations of anatomical differences, and on observations of
whether different populations were able to interbreed successfully, to distinguish species; both anatomy and
breeding behavior are still important to assigning species status. As a result of the revolutionary (and still
ongoing) advance in microbiological research techniques, including DNA analysis, in the last few decades, a
great deal of additional knowledge about the differences and similarities between species has become
available. Many populations formerly regarded as separate species are now considered a single taxon, and
many formerly grouped populations have been split. Any taxonomic level (species, genus, family, etc.) can
be synonymized or split, and at higher taxonomic levels, these revisions have been still more profound.
From a taxonomical point of view, groups within a species can be defined as being of a taxon
hierarchically lower than a species. In zoology only the subspecies is used, while in botany the variety,
subvariety, and form are used as well. In conservation biology, the concept of evolutionary significant units
(ESU) is used, which may be define either species or smaller distinct population segments. Identifying and
naming species is the providence of alpha taxonomy.
[edit] Historical development of the species concept

The following text needs to be harmonized with text in Species problem.

may be challenged and removed. (September 2009)
Linnaeus believed in the fixity of species.
In the earliest works of science, a species was simply an individual organism that represented a
group of similar or nearly identical organisms. No other relationships beyond that group were implied.
Aristotle used the words genus and species to mean generic and specific categories. Aristotle and other pre-
Darwinian scientists took the species to be distinct and unchanging, with an "essence", like the chemical
elements. When early observers began to develop systems of organization for living things, they began to
place formerly isolated species into a context. Many of these early delineation schemes would now be
considered whimsical and these included consanguinity based on color (all plants with yellow flowers) or
behavior (snakes, scorpions and certain biting ants).
In the 18th century Swedish scientist Carolus Linnaeus classified organisms according to differences
in the form of reproductive apparatus. Although his system of classification sorts organisms according to
degrees of similarity, it made no claims about the relationship between similar species. At that time, it was
still widely believed that there was no organic connection between species, no matter how similar they
appeared. This approach also suggested a type of idealism: the notion that each species existed as an "ideal
form". Although there are always differences (although sometimes minute) between individual organisms,
Linnaeus considered such variation problematic. He strove to identify individual organisms that were
exemplary of the species, and considered other non-exemplary organisms to be deviant and imperfect.
By the 19th century most naturalists understood that species could change form over time, and that
the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809
Zoological Philosophy, offered one of the first logical arguments against creationism. The new emphasis was
on determining how a species could change over time. Lamarck suggested that an organism could pass on
an acquired trait to its offspring, i.e., the giraffe's long neck was attributed to generations of giraffes stretching
to reach the leaves of higher treetops (this well-known and simplistic example, however, does not do justice
to the breadth and subtlety of Lamarck's ideas). With the acceptance of the natural selection idea of Charles
Darwin in the 1860s, however, Lamarck's view of goal-oriented evolution, also known as a teleological
process, was eclipsed. Recent interest in inheritance of acquired characteristics centers around epigenetic
processes, e.g. methylation, that do not affect DNA sequences, but instead alter expression in an inheritable
manner. Thus, neo-lamarckism, as it is sometimes termed, is not a challenge to the theory of evolution by
natural selection.
Charles Darwin and Alfred Wallace provided what scientists now consider as the most powerful and
compelling theory of evolution. Darwin argued that it was populations that evolved, not individuals. His
argument relied on a radical shift in perspective from that of Linnaeus: rather than defining species in ideal
terms (and searching for an ideal representative and rejecting deviations), Darwin considered variation
among individuals to be natural. He further argued that variation, far from being problematic, actually
provides the explanation for the existence of distinct species.
Darwin's work drew on Thomas Malthus' insight that the rate of growth of a biological population will
always outpace the rate of growth of the resources in the environment, such as the food supply. As a result,
Darwin argued, not all the members of a population will be able to survive and reproduce. Those that did will,
on average, be the ones possessing variations—however slight—that make them slightly better adapted to the
environment. If these variable traits are heritable, then the offspring of the survivors will also possess them.
Thus, over many generations, adaptive variations will accumulate in the population, while counter-adaptive
traits will tend to be eliminated.
Whether a variation is adaptive or non-adaptive depends on the environment: different environments
favor different traits. Since the environment effectively selects which organisms live to reproduce, it is the
environment (the "fight for existence") that selects the traits to be passed on. This is the theory of evolution
by natural selection. In this model, the length of a giraffe's neck would be explained by positing that proto-
giraffes with longer necks would have had a significant reproductive advantage to those with shorter necks.
Over many generations, the entire population would be a species of long-necked animals.
In 1859, when Darwin published his theory of natural selection, the mechanism behind the
inheritance of individual traits was unknown. Although Darwin made some speculations on how traits are
inherited (pangenesis), his theory relies only on the fact that inheritable traits exist, and are variable (which
makes his accomplishment even more remarkable.) Although Gregor Mendel's paper on genetics was
published in 1866, its significance was not recognized. It was not until 1900 that his work was rediscovered
by Hugo de Vries, Carl Correns and Erich von Tschermak, who realised that the "inheritable traits" in
Darwin's theory are genes.
The theory of the evolution of species through natural selection has two important implications for
discussions of species—consequences that fundamentally challenge the assumptions behind Linnaeus'
taxonomy. First, it suggests that species are not just similar, they may actually be related. Some students of
Darwin argue that all species are descended from a common ancestor. Second, it supposes that "species"
are not homogeneous, fixed, permanent things; members of a species are all different, and over time species
change. This suggests that species do not have any clear boundaries but are rather momentary statistical
effects of constantly changing gene-frequencies. One may still use Linnaeus' taxonomy to identify individual
plants and animals, but one can no longer think of species as independent and immutable.
The rise of a new species from a parental line is called speciation. There is no clear line demarcating
the ancestral species from the descendant species.
Although the current scientific understanding of species suggests that there is no rigorous and
comprehensive way to distinguish between different species in all cases, biologists continue to seek concrete
ways to operationalize the idea. One of the most popular biological definitions of species is in terms of
reproductive isolation; if two creatures cannot reproduce to produce fertile offspring of both sexes, then they
are in different species. This definition captures a number of intuitive species boundaries, but it remains
imperfect. It has nothing to say about species that reproduce asexually, for example, and it is very difficult to
apply to extinct species. Moreover, boundaries between species are often fuzzy: there are examples where
members of one population can produce fertile offspring of both sexes with a second population, and
members of the second population can produce fertile offspring of both sexes with members of a third
population, but members of the first and third population cannot produce fertile offspring, or can only produce
fertile offspring of the homozygous sex. Consequently, some people reject this definition of a species.
Richard Dawkins defines two organisms as conspecific if and only if they have the same number of
chromosomes and, for each chromosome, both organisms have the same number of nucleotides (The Blind
Watchmaker, p. 118). However, most if not all taxonomists would strongly disagree[citation needed]. For
example, in many amphibians, most notably in New Zealand's Leiopelma frogs, the genome consists of
"core" chromosomes that are mostly invariable and accessory chromosomes, of which exist a number of
possible combinations. Even though the chromosome numbers are highly variable between populations,
these can interbreed successfully and form a single evolutionary unit. In plants, polyploidy is extremely
commonplace with few restrictions on interbreeding; as individuals with an odd number of chromosome sets
are usually sterile, depending on the actual number of chromosome sets present, this results in the odd
situation where some individuals of the same evolutionary unit can interbreed with certain others and some
cannot, with all populations being eventually linked as to form a common gene pool.
The classification of species has been profoundly affected by technological advances that have
allowed researchers to determine relatedness based on molecular markers, starting with the comparatively
crude blood plasma precipitation assays in the mid-20th century to Charles Sibley's ground-breaking DNA-
DNA hybridization studies in the 1970s leading to DNA sequencing techniques. The results of these
techniques caused revolutionary changes in the higher taxonomic categories (such as phyla and classes),
resulting in the reordering of many branches of the phylogenetic tree (see also: molecular phylogeny). For
taxonomic categories below genera, the results have been mixed so far; the pace of evolutionary change on
the molecular level is rather slow, yielding clear differences only after considerable periods of reproductive
separation. DNA-DNA hybridization results have led to misleading conclusions, the Pomarine Skua – Great
Skua phenomenon being a famous example. Turtles have been determined to evolve with just one-eighth of
the speed of other reptiles on the molecular level, and the rate of molecular evolution in albatrosses is half of
what is found in the rather closely related storm-petrels. The hybridization technique is now obsolete and is
replaced by more reliable computational approaches for sequence comparison. Molecular taxonomy is not
directly based on the evolutionary processes, but rather on the overall change brought upon by these
processes. The processes that lead to the generation and maintenance of variation such as mutation,
crossover and selection are not uniform (see also molecular clock). DNA is only extremely rarely a direct
target of natural selection rather than changes in the DNA sequence enduring over generations being a result
of the latter; for example, silent transition-transversion combinations would alter the melting point of the DNA
sequence, but not the sequence of the encoded proteins and thus are a possible example where, for
example in microorganisms, a mutation confers a change in fitness all by itself.
[edit] Species as taxa

The scientific name of a species (often of Latin or Greek origin) in the binominal nomenclature
introduced by Carl Linnaeus in 1753 is composed of two parts, which are written in italic font and for which
there are different expressions in botany and zoology. The first part of that name is spelled upper case and is
in both disciplines known as the genus name (also called the generic name). The second part is always
spelled lower case and in botany it is called the specific epithet.
• Example: in the European beech (Fagus sylvatica) the component Fagus refers to the genus,
sylvatica is the specific epithet.
In zoology, the second part is called the specific name.
• Example: in the lion (Panthera leo) the component Panthera refers to the genus, leo is the
specific name.
The scientific name is completed when authors, years and parentheses are added.
In botany the name of the author is usually abbreviated, for example "L." stands for "Linnaeus".
• Example: shiitake Lentinula edodes (Berk.) Pegler
M. J. Berkeley was the first to describe the species, D. Pegler has placed it into the currently used
system.
In zoology, the addition of author and year are optional, Panthera leo is thus an entirely correct
name. The International Code of Zoological Nomenclature prescribes how to add author(s) (if possible not
abbreviated) and year (or author alone without year). If the species is cited in different genus than the one in
which it was originally described, author(s) and year are given in parentheses. Between author and year
often a comma is set (but not required).
• Example: lion Panthera leo (Linnaeus, 1758)
Carl Nilsson Linnæus described the lion first and as Felis leo. The person who first placed the lion in
the genus Panthera Oken, 1816 is not relevant in zoology. Instead of Linnæus, usually Linnaeus is
spelled.
[edit] See also

• Cline
• Cryptic species complex
• Encyclopedia of Life
• Endangered species
• Genetic pollution
• Genetic erosion
• Ring species
• Species problem
• Systematics

1. ^ a b "Just How Many Species Are There, Anyway?". 2003-05-26.
http://www.sciencedaily.com/releases/2003/05/030526103731.htm. Retrieved 2008-01-15
2. ^ Koch, H. 2010. Combining morphology and DNA barcoding resolves the taxonomy of
Western Malagasy Liotrigona Moure, 1961. African Invertebrates 51 (2): 413-421.[1]
3. ^ De Queiroz K (December 2007). "Species concepts and species delimitation". Syst. Biol.
56 (6): 879–86. doi:10.1080/10635150701701083. PMID 18027281.
4. ^ Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (February 2009). "The bacterial
species challenge: making sense of genetic and ecological diversity". Science (journal) 323 (5915):
741–6. doi:10.1126/science.1159388. PMID 19197054.
5. ^ a b c de Queiroz K (May 2005). "Ernst Mayr and the modern concept of species". Proc. Natl.
Acad. Sci. U.S.A. 102 Suppl 1: 6600–7. doi:10.1073/pnas.0502030102. PMID 15851674.
6. ^ Wilkins, John (2010-10-20). "How many species concepts are there?". The Guardian.
http://www.guardian.co.uk/science/punctuated-equilibrium/2010/oct/20/3. Retrieved 2010-10-19.
7. ^ David I. Williamson (2003). The Origins of Larvae. Kluwer. ISBN 1-4020-1514-3.
8. ^ Darwin 1859 p.59
9. ^ Darwin 1871 p. 24
10.^ Louis Menand (2001) The Metaphysical Club New York: Farrar, Straus and Giroux 123–124
11.^ Stackebrandt E, Goebel BM (1994). "Taxonomic note: a place for DNA-DNA reassociation
and 16S rRNA sequence analysis in the present species definition in bacteriology". Int. J. Syst.
Bacteriol. 44: 846–9. doi:10.1099/00207713-44-4-846.
12.^ Stackebrandt E, Ebers J (2006). "Taxonomic parameters revisited: tarnished gold
standards". Microbiol. Today 33: 152–5.
13.^ Michael Ruse (August 1969). "Definitions of Species in Biology". The British Journal for the
Philosophy of Science (Oxford University Press) 20 (2): 97–119. doi:10.1093/bjps/20.2.97.
http://www.jstor.org/stable/686173.
14.^ a b "Number of Species on Earth". Current Results. 2007-01-01.
http://www.currentresults.com/Environment-Facts/Plants-Animals/number-species.php. Retrieved
2010-04-23.
15.^ Sogin ML, Morrison HG, Huber JA, et al. (August 2006). "Microbial diversity in the deep sea
and the underexplored "rare biosphere"". Proc. Natl. Acad. Sci. U.S.A. 103 (32): 12115–20.
doi:10.1073/pnas.0605127103. PMID 16880384. PMC 1524930.
http://www.pnas.org/cgi/pmidlookup?view=long&pmid=16880384. Cheung L (Monday, 31 July 200).
"Thousands of microbes in one gulp". BBC. http://news.bbc.co.uk/1/hi/sci/tech/5232928.stm.
16.^ David L. Hawksworth (2001). "The magnitude of fungal diversity: the 1•5 million species
estimate revisited". Mycological Research 105 (12): 1422–1432. doi:10.1017/S0953756201004725.
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=95069.
17.^ "Census of marine life". Coml.org. http://www.coml.org/. Retrieved 2010-04-23.
18.^ Robin McKie and Zoe Corbyn (2005-09-25). "Discovery of new species and extermination
at high rate". London: Guardian.
http://www.guardian.co.uk/science/2005/sep/25/taxonomy.conservationandendangeredspecies.
Look up species in Wiktionary, the free dictionary.
Wikispecies has information related to: Species

• Barcoding of species
• European Species Names in Linnaean, Czech, English, German and French
• Catalogue of Life
• VisualTaxa
• Other Species Concepts Berkeley University
• "Gone", Mother Jones, May/June 2007.
• Speciation
• 2003-12-31, ScienceDaily: Working On The 'Porsche Of Its Time': New Model For Species
Determination Offered Quote: "...two species of dinosaur that are members of the same genera
varied from each other by just 2.2%. Translation of the percentage into an actual number results in
an average of just three skeletal differences out of the total 338 bones in the body. Amazingly, 58%
of these differences occurred in the skull alone. "This is a lot less variation than I'd expected", said
Novak..."
• 2003-08-08, ScienceDaily: Cross-species Mating May Be Evolutionarily Important And Lead
To Rapid Change, Say Indiana University Researchers Quote: "...the sudden mixing of closely
related species may occasionally provide the energy to impel rapid evolutionary change..."
• 2004-01-09 ScienceDaily: Mayo Researchers Observe Genetic Fusion Of Human, Animal
Cells; May Help Explain Origin Of AIDS Quote: "...The researchers have discovered conditions in
which pig cells and human cells can fuse together in the body to yield hybrid cells that contain
genetic material from both species... "What we found was completely unexpected", says Jeffrey Platt,
M.D."
• 2000-09-18, ScienceDaily: Scientists Unravel Ancient Evolutionary History Of
Photosynthesis Quote: "...gene-swapping was common among ancient bacteria early in evolution..."
[hide]v · d · eSpeciation
Basic concepts Species · Cline · Chronospecies · Speciation
Modes of Allopatric · Heteropatric · Peripatric · Parapatric · Sympatric ·

speciation Polyploidy · Paleopolyploidy
Auxiliary
mechanisms Sexual selection · Assortative mating · Punctuated equilibrium
Intermediate stages Hybrid · Species complex · Ring species · Haldane's rule

Magnorder
Phylum/Divisi
on
Infrakingdom/B
ranch
Retrieved from "http://en.wikipedia.org/wiki/Species"
Categories: Biology | Scientific classification | Zoological nomenclature

W000
W000
Evolution of mammals

Restoration of Thrinaxodon, a member of the cynodont group, which includes the ancestors of
mammals.
Further information: Evolutionary history of life
The evolution of mammals within the synapsid lineage (mammal-like-reptiles) was a gradual process
that took approximately 70 million years, beginning in the mid-Permian. By the mid-Triassic, there were many
species that looked like mammals, and the first true mammals appeared in the early Jurassic. The earliest
known marsupial, Sinodelphys, appeared 125 million years ago in the early Cretaceous, around the same
time as Eomaia, the first known eutherian (member of placentals' "parent" group); and the earliest known
monotreme, Teinolophos, appeared two million years later. After the Cretaceous-Tertiary extinction wiped out
the non-avian dinosaurs (birds are generally regarded as the surviving dinosaurs) and several other
mammalian groups, placental and marsupial mammals diversified into many new forms and ecological
niches throughout the Tertiary, by the end of which all modern orders had appeared.
From the point of view of phylogenetic nomenclature, mammals are the only surviving synapsids.
The synapsid lineage became distinct from the sauropsid ("reptile") lineage in the late Carboniferous period,
between 320 and 315 million years ago,[1] and were the most common and largest land vertebrates of the
Permian period.[2] But in the Triassic period a previously obscure group of sauropsids, the archosaurs,
became the dominant vertebrates and one archosaur group, the dinosaurs, dominated the rest of the
Mesozoic era. These changes forced the Mesozoic mammaliforms ("nearly mammals") into nocturnal niches,
and may have contributed greatly to the development of mammalian traits such as endothermy, hair and a
large brain. Later in the Mesozoic mammals spread into other ecological niches, for example aquatic, gliding
and even preying on dinosaurs.
Most of the evidence consists of fossils. For many years fossils of Mesozoic mammals and their
immediate ancestors were very rare and fragmentary, but since the mid 1990s there have been many
important new finds, especially in China. The relatively new techniques of molecular phylogenetics have also
shed light on some aspects of mammalian evolution by estimating the timing of important divergence points
for modern species. When used carefully, these techniques often, but not always, agree with the fossil
record.
Although mammary glands are a signature feature of modern mammals, little is known about the
evolution of lactation, and virtually nothing is known about the evolution of another distinctive feature, the
neocortex region of the brain. This is because these soft tissues are not often preserved in the fossil record.
Hence, most study of the evolution of mammals centers around the development of the middle ear bones
from components of the ancestral amniote jaw joint. Other much-studied aspects include the evolution of
erect limb posture, a bony secondary palate, fur and hair, and warm-bloodedness.
Contents
[hide]
• 1 Definition of "mammal"
• 2 The ancestry of mammals
• 2.1 Amniotes
• 2.2 Synapsids
• 3 Therapsids
• 3.1 Therapsid family tree
• 3.2 Biarmosuchia
• 3.3 Dinocephalians
• 3.4 Anomodonts
• 3.5 Theriodonts
• 3.6 Cynodonts
• 4 Triassic takeover
• 5 From cynodonts to true mammals
• 5.1 Many uncertainties
• 5.2 Mammals or mammaliformes?
• 5.3 Family tree — cynodonts to mammals
• 5.4 Multituberculates
• 5.5 Morganucodontidae
• 5.6 Docodonts
• 5.7 Hadrocodium
[edit] Definition of "mammal"
Mammalian and non-mammalian jaws. In the mammal configuration, the quadrate and articular
bones are much smaller and form part of the middle ear. Note that in mammals the lower jaw consists of only
the dentary bone.
Living mammal species can be identified by the presence of milk-producing mammary glands in
females. Other features are required when classifying fossils, since mammary glands and other soft-tissue
features are not visible in fossils.
Paleontologists therefore use a distinguishing feature that is shared by all living mammals (including
monotremes) but is not present in any of the early Triassic therapsids: Mammals use two bones for hearing
that all other amniotes use for eating. The earliest amniotes had a jaw joint composed of the articular (a small
bone at the back of the lower jaw) and the quadrate (a small bone at the back of the upper jaw). All non-
mammalian amniotes use this system including lizards, crocodilians, dinosaurs (and their descendants the
birds), and therapsids. But mammals have a different jaw joint, composed only of the dentary (the lower jaw
bone, which carries the teeth) and the squamosal (another small skull bone). In mammals, the quadrate and
articular bones have become the incus and malleus bones in the middle ear.[3][4]
Mammals also have a double occipital condyle; they have two knobs at the base of the skull that fit
into the topmost neck vertebra, and other vertebrates have a single occipital condyle.[3] But paleontologists
use only the jaw joint and middle ear as criteria for identifying fossil mammals, as it would be confusing if
they found a fossil that had one feature but not the other (e.g. a mammalian jaw and ear but a non-
mammalian single occipital condyle).
Due to the incremental changes in transitional fossils, it has been said
We may again ask the question, What is a mammal? Where we draw the line between reptile
and mammal has no biological significance. It is purely a matter of convenience. There are two
obvious choices, both immediately following a period of rapid evolution that make as definite a
break as we can hope to find.[5]
[edit] The ancestry of mammals

Tetrapods
Amphibians
Amniotes
Sauropsids (including
dinosaurs)
Synapsids
Pelycosaurs
Therapsids
Mammals
[edit] Amniotes
The first fully terrestrial vertebrates were amniotes — their eggs had internal membranes that allowed
the developing embryo to breathe but kept water in. This allowed amniotes to lay eggs on dry land, while
amphibians generally need to lay their eggs in water (a few amphibians, such as the Surinam toad, have
evolved other ways of getting round this limitation). The first amniotes apparently arose in the late
Carboniferous from the ancestral reptiliomorphs.
Within a few million years two important amniote lineages became distinct: mammals' synapsid
ancestors and the sauropsids, from which lizards, snakes, crocodilians, dinosaurs and birds are descended.
[1] The earliest known fossils of synapsids and sauropsids (such as Archaeothyris and Hylonomus resp.)
date from about 320 to 315 million years ago. Unfortunately it is difficult to be sure about when each of them
evolved, since vertebrate fossils from the late Carboniferous are very rare, and therefore the actual first
occurrences of each of these types of animal might have been considerably earlier.[6]
[edit] Synapsids
The original synapsid skull structure has one hole behind each eye, in a fairly low position on the
skull (lower right in this image).
Synapsid skulls are identified by the distinctive pattern of the holes behind each eye, which served
the following purposes:
• made the skull lighter without sacrificing strength.
• saved energy by using less bone.
• probably provided attachment points for jaw muscles. Having attachment points further away
from the jaw made it possible for the muscles to be longer and therefore to exert a strong pull over a
wide range of jaw movement without being stretched or contracted beyond their optimum range.
Early Permian terrestrial fossils indicate that one synapsid group, the pelycosaurs, were the most
common land vertebrates of their time and included the largest land animals of the time.[2]
[edit] Therapsids
Therapsids descended from pelycosaurs in the middle Permian and took over their position as the
dominant land vertebrates. They differ from pelycosaurs in several features of the skull and jaws, including
larger temporal fenestrae and incisors that are equal in size.[7]
The therapsids went through a series of stages, beginning with animals that were very like their
pelycosaur ancestors and ending with some that could easily be mistaken for mammals:[8]
• gradual development of a bony secondary palate. Most books and articles interpret this as a
prequisite for the evolution of mammals' high metabolic rate, because it enabled these animals to eat
and breathe at the same time. But some scientists point out that some modern ectotherms use a
fleshy secondary palate to separate the mouth from the airway, and that a bony palate provides a
surface on which the tongue can manipulate food, facilitating chewing rather than breathing.[9] The
interpretation of the bony secondary palate as an aid to chewing also suggests the development of a
faster metabolism, since chewing makes it possible to digest food more quickly. In mammals the
palate is formed by two specific bones, but various Permian therapsids had other combinations of
bones in the right places to function as a palate.
• the dentary gradually becomes the main bone of the lower jaw.
• progress towards an erect limb posture, which would increase the animals' stamina by
avoiding Carrier's constraint. But this process was erratic and very slow — for example: all
herbivorous therapsids retained sprawling limbs (some late forms may have had semi-erect hind
limbs); Permian carnivorous therapsids had sprawling forelimbs, and some late Permian ones also
had semi-sprawling hindlimbs. In fact, modern monotremes still have semi-sprawling limbs.
• in the Triassic, progress towards the mammalian jaw and middle ear.
• there is plausible evidence of hair in Triassic therapsids, but none for Permian therapsids
(see below).
• some scientists have argued that some Triassic therapsids show signs of lactation (see
below).
[edit] Therapsid family tree

(simplified from;[7] only those that are most relevant to the evolution of mammals are described
below)
Therapsids
Eutherapsida
Dinocephalia
Neotherapsida
Anomodonts
Dicynodonts
Theriodontia
Gorgonopsia
Eutheriodontia
Therocephalia
Cynodontia
(Mammals,
eventually)
Only the dicynodonts, therocephalians and cynodonts survived into the Triassic.
[edit] Biarmosuchia
The Biarmosuchia were the most primitive and pelycosaur-like of the therapsids.
[edit] Dinocephalians
Dinocephalians ("terrible heads") were large, some as large as a rhinoceros, and included both
carnivores and herbivores. Some of the carnivores had semi-erect hindlimbs, but all dinocephalians had
sprawling forelimbs. In many ways they were very primitive therapsids, for example they had no secondary
palate and their jaws were rather "reptilian".[10]
[edit] Anomodonts
Lystrosaurus, one of the few species of dicynodonts that survived the Permian-Triassic extinction
event
The anomodonts ("anomalous teeth") were the most successful of the herbivorous therapsids — one
sub-group, the dicynodonts, survived almost to the end of the Triassic. But anomodonts were very different
from modern herbivorous mammals, as their only teeth were a pair of fangs in the upper jaw and it is
generally agreed that they had beaks like those of birds or ceratopsians.[11]
[edit] Theriodonts
The theriodonts ("beast teeth") and their descendants had jaw joints in which the lower jaw's articular
bone tightly gripped the skull's very small quadrate bone. This allowed a much wider gape, and one group,
the carnivorous gorgonopsians ("gorgon faces"), took advantage of this to develop "sabre teeth". But the
theriodont's jaw hinge had a longer term significance — the much reduced size of the quadrate bone was an
important step in the development of the mammalian jaw joint and middle ear.
The gorgonopsians still had some primitive features: no bony secondary palate (but other bones in
the right places to perform the same functions); sprawling forelimbs; hindlimbs that could operate in both
sprawling and erect postures. But the therocephalians ("beast heads"), which appear to have arisen at about
the same time as the gorgonopsians, had additional mammal-like features, e.g. their finger and toe bones
had the same number of phalanges (segments) as in early mammals (and the same number that primates
have, including humans).[12]
[edit] Cynodonts
Artist's conception of the cynodont Trirachodon within a burrow

The cynodonts, a theriodont group that also arose in the late Permian, include the ancestors of all
mammals — one sub-group, the trithelodonts, is widely regarded as the most likely to contain mammals'
ancestor. Cynodonts' mammal-like features include further reduction in the number of bones in the lower jaw;
a secondary bony palate; cheek teeth with a complex pattern in the crowns; the brain filled the endocranial
cavity.[13]
Multi-chambered burrows have been found, containing as many as 20 skeletons of the Early Triassic
cynodont Trirachodon; the animals are thought to have been drowned by a flash flood. The extensive shared
burrows indicate that these animals were capable of complex social behaviors.[14]
[edit] Triassic takeover

The catastrophic Permian-Triassic mass extinction killed off about 70 percent of terrestrial vertebrate
species, and the majority of land plants. As a result[15]
• Ecosystems and food chains collapsed, and the recovery took about 6 million years.
• The survivors had to re-start the struggle for dominance of their former ecological niches —
even the cynodonts, which had seemed on the way to dominance at the end of the Permian.
But the cynodonts lost out to a previously obscure group of sauropsids, the archosaurs (which
include the ancestors of crocodilians, dinosaurs and birds). This reversal of fortunes is often called the
"Triassic takeover". Several explanations have been offered for it, but the most likely is that the early Triassic
was predominantly arid and therefore archosaurs' superior water conservation gave them a decisive
advantage (all known sauropsids have glandless skins and excrete uric acid, which requires less water to
keep it sufficiently liquid than urea, which marsupial and placental mammals excrete and presumably
therapsids excreted).[8][16] The Triassic takeover was gradual — in the earliest part of the Triassic cynodonts
were the main predators and lystrosaurs were the main herbivores, but by the mid-Triassic archosaurs
dominated all the large carnivore and herbivore niches.
But the Triassic takeover may have been a vital factor in the evolution of cynodonts into mammals.
The cynodonts' descendants were only able to survive as small, mainly nocturnal insectivores.[13] As a
result:
• The therapsid trend towards differentiated teeth with precise occlusion accelerated, because
of the need to hold captured arthropods and crush their exoskeletons.
• Nocturnal life required advances in thermal insulation and temperature regulation to enable
the ancestors of mammals to be active in the cool of the night.[17]
• Acute senses of hearing and smell became vital.
• This accelerated the development of the mammalian middle ear, and therefore of the
mammalian jaw since bones that had been part of the jaw joint became part of the middle
ear.
• The increase in the size of the olfactory and auditory lobes of the brain increased
brain weight as a total percentage of body weight. Brain tissue requires a disproportionate
amount of energy.[18][19] The need for more food to support the enlarged brains increased
the pressures for improvements in insulation, temperature regulation and feeding.
• As a side-effect of the nocturnal life, discerning colors became less important (they lost two
out of four opsins), and this is reflected in the fact that most mammals have poor color vision,
including the "lower primates" such as lemurs.[20]
[edit] From cynodonts to true mammals

[edit] Many uncertainties
While the Triassic takeover probably accelerated the evolution of mammals, it made life more difficult
for paleontologists because good fossils of the nearly-mammals are extremely rare, mainly because they
were mostly smaller than rats:
• They were largely restricted to environments that are less likely to provide good fossils. The
best terrestrial environments for fossilization are floodplains, where seasonal floods quickly cover
dead animals in a protective layer of silt that is later compressed into sedimentary rock. But
floodplains are dominated by medium to large animals, and the Triassic therapsids and near-
mammals could not compete with archosaurs in the medium to large size range.
• Their delicate bones were vulnerable to being destroyed before they could be fossilized — by
scavengers (including fungi and bacteria) and by being trodden on.
• Small fossils are harder to spot and more vulnerable to being destroyed by weathering and
other natural stresses before they are discovered.
In fact it was said as recently as the 1980s that all the Mesozoic fossils of mammals and near-
mammals could be contained in a few shoeboxes — and they were mostly teeth, which are the most durable
of all tissues.[21] Since then, the number of Mesozoic fossil mammals has increased, from 116 genera
known in 1979 to about 310 in 2007, with an increase in quality such that "at least 18 Mesozoic mammals are
represented by nearly complete skeletons".[22]
As a result:
• In many cases it is difficult to assign a Mesozoic mammal or near-mammal fossil to a genus.
• All the available fossils of a genus seldom add up to a complete skeleton, and hence it is
difficult to decide which genera are most like each other and therefore most likely to be closely-
related. In other words, it becomes very difficult to classify them by means of cladistics, which is the
most reliable and least subjective method currently available.
So the evolution of mammals in the Mesozoic is full of uncertainties, although there is no room for
doubt that true mammals did first appear in the Mesozoic.
[edit] Mammals or mammaliformes?
One result of these uncertainties has been a change in the paleontologists' definition of "mammal".
For a long time a fossil was considered a mammal if it met the jaw-ear criterion (the jaw joint consists only of
the squamosal and dentary; and the articular and the quadrate bones have become the middle ear's malleus
and incus). But more recently some paleontologists have usually defined "mammal" as the crown group
mammals, i.e. the last common ancestor of monotremes, marsupials and placentals and all of its
descendants. The need to address the animals that are more mammal-like than cynodonts, but less closely
related to monotremes, marsupials and placentals, lead to erecting the group mammaliformes to
accommodate these primitive forms. Mammaliformes is a paraphyletic taxon, representing the early radiation
of mammals after the jaw-ear criterion.[23] Although this now appears to be the majority approach, some
paleontologists have resisted it because it simply moves most of the problems into the new taxon (a
paraphyletic one at that) without solving the original problem; the Mammaliformes includes some animals
with "mammalian" jaw joints and some with "reptilian" (articular-to-quadrate) jaw joints; and the newer
definition of "mammal" and "mammaliformes" depend on last common ancestors of both groups, which have
not yet been found.[21] Despite these objections, this article follows the majority approach and treats most of
the cynodonts' Mesozoic descendants as mammaliformes.
[edit] Family tree — cynodonts to mammals

(based on Mammaliformes - Palaeos)
Cynodontia
Dvinia
Procynosuchidae
Epicynodontia
Eucynodontia
Probainognathia
Trithelodontidae
Chiniquodontidae
Mammaliaformes
Allotheria
Multituberc
Morganucodontidae
Docodonta
Hadrocodium
Symmetrodonta
Kuehneotheriidae
crown group
Mammals (all
descendants of the last
common ancestor of all
living mammals)
[edit] Multituberculates
Skull of the multituberculate Ptilodus

Multituberculates (named for the multiple tubercles on their "molars") are often called the "rodents of
the Mesozoic" but this is an example of convergent evolution rather than meaning that they are closely
related to the Rodentia. At first sight they look like mammals: their jaw joints consists of only the dentary and
squamosal bones, and the quadrate and articular bones are part of the middle ear; their teeth are
differentiated, occlude and have mammal-like cusps; they have a zygomatic arch; the structure of the pelvis
suggests that they gave birth to tiny helpless young, like modern marsupials. And they lived for over 120
million years (from mid Jurassic, about 160M years ago, to early Oligocene, about 35M years ago), which in
terms of clade longevity would make them the most successful mammaliformes ever. But a closer look
shows that they are very different from modern mammals:[23]
• Their "molars" have two parallel rows of tubercles, unlike the tribosphenic (three-peaked)
molars of early mammals.
• The chewing action is completely different. Mammals chew with a side-to-side grinding
action, which means that usually the molars occlude on only one side at a time. Multituberculates'
jaws were incapable of side-to-side movement and chewed by dragging the lower teeth backwards
against the upper ones as the jaw closed.
• The anterior (forward) part of the zygomatic arch mostly consists of the maxilla (upper
jawbone) rather than the jugal, and the jugal is a small bone in a little slot in the maxillary process
(extension).
• The squamosal does not form part of the braincase.
• The rostrum (snout) is unlike that of mammals, in fact it looks more like that of a pelycosaur
such as Dimetrodon. The multituberculate rostrum is box-like, with the large flat maxillae forming the
sides, the nasal the top, and the tall premaxilla at the front.
Morganucodontidae and other transitional forms had both types of jaw joint: dentary-squamosal
(front) and articular-quadrate (rear).
[edit] Morganucodontidae
The Morganucodontidae first appeared in the late Triassic, about 205M years ago. They are an
excellent example of transitional fossils, since they have both the dentary-squamosal and articular-quadrate
jaw joints.[24] They were also one of the first discovered and most thoroughly studied of the mammaliformes,
since an unusually large number of morganucodont fossils have been found.
[edit] Docodonts
Reconstruction of Castorocauda. Note the fur and the adaptations for swimming (broad, flat tail;
webbed feet) and for digging (robust limbs and claws).
The most notable member of the docodonts is Castorocauda ("beaver tail"), which lived in the mid
Jurassic about 164M years ago and was first discovered in 2004 and described in 2006. Castorocauda was
not a typical docodont (most were omnivores) and not a true mammal, but it is extremely important in the
study of the evolution of mammals because the first find was an almost complete skeleton (a real luxury in
paleontology) and it breaks the "small nocturnal insectivore" stereotype:[25]
• It was noticeably larger than most Mesozoic mammal-like fossils — about 17 in (43 cm) from
its nose to the tip of its 5-inch (130 mm) tail, and may have weighed 500–800 g (18–28 oz).
• It provides the earliest absolutely certain evidence of hair and fur. Previously the earliest was
Eomaia, a true mammal from about 125M years ago.
• It had aquatic adaptations including flattened tail bones and remnants of soft tissue between
the toes of the back feet, suggesting that they were webbed. Previously the earliest known semi-
aquatic mammal-like animals were from the Eocene, about 110M years later.
• Castorocauda's powerful forelimbs look adapted for digging. This feature and the spurs on its
ankles make it resemble the platypus, which also swims and digs.
• Its teeth look adapted for eating fish: the first two molars had cusps in a straight row, which
made them more suitable for gripping and slicing than for grinding; and these molars are curved
backwards, to help in grasping slippery prey.
[edit] Hadrocodium
Hadrocodium skull. The jaw joint is fully mammalian (squamosal-dentary only) and farther forward
than in earlier transitional forms.
The consensus family tree above shows Hadrocodium as an "aunt" of true mammals, while
symmetrodonts and kuehneotheriids are more closely related to true mammals. But fossils of symmetrodonts
and kuehneotheriids are so few and fragmentary that they are poorly understood and may be paraphyletic.
[26] On the other hand there are good fossils of Hadrocodium (about 195M years ago in the very early
Jurassic) and they have some important features: [27]
• The jaw joint consists only of the squamosal and dentary bones, and the jaw contains no
smaller bones to the rear of the dentary, unlike the therapsid design.
• In therapsids and most mammaliformes the eardrum stretched over a trough at the rear of
the lower jaw. But Hadrocodium had no such trough, which suggests its ear was part of the cranium,
as it is in mammals — and hence that the former articular and quadrate had migrated to the middle
ear and become the malleus and incus. On the other hand the dentary has a "bay" at the rear that
mammals lack. This suggests that Hadrocodium's dentary bone retained the same shape that it
would have had if the articular and quadrate had remained part of the jaw joint, and therefore that
Hadroconium or a very close ancestor may have been the first to have a fully mammalian middle ear.
• Therapsids and earlier mammaliforms had their jaw joints very far back in the skull, partly
because the ear was at the rear end of the jaw but also had to be close to the brain. This
arrangement limited the size of the braincase, because it forced the jaw muscles to run round and
over it. Hadrocodium's braincase and jaws were no longer bound to each other by the need to
support the ear, and its jaw joint was further forward. In its descendants or those of animals with a
similar arrangement, the brain case was free to expand without being constrained by the jaw and the
jaw was free to change without being constrained by the need to keep the ear near the brain — in
other words it now became possible for mammal-like animals both to develop large brains and to
adapt their jaws and teeth in ways that were purely specialized for eating.
[edit] The earliest true mammals

This part of the story introduces new complications, since true mammals are the only group that still
has living members:
• One has to distinguish between extinct groups and those that have living representatives.
• One often feels compelled to try to explain the evolution of features that do not appear in
fossils. This endeavor often involves Molecular phylogenetics, a technique that has become popular
since the mid-1980s but is still often controversial because of its assumptions, especially about the
reliability of the molecular clock.
[edit] Family tree of early true mammals
(based on Mammalia: Overview - Palaeos; X marks extinct groups)
Mammals
Australosphenida
Ausktribosphenidae X
Monotremes
Triconodonta
X
Spalacotheroidea
X
Cladotheria
Dryolestoidea
X
Theria
Metatheria
Eutheria
[edit] Australosphenida and Ausktribosphenidae
Ausktribosphenidae is a group name that has been given to some rather puzzling finds that:[28]
• appear to have tribosphenic molars, a type of tooth that is otherwise known only in placentals
and marsupials.[29]
• come from mid Cretaceous deposits in Australia — but Australia was connected only to
Antarctica, and placentals originated in the northern hemisphere and were confined to it until
continental drift formed land connections from North America to South America, from Asia to Africa
and from Asia to India (the late Cretaceous map at [1] shows how the southern continents are
separated).
• are represented only by skull and jaw fragments, which is not very helpful.
Australosphenida is a group that has been defined in order to include the Ausktribosphenidae and
monotremes. Asfaltomylos (mid- to late Jurassic, from Patagonia) has been interpreted as a basal
australosphenid (animal that has features shared with both Ausktribosphenidae and monotremes; lacks
features that are peculiar to Ausktribosphenidae or monotremes; also lacks features that are absent in
Ausktribosphenidae and monotremes) and as showing that australosphenids were widespread throughout
Gondwanaland (the old Southern hemisphere super-continent).[30]
But recent analysis of Teinolophos suggests Teinolophos (about 115M years ago) was a "crown
group" (advanced and relatively specialised) monotreme, so the basal (most primitive) monotremes must
have appeared considerably earlier; that some alleged Australosphenids were also "crown group"
monotremes (e.g. Steropodon); and that other alleged Australosphenids (e.g. Ausktribosphenos, Bishops,
Ambondro, Asfaltomylos) are therefore more closely related to and possibly members of the Therian
mammals (group that includes marsupials and placentals, see below).[31]
[edit] Monotremes
The earliest known monotreme is Teinolophos, which lived about 123M years ago in Australia.
Recent (2007, published 2008) analysis suggest that it was not a basal (primitive, ancestral) monotreme but
a full-fledged platypus, and therefore that the platypus and echidna lineages diverged considerably earlier
and that basal monotremes were even earlier.[31]
A more recent study (2009), however, has suggested that while Teinolophis was a type of platypus, it
also was a basal monotreme and predated the radiation of modern monotremes. The semi-aquatic lifestyle of
platypuses prevented them from being outcompeted by the marsupials that migrated to Australia millions of
years ago, since joeys need to keep attached to their mothers and would drown if their mothers ventured into
water. Genetic evidence has determined that echidnas diverged from the platypus lineage as recently as 19-
48M when they made their transition from semi-aquatic to terrestrial lifestyle.[32]
Monotremes have some features that may be inherited from the original amniotes:
• they use the same orifice to urinate, defecate and reproduce ("monotreme" means "one
hole") — as lizards and birds also do.
• they lay eggs that are leathery and uncalcified, like those of lizards, turtles and crocodilians.
Unlike in other mammals, female monotremes do not have nipples and feed their young by
"sweating" milk from patches on their bellies.
Of course these features are not visible in fossils, and the main characteristics from paleontologists'
point of view are:[28]
• a slender dentary bone in which the coronoid process is small or non-existent.
• the external opening of the ear lies at the posterior base of the jaw.
• the jugal bone is small or non-existent.
• a primitive pectoral girdle with strong ventral elements: coracoids, clavicles and interclavicle.
Note: therian mammals have no interclavicle.[33]
• sprawling or semi-sprawling forelimbs.
[edit] Theria
Theria ("beasts") is a name applied to the hypothetical group from which both metatheria (which
include marsupials) and eutheria (which include placentals) descended. Although no convincing fossils of
basal therians have been found (just a few teeth and jaw fragments), metatheria and eutheria share some
features that one would expect to have been inherited from a common ancestral group:[34]
Therian form of crurotarsal ankle. Adapted with permission from Palaeos
• no interclavicle.[33]
• coracoid bones non-existent or fused with the shoulder blades to form coracoid processes.
• a type of crurotarsal ankle joint in which: the main joint is between the tibia and astragalus;
the calcaneum has no contact with the tibia but forms a heel to which muscles can attach. (The other
well-known type of crurotarsal ankle is seen in crocodilians and works differently — most of the
bending at the ankle is between the calcaneum and astragalus).
• tribosphenic molars.[29]
Tribosphenic molars have been found in fossils from Madagascar, which indicates that therian
mammals are at least 167 million years old.[35]
[edit] Metatheria
The living Metatheria are all marsupials ("animals with pouches"). A few fossil genera such as the
Mongolian late Cretaceous Asiatherium may be marsupials or members of some other metatherian group(s).
[36][37]
The oldest known marsupial is Sinodelphys, found in 125M-year old early Cretaceous shale in
China's northeastern Liaoning Province. The fossil is nearly complete and includes tufts of fur and imprints of
soft tissues.[38]
Didelphimorphia (common opossums of the Western Hemisphere) first appeared in the late
Cretaceous and still have living representatives, probably because they are mostly semi-arboreal
unspecialized omnivores.[39]
The best-known feature of marsupials is their method of reproduction:
• The mother develops a kind of yolk sack in her womb that delivers nutrients to the embryo.
Embryos of bandicoots, koalas and wombats additionally form placenta-like organs that connect
them to the uterine wall, although the placenta-like organs are smaller than in placental mammals
and it is not certain that they transfer nutrients from the mother to the embryo.[40]
• Pregnancy is very short, typically 4 to 5 weeks. The embryo is born at a very young age of
development, and is usually less than 2 in (5.1 cm) long at birth. It has been suggested that the short
pregnancy is necessary to reduce the risk that the mother's immune system will attack the embryo.
• The newborn marsupial uses its forelimbs (with relatively strong hands) to climb to a nipple,
which is usually in a pouch on the mother's belly. The mother feeds the baby by contracting muscles
over her mammary glands, as the baby is too weak to suck. The newborn marsupial's need to use its
forelimbs in climbing to the nipple has prevented the forelimbs from evolving into paddles or wings
and has therefore prevented the appearance of aquatic or truly flying marsupials (although there are
several marsupial gliders).
Palate of thylacine, showing one of the paired palatal fenestrae (top left), which are a signature
feature of marsupials.
Although some marsupials look very like some placentals (the thylacine or "marsupial wolf" is a good
example), marsupial skeletons have some features that distinguish them from placentals:[41]
• Some, including the thylacine, have 4 molars. No placentals have more than 3.
• All have a pair of palatal fenestrae, window-like openings on the bottom of the skull (in
addition to the smaller nostril openings).
Marsupials also have a pair of marsupial bones (sometimes called "epipubic bones"), which support
the pouch in females. But these are not unique to marsupials, since they have been found in fossils of
multituberculates, monotremes, and even eutherians — so they are probably a common ancestral feature that
disappeared at some point after the ancestry of living placental mammals diverged from that of marsupials.
[42][43] Some researchers think the epipubic bones' original function was to assist locomotion by supporting
some of the muscles that pull the thigh forwards.[44]
[edit] Eutheria
Main article: Eutheria
The living Eutheria ("true beasts") are all placentals. But the earliest known eutherian, Eomaia, found
in China and dated to 125M years ago, has some features that are more like those of marsupials (the
surviving metatherians):[45]
Fossil of Eomaia in the Hong Kong Science Museum.
• Epipubic bones extending forwards from the pelvis, which are not found in any modern
placental, but are found in all other mammals — non-placental eutherians, marsupials, monotremes
and mammaliformes — and even in the cynodont therapsids that are closest to mammals. Their
function is to stiffen the body during locomotion.[46] This stiffening would be harmful in pregnant
placentals, whose abdomens need to expand.[47]
• A narrow pelvic outlet, which indicates that the young were very small at birth and therefore
pregnancy was short, as in modern marsupials. This suggests that the placenta was a later
development.
• 5 incisors in each side of the upper jaw. This number is typical of metatherians, and the
maximum number in modern placentals is 3, except for homodonts such as the armadillo. But
Eomaia's molar to premolar ratio (it has more pre-molars than molars) is typical of eutherians,
including placentals, and not normal in marsupials.
Eomaia also has a Meckelian groove, a primitive feature of the lower jaw that is not found in modern
placental mammals.
These intermediate features are consistent with molecular phylogenetics estimates that the
placentals diversified about 110M years ago, 15M years after the date of the Eomaia fossil.
Eomaia also has many features that strongly suggest it was a climber, including several features of
the feet and toes; well-developed attachment points for muscles that are used a lot in climbing; and a tail that
is twice as long as the rest of the spine.
Placentals' best-known feature is their method of reproduction:
• The embryo attaches itself to the uterus via a large placenta via which the mother supplies
food and oxygen and removes waste products.
• Pregnancy is relatively long and the young are fairly well-developed at birth. In some species
(especially herbivores living on plains) the young can walk and even run within an hour of birth.
It has been suggested that the evolution of placental reproduction was made possible by retroviruses
that:[48]
• make the interface between the placenta and uterus into a syncytium, i.e. a thin layer of cells
with a shared external membrane. This allows the passage of oxygen, nutrients and waste products
but prevents the passage of blood and other cells, which would cause the mother's immune system
to attack the fetus.
• reduce the aggressiveness of the mother's immune system (which is good for the foetus but
makes the mother more vulnerable to infections).
From a paleontologist's point of view, eutherians are mainly distinguished by various features of their
teeth,[49] ankles and feet.[50]
[edit] Expansion of ecological niches in the Mesozoic

There is still some truth in the "small, nocturnal insectivores" stereotype but recent finds, mainly in
China, show that some mammaliforms and true mammals were larger and had a variety of lifestyles. For
example:
• Castorocauda, a member of Docodonta which lived in the middle Jurassic about 164 million
years, was about 42.5 cm (16.7 in) long, weighed 500–800 g (18–28 oz), had limbs that were adapted
for swimming and digging and teeth adapted for eating fish.[25]
• Multituberculates, are allotherians that survived for over 125 million years (from mid Jurassic,
about 160M years ago, to early Oligocene, about 35M years ago) are often called the "rodents of the
Mesozoic", because they had continuously-growing incisors like those of modern rodents.[23]
Repenomamus sometimes preyed on young dinosaurs

• Fruitafossor, from the late Jurassic period about 150 million years ago, was about the size of
a chipmunk and its teeth, forelimbs and back suggest that it broke open the nest of social insects to
prey on them (probably termites, as ants had not yet appeared).[51]
• Volaticotherium, allotherians from the boundary the early Cretaceous about 125M years ago,
is the earliest-known gliding mammal and had a gliding membrane that stretched out between its
limbs, rather like that of a modern flying squirrel. This also suggests it was active mainly during the
day.[52]
• Repenomamus, tricodonts from the early Cretaceous 130 million years ago, was a stocky,
badger-like predator that sometimes preyed on young dinosaurs. Two species have been
recognized, one more than 1 m (39 in) long and weighing about 12–14 kg (26–31 lb), the other less
than 0.5 m (20 in) long and weighing 4–6 kg (8.8–13 lb).[53][54]
[edit] Evolution of major groups of living mammals

There are currently vigorous debates between traditional paleontologists ("fossil-hunters") and
molecular phylogeneticists about how and when the true mammals diversified, especially the placentals.
Generally the traditional paelontologists date the appearance of a particular group by the earliest known
fossil whose features make it likely to be a member of that group, while the molecular phylogeneticists
suggest that each lineage diverged earlier (usually in the Cretaceous) and that the earliest members of each
group were anatomically very similar to early members of other groups and differed only in their genes.
These debates extend to the definition of and relationships between the major groups of placentals — the
controversy about Afrotheria is a good example.
[edit] Fossil-based family tree of placental mammals

Here is a very simplified version of a typical family tree based on fossils, based on Cladogram of
Mammalia - Palaeos. It tries to show the nearest thing there is at present to a consensus view, but some
paleontologists have very different views, for example:[55]
• The most common view is that placentals originated in the southern hemisphere, but some
paleontologists argue that they first appeared in Laurasia (old supercontinent containing modern
Asia, N. America and Europe).
• Paleontologists differ about when the first placentals appeared, with estimates ranging from
20M years before the end of the Cretaceous to just after the end of the Cretaceous. And molecular
biologists argue for a much earlier origin.
• Most paleontologists suggest that placentals should be divided into Xenarthra and the rest,
but a few think these animals diverged later.
For the sake of brevity and simplicity the diagram omits some extinct groups in order to focus on the
ancestry of well-known modern groups of placentals — X marks extinct groups. The diagram also shows the
following:
• the age of the oldest known fossils in many groups, since one of the major debates between
traditional paleontologists and molecular phylogeneticists is about when various groups first became
distinct.
• well-known modern members of most groups.
Eutheria
Epitheria (latest Cretaceous)

Anagalida
Zalambdalestidae X
(late Cretaceous)
Macroscelidea
(late Eocene)
(elephant shrews)
Anagaloidea
X
Glires (early Paleocene)

Lagomorpha
(Eocene)
(rabbits, hares, pikas)
Rodentia (late
Paleocene)
(mice & rats, squirrels,
porcupines)
Archonta
Scandentia (mid
Eocene)
(tree shrews)
Primatomorpha
Plesiadapiformes X
Primates (early Paleocene)
(tarsiers, lemurs, monkeys, apes including humans)
Dermoptera (late Eocene)

(colugos)
Chiroptera (late Paleocene)

(bats)
Carnivora
(early Paleocene)
(cats, dogs, bears,
seals)
Ungulatomorpha (late Cretaceous)
Eparctocyona (late Cretaceous)
(some
extinct groups)
X
Arctostylopida
X (late Paleocene)
Mesonychia
X (mid Paleocene)
(predators /
scavengers, but not
closely related to
modern carnivores)
Cetartiodactyla
Cetacea
(early Eocene)
(whales, dolphins,
porpoises)
Artiodactyla
(early Eocene)
(even-toed
ungulates: pigs,
hippos, camels,
giraffes, cattle,
deer)
Altungulata
Hilalia
X
Perissodactyla (late Paleocene)

(odd-toed ungulates: horses, rhinos, tapirs)
Tubulidentata (early Miocene)

(aardvarks)
Paenungulata ("not quite ungulates")

Hyracoidea (early
Eocene)
(hyraxes)
Sirenia (early
Eocene)
(manatees, dugongs)
Proboscidea (early
Eocene)
(elephants)
This family tree contains some surprises and puzzles. For example:
• The closest living relatives of cetaceans (whales, dolphins, porpoises) are artiodactyls,
hoofed animals, which are almost all pure vegetarians.
• Bats are fairly close relatives of primates.
• The closest living relatives of elephants are the aquatic sirenians, while their next relatives
are hyraxes, which look more like well-fed guinea pigs.
• There is little correspondence between the structure of the family (what was descended from
what) and the dates of the earliest fossils of each group. For example the earliest fossils of
perissodactyls (the living members of which are horses, rhinos and tapirs) date from the late
Paleocene but the earliest fossils of their "sister group" the Tubulidentata date from the early
Miocene, nearly 50M years later. Paleontologists are fairly confident about the family relationships,
which are based on cladistic analyses, and believe that fossils of the ancestors of modern aardvarks
have simply not been found yet.
[edit] Family tree of placental mammals according to molecular
phylogenetics
Molecular phylogenetics uses features of organisms' genes to work out family trees in much the
same way as paleontologists do with features of fossils — if two organisms' genes are more similar to each
other than to those of a third organism, the two organisms are more closely related to each other than to the
third.
Molecular phylogeneticists have proposed a family tree that is very different from the one with which
paleontologists are familiar. Like paleontologists, molecular phylogeneticists have different ideas about
various details, but here is a typical family tree according to molecular phylogenetics:[56][57] Note that the
diagram shown here omits extinct groups, as one cannot extract DNA from fossils.
Eutheria
Atlantogenata ("born round the Atlantic ocean")
Xenarthra
(armadillos,
anteaters, sloths)
Afrotheria
Afroinsectiphilia
(golden moles, tenrecs,
otter shrews)
unnamed
Macroscelidea (elephant
shrews)
Tubulidentata (aardvarks)
Paenungulata ("not quite ungulate

s")
Hyracoidea (hyraxes)
Proboscidea (elephants)
Sirenia (manatees,
dugongs)
Boreoeutheria ("northern true / placental mammals")
Laurasiatheria
Erinaceomorpha (hedgehogs,
gymnures)
Soricomorpha (moles, shrews,

solenodons)
Cetartiodactyla
Pegasoferae
Pholidota (pangolins)
Chiroptera (bats)
Carnivora (cats, dogs, bears,
seals)
Perissodactyla (horses,
rhinos, tapirs).
Euarchontoglires
Glires
Lagomorpha (rabbits, hares, pikas)
Rodentia (late Paleocene)(mice & rats, squirrels,

porcupines)
Euarchonta
Scandentia (tree shrews)
Dermoptera (colugos)
Primates (tarsiers, lemurs, monkeys, apes including

humans)
Here are the most significant of the many differences between this family tree and the one familiar to
paleontologists:
• The top-level division is between Atlantogenata and Boreoeutheria, instead of between
Xenarthra and the rest. But some molecular phylogeneticists have proposed a 3-way top-level split
between Xenarthra, Afrotheria and Boreoeutheria.
• Afrotheria contains several groups that are only distantly related according to the
paleontologists' version: Afroinsectiphilia ("African insectivores"), Tubulidentata (aardvarks, which
paleontologists regard as much closer to odd-toed ungulates than to other members of Afrotheria),
Macroscelidea (elephant shrews, usually regarded as close to rabbits and rodents). The only
members of Afrotheria that paleontologists would regard as closely related are Hyracoidea (hyraxes),
Proboscidea (elephants) and Sirenia (manatees, dugongs).
• Insectivores are split into 3 groups: one is part of Afrotheria and the other two are distinct
sub-groups within Boreoeutheria.
• Bats are closer to Carnivora and odd-toed ungulates than to primates and Dermoptera
(colugos).
• Perissodactyla (odd-toed ungulates) are closer to Carnivora and bats than to Artiodactyla
(even-toed ungulates).
The grouping together of the Afrotheria has some geological justification. All surviving members of
the Afrotheria originate from South American or (mainly) African lineages — even the Indian elephant, which
diverged from an African lineage about 7.6 million years ago.[58] As Pangaea broke up Africa and South
America separated from the other continents less than 150M years ago, and from each other between 100M
and 80M years ago.[59][60] The earliest known eutherian mammal is Eomaia, from about 125M years ago.
So it would not be surprising if the earliest eutherian immigrants into Africa and South America were isolated
there and radiated into all the available ecological niches.
Nevertheless these proposals have been controversial. Paleontologists naturally insist that fossil
evidence must take priority over deductions from samples of the DNA of modern animals. More surprisingly,
these new family trees have been criticised by other molecular phylogeneticists, sometimes quite harshly:[61]
• Mitochondrial DNA's mutation rate in mammals varies from region to region — some parts
hardly ever change and some change extremely quickly and even show large variations between
individuals within the same species.[62][63]
• Mammalian mitochondrial DNA mutates so fast that it causes a problem called "saturation",
where random noise drowns out any information that may be present. If a particular piece of
mitochondrial DNA mutates randomly every few million years, it will have changed several times in
the 60 to 75M years since the major groups of placental mammals diverged.[64]
[edit] Timing of placental evolution

Recent molecular phylogenetic studies suggest that most placental orders diverged about 100M to
85M years ago, but that modern families first appeared in the late Eocene and early Miocene.[65]
Some paleontologists object that no placental fossils have been found from before the end of the
Cretaceous — for example Maelestes gobiensis, from about 75M years ago, is a eutherian but not a true
placental.[66] Many Cretaceous fossil sites contain well-preserved lizards, salamanders, birds, and
mammals, but not the modern forms of mammals. It is likely that they simply did not exist, and that the
molecular clock runs fast during major evolutionary radiations.[67] On the other hand there is fossil evidence
from 85 million years ago of hoofed animals that may be ancestors of modern ungulates.[68]
Fossils of the earliest members of most modern groups date from the Paleocene, a few date from
later and very few from the Cretaceous, before the extinction of the dinosaurs. But some paleontologists,
influenced by molecular phylogenetic studies, have used statistical methods to extrapolate backwards from
fossils of members of modern groups and concluded that primates arose in the late Cretaceous.[69] However
statistical studies of the fossil record confirm that mammals were restricted in size and diversity right to the
end of the Cretaceous, and rapidly grew in size and diversity during the Early Paleocene.[70][71]
[edit] Evolution of mammalian features

[edit] Jaws and middle ears
See also Evolution of mammalian auditory ossicles
Hadrocodium, whose fossils date from the early Jurassic, provides the first clear evidence of fully
mammalian jaw joints and middle ears, in which the jaw joint is formed by the dentary and squamosal bones
while the articular and quadrate move to the middle ear, where they are known as the incus and malleus.
Curiously it is usually classified as a member of the mammaliformes rather than a as a true mammal.
One analysis of the monotreme Teinolophos suggested that this animal had a pre-mammalian jaw
joint formed by the angular and quadrate bones and that the typical mammalian middle ear evolved twice
independently, in monotremes and in therian mammals, but this idea has been disputed.[72] In fact 2 of the
suggestion's authors co-authored a later paper that reinterpreted the same features as evidence that
Teinolophos was a full-fledged platypus, which means it would have had a mammalian jaw joint and middle
ear.[31]
[edit] Milk production (lactation)

It has been suggested that lactation's original function was to keep eggs moist. Much of the argument
is based on monotremes (egg-laying mammals):[73][74][75]
• Monotremes do not have nipples but secrete milk from a hairy patch on their bellies.
• During incubation, monotremes' eggs are covered in a sticky substance whose origin is not
known. Before the eggs are laid, their shells have only three layers. Afterwards a fourth layer
appears, and its composition is different from that of the original three. The sticky substance and the
fourth layer may be produced by the mammary glands.
• If so, that may explain why the patches from which monotremes secrete milk are hairy — it is
easier to spread moisture and other substances over the egg from a broad, hairy area than from a
small, bare nipple.
[edit] Hair and fur

See also: Evolution of hair
The first clear evidence of hair or fur is in fossils of Castorocauda, from 164M years ago in the mid
Jurassic.
From 1955 onwards some scientists have interpreted the foramina (passages) in the maxillae (upper
jaws) and premaxillae (small bones in front of the maxillae) of cynodonts as channels that supplied blood
vessels and nerves to vibrissae (whiskers), and suggested that this was evidence of hair or fur.[76][77] But
foramina do not necessarily show that an animal had vibrissae — for example the modern lizard Tupinambis
has foramina that are almost identical to those found in the non-mammalian cynodont Thrinaxodon.[9][78]
[edit] Erect limbs

The evolution of erect limbs in mammals is incomplete — living and fossil monotremes have sprawling
limbs. In fact some scientists think that the parasagittal (non-sprawling) limb posture is a synapomorphy
(distinguishing characteristic) of the Boreosphenida, a group that contains the Theria and therefore includes
the last common ancestor of modern marsupials and placentals — and therefore that all earlier mammals had
sprawling limbs.[79]
Sinodelphys (the earliest known marsupial) and Eomaia (the earliest known eutherian) lived about
125M years ago, so erect limbs must have evolved before then.
[edit] Warm-bloodedness
"Warm-bloodedness" is a complex and rather ambiguous term, because it includes some or all of the
following:
• Endothermy, i.e. the ability to generate heat internally rather than via behaviors such as
basking or muscular activity.
• Homeothermy, i.e. maintaining a fairly constant body temperature.
• Tachymetabolism, i.e. maintaining a high metabolic rate, particularly when at rest. This
requires a fairly high and stable body temperature, since biochemical processes run about half as
fast if an animal's temperature drops by 10°C; most enzymes have an optimum operating
temperature and their efficiency drops rapidly outside the preferred range.
Since scientists cannot know much about the internal mechanisms of extinct creatures, most
discussion focuses on homeothermy and tachymetabolism.
Modern monotremes have a lower body temperature and more variable metabolic rate than
marsupials and placentals.[80] So the main question is when a monotreme-like metabolism evolved in
mammals. The evidence found so far suggests Triassic cynodonts may have had fairly high metabolic rates,
but is not conclusive.
[edit] Respiratory turbinates
Modern mammals have respiratory turbinates, convoluted structures of thin bone in the nasal cavity.
These are lined with mucous membranes that warm and moisten inhaled air and extract heat and moisture
from exhaled air. An animal with respiratory turbinates can maintain a high rate of breathing without the
danger of drying its lungs out, and therefore may have a fast metabolism. Unfortunately these bones are very
delicate and therefore have not yet been found in fossils. But rudimentary ridges like those that support
respiratory turbinates have been found in Triassic therapsids such as Thrinaxodon and Diademodon, which
suggests that they may have had fairly high metabolic rates. [76] [81][82]
[edit] Bony secondary palate

Mammals have a secondary bony palate, which separates the respiratory passage from the mouth,
allowing them to eat and breathe at the same time. Secondary bony palates have been found in the more
advanced cynodonts and have been used as evidence of high metabolic rates.[76][77][83] But some cold-
blooded vertebrates have secondary bony palates (crocodilians and some lizards), while birds, which are
warm-blooded, do not have them.[9]
[edit] Diaphragm
A muscular diaphragm helps mammals to breathe, especially during strenuous activity. For a
diaphragm to work, the ribs must not restrict the abdomen, so that expansion of the chest can be
compensated for by reduction in the volume of the abdomen and vice versa. The advanced cynodonts have
very mammal-like rib cages, with greatly reduced lumbar ribs. This suggests that these animals had
diaphragms, were capable of strenuous activity for fairly long periods and therefore had high metabolic rates.
[76][77] On the other hand these mammal-like rib cages may have evolved to increase agility.[9] But the
movement of even advanced therapsids was "like a wheelbarrow", with the hindlimbs providing all the thrust
while the forelimbs only steered the animal, in other words advanced therapsids were not as agile as either
modern mammals or the early dinosaurs.[84] So the idea that the main function of these mammal-like rib
cages was to increase agility is doubtful.
[edit] Limb posture

The therapsids had sprawling forelimbs and semi-erect hindlimbs.[77][85] This suggests that
Carrier's constraint would have made it rather difficult for them to move and breathe at the same time, but not
as difficult as it is for animals such as lizards, which have completely sprawling limbs.[86] But cynodonts
(advanced therapsids) had costal plates that stiffened the rib cage and therefore may have reduced sideways
flexing of the trunk while moving, which would have made it a little easier for them to breathe while moving .
[87] These facts suggest that advanced therapsids were significantly less active than modern mammals of
similar size and therefore may have had slower metabolisms.
[edit] Insulation (hair and fur)

Insulation is the "cheapest" way to maintain a fairly constant body temperature, without consuming
energy to produce more body heat. Therefore, possession of hair or fur would be good evidence of
homeothermy but would not be such strong evidence of a high metabolic rate.[88] [89]
The first clear evidence of hair or fur is in fossils of Castorocauda, from 164M years ago in the mid
Jurassic;[25] arguments that advanced therapsids had hair are unconvincing.
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68.^ Archibald, J.D. (May 1996). "Fossil Evidence for a Late Cretaceous Origin of "Hoofed"
Mammals". Science 272 (5265): 1150–1153. doi:10.1126/science.272.5265.1150. PMID 8662448.
69.^ Martin, R.D.; Soligo, C.; Tavaré, S. (2007). "Primate Origins: Implications of a Cretaceous
Ancestry" (PDF). Folia Primatologica 78 (78): 277–296. doi:10.1159/000105145. PMID 17855783.
http://content.karger.com/ProdukteDB/produkte.asp?
Aktion=ShowPDF&ArtikelNr=105145&Ausgabe=233328&ProduktNr=223842&filename=105145.pdf.
— a similar paper by these authors is free online at New light on the dates of primate origins and
divergence
70.^ Alroy J. (March 1999). "The fossil record of North American mammals: evidence for a
Paleocene evolutionary radiation". Systematic biology 48 (1): 107–18.
doi:10.1080/106351599260472. PMID 12078635.
71.^ Archibald J.D., and Deutschman D.H. (June 2001). "Quantitative Analysis of the Timing of
the Origin and Diversification of Extant Placental Orders". Journal of Mammalian Evolution 8 (2): 107–
124. doi:10.1023/A:1011317930838.
http://www.ingentaconnect.com/content/klu/jomm/2001/00000008/00000002/00342277. Retrieved
2008-09-24.
72.^ Rich, T.H., Hopson, J.A., Musser, A.M., Flannery., T.GF., and Vickers-Rich, P. (11
February 2005). "Independent Origins of Middle Ear Bones in Monotremes and Therians". Science
307 (5711): 910–914. doi:10.1126/science.1105717. PMID 15705848.
http://www.sciencemag.org/cgi/content/abstract/307/5711/910. For other opinions see "Technical
comments" linked from same Web page
73.^ Oftedal, O.T. (2002). "The mammary gland and its origin during synapsid evolution".
Journal of Mammary Gland Biology and Neoplasia 7 (3): 225–252. doi:10.1023/A:1022896515287.
PMID 12751889.
74.^ Oftedal, O.T. (2002). The origin of lactation as a water source for parchment-shelled
eggs=Journal of Mammary Gland Biology and Neoplasia. 7. pp. 253–266.
75.^ Lactating on Eggs
76.^ a b c d Brink, A.S. (1955). "A study on the skeleton of Diademodon". Palaeontologia
Africana 3: 3–39.
77.^ a b c d Kemp, T.S. (1982). Mammal-like reptiles and the origin of mammals . London:
Academic Press. pp. 363. ISBN 0124041205.
78.^ Estes, R. (1961). "Cranial anatomy of the cynodont reptile Thrinaxodon liorhinus". Bulletin
of the Museum of Comparative Zoology (1253): 165–180.
79.^ Kielan−Jaworowska, Z.; Hurum, J.H.. (2006). "Limb posture in early mammals: Sprawling
or parasagittal" (PDF). Acta Palaeontologica Polonica 51 (3): 10237–10239.
http://www.app.pan.pl/archive/published/app51/app51-393.pdf. Retrieved 2008-09-24.
80.^ Paul, G.S. (1988). Predatory Dinosaurs of the World. New York: Simon and Schuster.
pp. 464. ISBN 0671619462.
81.^ Hillenius, W.H. (1992). "The evolution of nasal turbinates and mammalian endothermy".
Paleobiology 18 (1): 17–29.
82.^ Ruben, J. (1995). "The evolution of endothermy in mammals and birds: from physiology to
fossils". Annual Review of Physiology 57: 69–95. doi:10.1146/annurev.ph.57.030195.000441.
PMID 7778882.
83.^ McNab, B.K. (1978). "The evolution of endothermy in the phylogeny of mammals".
American Naturalist 112: 1–21. doi:10.1086/283249.
84.^ Ccowen, R. (2000). History of Life. Oxford: Blackwell Science. pp. 432.
85.^ Jenkins, F.A., Jr (1971). "The postcranial skeleton of African cynodonts". Bulletin of the
Peabody Museum of Natural History (36): 1–216.
86.^ Pough, F.H; Heiser, J.B.; McFarland, W.N. (1996). Vertebrate Life. New Jersey: Prentice-
Hall. pp. 798. ISBN 0023963700.
87.^ Sidor, C.A.; Hopson, J.A. (1998). "Ghost lineages and "mammalness": assessing the
temporal pattern of character acquisition in the Synapsida". Paleobiology (24): 254–273.
88.^ Schmidt-Nielsen, K. (1975). Animal physiology: Adaptation and environment . Cambridge:
Cambridge University Press. pp. 699. ISBN 0521381967.
89.^ Withers, P.C. (1992). Comparative Animal Physiology. Fort Worth: Saunders College.
pp. 949. ISBN 0030128471.
[edit] Bibliography
• Robert L. Carroll, Vertebrate Paleontology and Evolution, W. H. Freeman and Company,
New York, 1988 ISBN 0-716-71822-7. Chapters XVII through XXI
• Nicholas Hotton III, Paul D. MacLean, Jan J. Roth, and E. Carol Roth, editors, The Ecology
and Biology of Mammal-like Reptiles, Smithsonian Institution Press, Washington and London, 1986
ISBN 0-87474-524-1
• T. S. Kemp, The Origin and Evolution of Mammals , Oxford University Press, New York, 2005
ISBN 0-19-850760-7
• Zofia Kielan-Jaworowska, Richard L. Cifelli, and Zhe-Xi Luo, Mammals from the Age of
Dinosaurs: Origins, Evolution, and Structure, Columbia University Press, New York, 2004 ISBN 0-
231-11918-6. Comprehensive coverage from the first mammals up to the time of the K-T mass
extinction.
• Zhe-Xi Luo, "Transformation and diversification in early mammal evolution", Nature volume
450 number 7172 (13 December 2007) pages 1011–1019. doi:10.1038/nature06277. A survey article
with 98 references to the scientific literature.

• The Cynodontia covers several aspects of the evolution of cynodonts into mammals, with
plenty of references.
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_mammals"
Categories: Evolution by taxon | Mammals | Synapsids | Mammalogy | Paleontology | Mammal

anatomy | Prehistoric mammals
W000
The Evolution of the Genome


This article may not meet the general notability guideline. Please help to establish
notability by adding reliable, secondary sources about the topic. If notability cannot be
established, the article is likely to be merged, redirected, or deleted. (May 2009)
The Evolution of the Genome is a book edited by Dr. T. Ryan Gregory of the University of Guelph, in
Guelph, Ontario, Canada, covering a wide range of topics in the study of genome evolution. The book
includes chapters by 16 authors and deals with the topics of genome size evolution, genomic parasites
(transposable elements and B chromosomes), polyploidy, gene duplication, ancient genome duplication,
comparative genomics, and macroevolution. It was released in December 2004 by Elsevier, ISBN 0-12-
301463-8.
[edit] Chapters and authors
Part I: The C-value enigma
• Chapter 1: Genome size evolution in animals
by T. Ryan Gregory
• Chapter 2: Genome size evolution in plants
by Michael D. Bennett and Ilia J. Leitch
Part II: The evolution of genomic parasites
• Chapter 3: Transposable elements
by Margaret G. Kidwell
• Chapter 4: B chromosomes
by Juan Pedro M. Camacho
Part III: Duplications, duplications...
• Chapter 5: Small-scale gene duplications
by John S. Taylor and Jeroen Raes
• Chapter 6: Large-scale gene and ancient genome duplications
by Yves Van de Peer and Axel Meyer
Part IV: ...and more duplications
• Chapter 7: Polyploidy in plants
by Jennifer Tate, Douglas E. Soltis, and Pamela S. Soltis
• Chapter 8: Polyploidy in animals
by T. Ryan Gregory and Barbara K. Mable
Part V: Sequence and structure
• Chapter 9: Comparative genomics in eukaryotes
by Alan Filipski and Sudhir Kumar
• Chapter 10: Comparative genomics in prokaryotes
by T. Ryan Gregory and Rob DeSalle
Part VI: The genome in evolution
• Chapter 11: Macroevolution and the genome
by T. Ryan Gregory
[edit] Trivia
• The cover contains numerous images of animals, plants, and other organisms, most of which
apparently have personal meaning for Dr. Gregory, including one image on the back cover that is
reported to be a modified image of his own red blood cells.
• The timeline of production discussed in the preface indicates that Dr. Gregory began work on
this book while still a graduate student.
• As described in the preface, the book was originally to be published by Academic Press, but
part way through production the company was purchased by Elsevier. The former Academic Press
editor in charge of the project left the company while the book was being produced.

• Author's book page
• The Gregory Lab at the University of Guelph
• Animal Genome Size Database
• Plant DNA C-values Database
• Fungal Genome Size Database
• Genomes OnLine Database (GOLD)
• TIGR Comprehensive Microbial Resource
• Genome News Network
Retrieved from "http://en.wikipedia.org/wiki/The_Evolution_of_the_Genome"
Categories: Science books | Genetics books | 2004 books

W000
Evolution of color vision in primates


The evolution of color vision in primates is unique compared to most eutherian mammals. A remote
vertebrate ancestor of primates possessed tetrachromacy,[1] but nocturnal, warm-blooded, mammalian
ancestors lost two of four cones in the retina at the time of dinosaurs. Most teleost fish, reptiles and birds are
therefore tetrachromatic while all mammals, with the exception of some primates and marsupials,[2] are
strictly dichromats.
Primates achieve trichromacy through color photoreceptors (cone cells), with spectral peaks in the
violet (short wave, S), green (middle wave, M), and yellow-green (long wave, L) wavelengths. Opsin is the
primary photopigment in primate eyes, and the sequence of an organism's opsin proteins determines the
spectral sensitivity of its cone cells. Not all primates, however, are capable of trichromacy. The catarrhines
(Old World monkeys and apes) are routine trichromats, meaning both males and females possess three
opsins (pigments) sensitive to 430 nm, 530 nm, and 560 nm wavelengths.[3] In contrast, with the exception of
Alouatta and Aotus, all platyrrhines (New World monkeys) are allelic or polymorphic trichromats.[4]
Contents
[hide]
• 1 Mechanism of color vision
• 2 Hypotheses
• 2.1 Polymorphism
• 2.2 Gene duplication
• 3 New World monkeys
• 3.1 Aotus and Alouatta
• 4 See also
• 5 References
[edit] Mechanism of color vision

Genetically, there are two ways for a primate to be a trichromat. All primates share an S opsin
encoded by an autosomal gene on chromosome 7. Catarrhine primates have two adjacent opsin genes on
the X chromosome which code of L and M opsin pigments.[5]
In contrast, platyrrhines have only a single, polymorphic X chromosome M/L opsin gene locus.[5]
Therefore, every male platyrrhine is dichromatic because it can only receive either the M or L photopigment
on its single X chromosome in addition to its S photopigment. However, the X chromosome gene locus is
polymorphic for M and L alleles, rendering heterozygous platyrrhine females with trichromatic vision, and
homozygous females with dichromatic vision.[6]
[edit] Hypotheses
Some evolutionary biologists believe that the L and M photopigments of New World and Old World
primates had a common evolutionary origin; molecular studies demonstrate that the spectral tuning
(response of a photopigment to a specific wavelength of light) of the three pigments in both sub-orders is the
same.[7] There are two popular hypotheses that explain the evolution of the primate vision differences from
this common origin.
[edit] Polymorphism
The first hypothesis is that the two-gene (M and L) system of the catarrhine primates evolved from a
crossing-over mechanism. Unequal crossing over between the chromosomes carrying alleles for L and M
variants could have resulted in a separate L and M gene located on a single X chromosome.[5] This
hypothesis requires that the evolution of the polymorphic system of the platyrrhine pre-dates the separation
of the Old World and New World monkeys.[8]
This hypothesis proposes that this crossing over event occurred in a heterozygous catarrhine female
sometime after the platyrrhine/catarrhine divergence.[4] A genetic phenomenon known as X-inactivation
permits each cone cell to express only an M or an L opsin (not both), which endowed the catarrhines with
routine trichromacy.
[edit] Gene duplication
The alternate hypothesis is that opsin polymorphism arose in platyrrhines after they diverged from
catarrhines. By this hypothesis, a single X-opsin allele was duplicated in catarrhines and M and L opsins
diverged later by small changes in the gene sequences. Geneticists use the “molecular clocks” technique to
determine an evolutionary sequence of events. It deduces elapsed time from a number of minor differences
in DNA sequences.;[9][10] Nucleotide sequencing of opsin genes suggests that the genetic divergence
between New World primate opsin alleles (2.6%) is considerably smaller than the divergence between Old
World primate genes (6.1%).[8] Hence, the New World primate color vision alleles are likely to have arisen
after Old World gene duplication.[4] It is also proposed that the polymorphism in the opsin gene might have
arisen independently through point mutation on one or more occasions,[4] and that the spectral tuning
similarities are due to convergent evolution.Despite the homogenization of genes in the New World monkeys,
there has been a preservation of trichromacy in the heterozygous females suggesting that the critical amino
acid that define these alleles have been maintained.[11]
[edit] New World monkeys

These two conflicting forces (homogenization and polymorphism) suggest that a balancing selection
for trichromacy is present in the form of heterozygote advantage. Diurnal primates generally eat fruits and
young leaves, and it has been argued that trichromatic color vision is an adaptation for folivory and frugivory.
Trichromacy is observed in nearly all New World primates, and can offer a selective advantage in the
discrimination for the most nutritive, colorful items; behavioral studies have shown that trichromats are 50%
more likely to detect fruits compared to dichromats. However, in dim light, trichromats have exhibited a slight
disadvantage for discriminating fruit from foliage.[12] In many situations, dichromats have a foraging
advantage when food is camouflaged or similar in color to the background.[13] Since almost all New World
monkeys are known to search for food cooperatively, the entire group can benefit from the advantages of
trichromacy and dichromacy.[14]
[edit] Aotus and Alouatta

There are two noteworthy genera within the New World monkeys that exhibit how different
environments with different selective pressures can affect the type of vision in a population.[6] For example,
the night monkeys (Aotus) have lost their S photopigments and polymorphic M/L opsin gene. Because these
anthropoids are and were nocturnal, operating most often in a world where color is less important, selection
pressure on color vision relaxed. On the opposite side of the spectrum, diurnal howler monkeys (Alouatta)
have reinvented routine trichromacy through a relatively recent gene duplication of the M/L gene.[6] This
duplication has allowed trichromacy for both sexes; its X chromosome gained two loci to house both the
green allele and the red allele. The reccurence and spread of routine trichromacy in howler monkeys
suggests that it provides them with an evolutionary advantage.
Howler monkeys are perhaps the most folivorous of the New World monkeys. Fruits make up a
relatively small portion of their diet,[15] and the type of leaves they consume (young, nutritive, digestible,
often reddish in color), are best detected by a red-green signal. Field work exploring the dietary preferences
of howler monkeys suggest that routine trichromacy was environmentally selected for as a benefit to folivore
foraging.[4][6][16]
[edit] See also

• Evolution of color vision
[edit] References
1. ^ Jacobs, G. H. (2009). "Evolution of colour vision in mammals". Phil. Trans. R. Soc. B 364
(1531): 2957–2967. doi:10.1098/rstb.2009.0039. PMID 19720656.
2. ^ Arrese, C. A., et al. (2005). "Cone topography and spectral sensitivity in two potentially
trichromatic marsupials, the quokka (Setonix brachyurus) and quenda (Isoodon obesulus)". Proc.
Biol. Sci. 272 (1565): 791–796. doi:10.1098/rspb.2004.3009. PMID 15888411.
3. ^ Bowmaker, J. K., and S. Astell (1991). "Photosensitive and photostable pigments in the
retinae of Old World monkeys". J Exp Biol. 156: 1–19. PMID 2051127.
4. ^ a b c d e Surridge, A. K., and D. Osorio (2003). "Evolution and selection of trichromatic
vision in primates". Trends in Ecol. And Evol. 18: 198–205. doi:10.1016/S0169-5347(03)00012-0.
5. ^ a b c Nathans, J., and D Thomas (1986). "Molecular genetics of human color vision: the
genes encoding blue, green and red pigments". Science 232 (4747): 193–203.
doi:10.1126/science.2937147. PMID 2937147.
6. ^ a b c d Lucas, P. W., Dominy, N. J., Riba-Hernandez, P., Stoner, K. E., Yamashita, N.,
Loría-Calderón, E., Petersen-Pereira, W., Rojas-Durán, Salas-Pena, R., Solis-Madrigal, S,. Osorio,
D., and B. W. Darvell (2003). "Evolution and function of routine trichromatic vision in primates".
Evolution 57 (11): 2636–2643. doi:10.1554/03-168. PMID 14686538.
7. ^ Neitz, M., and J. Neitz (1991). "Spectral tuning of pigments underlying red-green color
vision". Science 252 (5008): 971–974. doi:10.1126/science.1903559. PMID 1903559.
8. ^ a b Hunt, D. M., and K. S. Dulai (1998). "Molecular evolution of trichromacy in primates".
Vision Research 38 (21): 3299–3306. doi:10.1016/S0042-6989(97)00443-4. PMID 9893841.
9. ^ Hillis, D. M. (1996). "Inferring complex phytogenies". Nature 383 (6596): 130–131.
doi:10.1038/383130a0. PMID 8774876.
10.^ Shyue, S. K., and D. Hewett-Emmett (1995). "Adaptive evolution of color vision genes in
higher primates". Science 269 (5228): 1265–1267. doi:10.1126/science.7652574. PMID 7652574.
11.^ Mollon, J. D., and O. Estevez (1990). The two subsystems of colour vision and their role in
wavelength discrimination. Found in: Vision—Coding and Efficiency . Cambridge, UK: Cambridge
12.^ Osorio, D., and M. Vorobyev (1996). "Colour vision as an adaptation to frugivory in
primates". Proc. R. Soc. Lond 263 (1370): 593–599. doi:10.1098/rspb.1996.0089. PMID 8677259.
13.^ Saito, A., A. Mikami, S. Kawamura, Y. Ueno, C. Hiramatsu, K. A. Widayati, B. Suryobroto
(2005). "Advantage of dichromats over trichromats in discrimination of color-camouflaged stimuli in
nonhuman primates". American Journal of Primatology 67 (4): 425–436. doi:10.1002/ajp.20197.
PMID 16342068.
14.^ Tovee, M. J., and J. K. Bowmaker (1991). "The relationship between cone pigments and
behavioral sensitivity in a New World monkey (Callithrix jacchus jacchus)". Vision Res. 32 (5): 867–
878. doi:10.1016/0042-6989(92)90029-I. PMID 1604855.
15.^ Robert W. Sussman (2003). Primate Ecology and Social Structure, Volume 2: New World
Monkeys (Revised First ed.). Boston, MA: Pearson Custom Publ. p. 133. ISBN 0-536-74364-9.
16.^ Dominy, N. J., Svenning, J., and W. Li (2003). "Historical contingency in the evolution of
primate color vision". Journal of Human Evolution 44 (44): 25–45. doi:10.1016/S0047-2484(02)00167-
7.
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_color_vision_in_primates"
Categories: Evolution by phenotype | Evolution by taxon | Primatology | Color | Vision

W000
Lamarckism

Lamarckism (or Lamarckian inheritance) is the idea that an organism can pass on characteristics that
it acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft
inheritance). It is named after the French biologist Jean-Baptiste Lamarck (1744–1829), who incorporated the
action of soft inheritance into his evolutionary theories. He is often incorrectly cited[ citation needed] as the
founder of soft inheritance, which proposes that individual efforts during the lifetime of the organisms were
the main mechanism driving species to adaptation, as they supposedly would acquire adaptive changes and
pass them on to offspring.
Theories of Evolution
• Based on Essentialism:
• Transmutationism
(saltationism)
• Transformationism
• Orthogenesis
• Lamarcki
sm
• Based on population biology:
• Darwinian evolution
After publication of Charles Darwin's theory of natural selection, the importance of individual efforts in
the generation of adaptation was considerably diminished. Later, Mendelian genetics supplanted the notion
of inheritance of acquired traits, eventually leading to the development of the modern evolutionary synthesis,
and the general abandonment of the Lamarckian theory of evolution in biology. In a wider context, soft
inheritance is of use when examining the evolution of cultures and ideas, and is related to the theory of
Memetics.
Contents
[hide]
• 1 History
• 2 Lamarck's theory
• 3 Current views
• 4 Neo-Lamarckism
• 5 Lamarckism and single-celled organisms
• 6 Lamarckism and societal change
• 7 See also
• 8 References
[edit] History
Jean-Baptiste Lamarck
Between 1794 and 1796 Erasmus Darwin wrote Zoönomia suggesting "that all warm-blooded
animals have arisen from one living filament... with the power of acquiring new parts" in response to stimuli,
with each round of "improvements" being inherited by successive generations. Subsequently Jean-Baptiste
Lamarck repeated in his Philosophie Zoologique of 1809 the folk wisdom that characteristics which were
"needed" were acquired (or diminished) during the lifetime of an organism then passed on to the offspring.
He incorporated this mechanism into his thoughts on evolution, seeing it as resulting in the adaptation of life
to local environments.
Lamarck founded a school of French Transformationism which included Étienne Geoffroy Saint-
Hilaire, and which corresponded with a radical British school of anatomy based in the extramural anatomy
schools in Edinburgh which included the surgeon Robert Knox and the comparative anatomist Robert
Edmund Grant. In addition, the Regius Professor of Natural History, Robert Jameson, was the probable
author of an anonymous paper in 1826 praising "Mr. Lamarck" for explaining how the higher animals had
"evolved" from the "simplest worms" – this was the first use of the word "evolved" in a modern sense. As a
young student, Charles Darwin was tutored by Grant, and worked with him on marine creatures.
The Vestiges of the Natural History of Creation, authored by Robert Chambers in St Andrews and
published anonymously in England in 1844, proposed a theory which combined radical phrenology with
Lamarckism, causing political controversy for its radicalism and unorthodoxy, but exciting popular interest
and preparing a huge and prosperous audience for Darwin.
Darwin's Origin of Species proposed natural selection as the main mechanism for development of
species, but did not rule out a variant of Lamarckism as a supplementary mechanism.[1] Darwin called his
Lamarckian hypothesis Pangenesis, and explained it in the final chapter of his book Variation in Plants and
Animals under Domestication, after describing numerous examples to demonstrate what he considered to be
the inheritance of acquired characteristics. Pangenesis, which he emphasised was a hypothesis, was based
on the idea that somatic cells would, in response to environmental stimulation (use and disuse), throw off
'gemmules' or 'pangenes' which travelled around the body (though not necessarily in the bloodstream).
These pangenes were microscopic particles that supposedly contained information about the characteristics
of their parent cell, and Darwin believed that they eventually accumulated in the germ cells where they could
pass on to the next generation the newly acquired characteristics of the parents. Darwin's half-cousin,
Francis Galton carried out experiments on rabbits, with Darwin's cooperation, in which he transfused the
blood of one variety of rabbit into another variety in the expectation that its offspring would show some
characteristics of the first. They did not, and Galton declared that he had disproved Darwin's hypothesis of
Pangenesis, but Darwin objected, in a letter to Nature, that he had done nothing of the sort, since he had
never mentioned blood in his writings. He pointed out that he regarded Pangenesis as occurring in Protozoa
and plants, which have no blood.[2] With the development of the modern synthesis of the theory of evolution
and a lack of evidence for either a mechanism or even the heritability of acquired characteristics, Lamarckism
largely fell from favor.
In the 1920s, experiments by Paul Kammerer on amphibians, particularly the midwife toad, appeared
to find evidence supporting Lamarckism, but his specimens with supposedly-acquired black foot-pads were
found to have been tampered with. In The Case of the Midwife Toad Arthur Koestler surmised that the
specimens had been faked by a Nazi sympathiser to discredit Kammerer for his political views.
A form of Lamarckism was revived in the Soviet Union of the 1930s when Trofim Lysenko promoted
Lysenkoism which suited the ideological opposition of Joseph Stalin to Genetics. This ideologically driven
research influenced Soviet agricultural policy which in turn was later blamed for crop failures.
Since 1988 certain scientists have produced work proposing that Lamarckism could apply to single
celled organisms. A version of Lamarckian acquisition in higher order animals is still posited in certain
branches of psychology, as, for example, in the Jungian racial memory.
Neo-Lamarckism is a theory of inheritance based on a modification and extension of Lamarckism,
essentially maintaining the principle that genetic changes can be influenced and directed by environmental
factors.
[edit] Lamarck's theory
The evolution of necks is often used as the example in explanations of Lamarckism.

The identification of Lamarckism with the inheritance of acquired characteristics is regarded by some
as an artifact of the subsequent history of evolutionary thought, repeated in textbooks without analysis.
Stephen Jay Gould wrote that late 19th century evolutionists "re-read Lamarck, cast aside the guts of it ...
and elevated one aspect of the mechanics - inheritance of acquired characters - to a central focus it never
had for Lamarck himself."[3] He argued that "the restriction of "Lamarckism" to this relatively small and non-
distinctive corner of Lamarck's thought must be labelled as more than a misnomer, and truly a discredit to the
memory of a man and his much more comprehensive system ".[4] Gould advocated defining "Lamarckism"
more broadly, in line with Lamarck's overall evolutionary theory.
Lamarck incorporated two ideas into his theory of evolution, in his day considered to be generally
true:
1. Use and disuse – Individuals lose characteristics they do not require (or use) and develop
characteristics that are useful.
2. Inheritance of acquired traits – Individuals inherit the traits of their ancestors.
Examples of what is traditionally called "Lamarckism" would include:
• Giraffes stretching their necks to reach leaves high in trees (especially Acacias), strengthen
and gradually lengthen their necks. These giraffes have offspring with slightly longer necks (also
known as "soft inheritance").
• A blacksmith, through his work, strengthens the muscles in his arms. His sons will have
similar muscular development when they mature.
With this in mind, Lamarck has been credited in some textbooks[ which?] and popular culture[which?]
with developing two laws:
1. In every animal which has not passed the limit of its development, a more frequent and
continuous use of any organ gradually strengthens, develops and enlarges that organ, and gives it a
power proportional to the length of time it has been so used; while the permanent disuse of any
organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional
capacity, until it finally disappears.
2. All the acquisitions or losses wrought by nature on individuals, through the influence of the
environment in which their race has long been placed, and hence through the influence of the
predominant use or permanent disuse of any organ; all these are preserved by reproduction to the
new individuals which arise, provided that the acquired modifications are common to both sexes, or
at least to the individuals which produce the young. [5]
In essence, a change in the environment brings about change in "needs" ( besoins), resulting in
change in behavior, bringing change in organ usage and development, bringing change in form over time —
and thus the gradual transmutation of the species.
However, as historians of science such as Michael Ghiselin and Stephen Jay Gould have pointed
out, none of these views were original to Lamarck.[6][7] On the contrary, Lamarck's contribution was a
systematic theoretical framework for understanding evolution. He saw evolution as comprising two
processes;
1. Le pouvoir de la vie (a complexifying force) - in which the natural, alchemical movements of
fluids would etch out organs from tissues, leading to ever more complex construction regardless of
the organ's use or disuse. This would drive organisms from simple to complex forms.
2. L'influence des circonstances (an adaptive force) - in which the use and disuse of characters
led organisms to become more adapted to their environment. This would take organisms sideways
off the path from simple to complex, specialising them for their environment.
[edit] Current views

Interest in Lamarckism has recently increased, as several studies in the field of epigenetics have
highlighted the possible inheritance of behavioral traits acquired by the previous generation. A recent such
study examined foraging behavior in chickens as a function of stress,[8] concluding:
Our findings suggest that unpredictable food access caused seemingly adaptive responses in
feeding behavior, which may have been transmitted to the offspring by means of epigenetic
mechanisms, including regulation of immune genes. This may have prepared the offspring for
coping with an unpredictable environment.... Transmissions of information across generations
which does not involve traditional inheritance of DNA-sequence alleles is often referred to as
soft inheritance [9] or 'Lamarckian inheritance'.[8]
The evolution of acquired characteristics has also been shown in human populations who have
experienced starvation, resulting in altered gene function in both the starved population and their offspring.
[10] The process of DNA methylation is thought to be behind such changes.
In October 2010, further evidence linking food intake to traits inherited by the offspring were shown in
a study of rats conducted by several Australian universities.[11] The study strongly suggested that fathers
can transfer a propensity for obesity to their daughters as a result of the fathers' food intake, and not their
genetics (or specific genes), prior to the conception of the daughter. A "paternal high-fat diet" was shown to
cause cell dysfunction in the daughter, which in turn led to obesity for the daughter.
Several historians have argued that Lamarck's name is linked somewhat unfairly to the theory that
has come to bear his name, and that Lamarck deserves credit for being an influential early proponent of the
concept of biological evolution, far more than for the mechanism of evolution, in which he simply followed the
accepted wisdom of his time. Lamarck died 30 years before the first publication of Charles Darwin's Origin of
Species. According to Stephen Jay Gould, if Lamarck had been aware of Darwin's proposed mechanism of
natural selection, there is no reason to assume he would not have accepted it as a more likely alternative to
his own mechanism. Note also that Darwin, like Lamarck, lacked a plausible alternative mechanism of
inheritance - the particulate nature of inheritance was only observed by Gregor Mendel somewhat later, and
published in 1866. Its full significance was not appreciated until the Modern evolutionary synthesis in the
early 1920s. An important point in its favour at the time was that Lamarck's theory contained a mechanism
describing how variation is maintained, which Darwin’s own theory lacked.[ citation needed]
Several recent studies, one conducted by researchers at MIT and another by researchers at the Tufts
University School of Medicine, have rekindled the debate once again. As reported in MIT's Technology
Review in February 2009, "The effects of an animal's environment during adolescence can be passed down
to future offspring ... The findings provide support for a 200-year-old theory of evolution that has been largely
dismissed: Lamarckian evolution, which states that acquired characteristics can be passed on to offspring."
[edit] Neo-Lamarckism
Unlike neo-Darwinism, the term neo-Lamarckism refers more to a loose grouping of largely
heterodox theories and mechanisms that emerged after Lamarck's time, than to any coherent body of
theoretical work.
In the 1920s, Harvard University researcher William McDougall studied the abilities of rats to
correctly solve mazes. He found that offspring of rats that had learned the maze were able to run it faster.
The first rats would get it wrong 165 times before being able to run it perfectly each time, but after a few
generations it was down to 20. McDougall attributed this to some sort of Lamarckian evolutionary process.
[12] Oscar Werner Tiegs and Wilfred Eade Agar later showed McDougall's results to be incorrect, caused by
poor experimental controls.[13][14][15][16][17]
At around the same time, Ivan Pavlov, who was also a Lamarckist, claimed to have observed a
similar phenomenon in animals being subject to conditioned reflex experiments. He claimed that with each
generation, the animals became easier to condition. However, Pavlov never suggested a mechanism to
explain these observations.
Soma to germ-line feedback
In the 1970s the immunologist Ted Steele, formerly of the University of Wollongong, and colleagues,
proposed a neo-Lamarckian mechanism to try to explain why homologous DNA sequences from the VDJ
gene regions of parent mice were found in their germ cells and seemed to persist in the offspring for a few
generations. The mechanism involved the somatic selection and clonal amplification of newly acquired
antibody gene sequences that were generated via somatic hyper-mutation in B-cells. The mRNA products of
these somatically novel genes were captured by retroviruses endogenous to the B-cells and were then
transported through the blood stream where they could breach the soma-germ barrier and retrofect (reverse
transcribe) the newly acquired genes into the cells of the germ line. Although Steele was advocating this
theory for the better part of two decades, little more than indirect evidence was ever acquired to support it. An
interesting attribute of this idea is that it strongly resembles Darwin's own theory of pangenesis, except in the
soma to germ line feedback theory, pangenes are replaced with realistic retroviruses.[18]
Science philosopher Ross Honeywill extended Steele's work by proposing Meta-Lamarckism 'The
real issue is whether a modern, well-supported Lamarckian theory can be devised, consistent with well-
documented parts of modern molecular genetics, and be able to be articulated with a surviving core of
Darwinian natural selection: a kind of Meta-Lamarckism that combines the best of both Darwin and
Lamarck.Steele identified RNA as the critical transcription vehicle because unlike DNA, it was the medium
that was out there in contact with what was going on in the body. It was the obedient servant that knew the
secret language, the secret handshake. What a breakthrough it was to discover from Lamarck via Steele that
RNA could take vital changes back to the DNA for generational improvements. But imagine what it means if
the RNA is capable of carrying its own information through generations; imagine the Meta-Lamarckian
consequences and opportunities written all over these discoveries.'[19]
Epigenetic inheritance
Forms of 'soft' or epigenetic inheritance within organisms have been suggested as neo-Lamarckian
in nature by such scientists as Eva Jablonka and Marion J. Lamb. In addition to 'hard' or genetic inheritance,
involving the duplication of genetic material and its segregation during meiosis, there are other hereditary
elements that pass into the germ cells also. These include things like methylation patterns in DNA and
chromatin marks, both of which regulate the activity of genes. These are considered "Lamarckian" in the
sense that they are responsive to environmental stimuli and can differentially affect gene expression
adaptively, with phenotypic results that can persist for many generations in certain organisms. Although the
reality of epigenetic inheritance is not doubted (as many experiments have validated it), its significance to the
evolutionary process is uncertain. Most neo-Darwinians consider[ citation needed] epigenetic inheritance
mechanisms to be little more than a specialized form of phenotypic plasticity, with no potential to introduce
evolutionary novelty into a species lineage.[20]
[edit] Lamarckism and single-celled organisms

While Lamarckism has been discredited as an evolutionary influence for larger lifeforms, some
scientists controversially argue that it can be observed among microorganisms.[21] Whether such mutations
are directed or not also remains in contention. (see Horizontal Gene Transfer)
In 1988, John Cairns at the Radcliffe Infirmary in Oxford, England, and a group of other scientists
renewed the Lamarckian controversy (which at that point had been a dead debate for many years).[22] The
group took a mutated strain of E. coli that was unable to consume the sugar lactose and placed it in an
environment where lactose was the only food source. They observed over time that mutations occurred
within the colony at a rate that suggested the bacteria were overcoming their handicap by altering their own
genes. Cairns, among others, dubbed the process adaptive mutation.
If bacteria that had overcome their own inability to consume lactose passed on this "learned" trait to
future generations, it could be argued as a form of Lamarckism; though Cairns later chose to distance himself
from such a position.[23] More typically, it might be viewed as a form of ontogenic evolution.
There has been some research into Lamarckism and prions. A group of researchers, for example,
discovered that in yeast cells containing a specific prion protein Sup35, the yeast were able to gain new
genetic material, some of which gave them new abilities such as resistance to a particular herbicide. When
the researchers crossed the yeast cells with cells not containing the prion, the trait reappeared in some of the
resulting offspring, indicating that some information indeed was passed down, though whether or not the
information is genetic is debatable: trace prion amounts in the cells may be passed to their offspring, giving
the appearance of a new genetic trait where there is none.[24]
Finally, there is growing evidence that cells can activate low-fidelity DNA polymerases in times of
stress to induce mutations. While this does not directly confer advantage to the organism on the organismal
level, it makes sense at the gene-evolution level. While the acquisition of new genetic traits is random, and
selection remains Darwinian, the active process of identifying the necessity to mutate is considered to be
Lamarckian.
[edit] Lamarckism and societal change

Jean Molino (2000) has proposed that Lamarckian evolution may be accurately applied to cultural
evolution. This was also previously suggested by Peter Medawar (1959) and Conrad Waddington (1961). K.
N. Laland and colleagues have recently suggested that human culture can be looked upon as an ecological
niche like phenomena, where the effects of cultural niche construction are transmissible from one generation
to the next. One interpretation of the Meme theory is that memes are both Darwinian and Lamarckian in
nature, as in addition to being subject to selection pressures based on their ability to differentially influence
Human minds, memes can be modified and the effects of that modification passed on. Richard Dawkins
notes (in Blackmore 2000: The Meme machine, page 13), that Memes can be copied in a Lamarckian way
(copying of the product) or in a Weismann-type evolutionary way (copying of the instruction) which is much
more resistant against changes.
[edit] See also

Book:Evolution

• Jean-Baptiste Lamarck
• Baldwinian evolution
• Darwinism
• Epigenetic inheritance
• Epigenetics
• Evolution
• Inheritance of acquired characters
• Lysenkoism
• Memetics
• Obsolete scientific theories
• Orthogenesis
• Marcus Pembrey
• Racial memory
• Ted Steele
• Eclipse of Darwinism
[edit] References
1. ^ Desmond, A. & Moore, J. (1991) Darwin Penguin Books p.617 "Darwin was loathe to let go
of the notion that a well-used and strengthened organ could be inherited"
2. ^ Charles Darwin (27 April 1871). "Pangenesis". Nature. A Weekly Illustrated Journal of
Science. pp. 502–503. http://darwin-online.org.uk/content/frameset?
viewtype=text&itemID=F1751&pageseq=1. Retrieved 2007-11-08.
3. ^ Gould, Stephen J. "Shades of Lamarck", reprinted in The Panda's Thumb (1980) pp.65-71.
Quote from page 66.
4. ^ Gould, Stephen J. (2002). The Structure of Evolutionary Theory. Harvard: Belknap Harvard.
pp. 177–178. ISBN 0-674-00613-5.
5. ^ Jean-Baptiste Lamarck Zoological Philosophy trans. Hugh Elliot, U. Chicago Press, 1984,
p.113
6. ^ The Imaginary Lamarck: a look at bogus "history" in schoolbooks by Michael Ghiselin
7. ^ Gould, S.J. (2002) The Structure of Evolutionary Theory
8. ^ a b http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006405
9. ^ Richards EJ (2006) Inherited epigenetic variation–revisiting soft inheritance. Nat Rev Genet
7(5): 395–401.
10.^ http://cat.inist.fr/?aModele=afficheN&cpsidt=3596539
11.^ http://www.nature.com/nature/journal/v467/n7318/full/nature09491.html
12.^ McDougall, 1938. British Journal of Psychology 28:321-345
13.^ Pantin, C F A (November 1957). "Oscar Werner Tiegs". Biographical Memiors of Fellows of
the Royal Society (The Royal Society) 3: 247.
14.^ W E Agar, F H Drummond (1935). "First report on a test of McDougall's Lamarckian
experiment on the training of rats". Journal of Experimental Biology 12: 191.
15.^ W E Agar, F H Drummond (1942). "Second report on a test of McDougall's Lamarckian
16.^ W E Agar, F H Drummond (1948). "Third report on a test of McDougall's Lamarckian
17.^ W E Agar, F H Drummond, M M Gunson (1954). "Fourth (final) report on a test of
McDougall's Lamarckian experiment on the training of rats". Journal of Experimental Biology 31:
308.
18.^ Lamarck's Signature: how retrogenes are changing Darwin's natural selection paradigm .
Edward J. Steele, Robyn A. Lindley, Robert V. Blanden. Perseus Books, 1998
19.^ http://lamarcksevolution.com/the-case-for-meta-lamarckism/
20.^ Epigenetic Inheritance and Evolution: The Lamarckian Dimension . Eva Jablonka, Marion J.
Lamb. Oxford University Press, 1995
21.^ Adaptive mutation Genetics, Vol. 148, April 1998
22.^ Adaptive mutation in bacteria
23.^ Adaptive mutation in E. coli, Journal of Bacteriology, August 2004, Vol. 186, No. 15
24.^ Lamarckism and prions, New Scientist, 21 August 2004, Issue #2461
• Burkeman, Oliver. Why everything you've been told about evolution is wrong, The Guardian,
March 19, 2010.
• Desmond, Adrian (1989). The Politics of Evolution: Morphology, Medicine, and Reform in
Radical London. Chicago: University of Chicago Press. ISBN 0-226-14374-0.
• Gould, Stephen J. (2002). The Structure of Evolutionary Theory. Harvard: Belknap Harvard.
pp. 170–197 on Lamarck. ISBN 0-674-00613-5.
• Medawar, Peter (1959). "The threat and the glory". BBC Reith Lectures No. 6.
• Molino, Jean (2000). "Toward an Evolutionary Theory of Music and Language". In Brown,
Merker & Wallin (Eds.), The Origins of Music, ISBN 0-262-23206-5.
• Waddington, Conrad (1961). "The human evolutionary system". In: Michael Banton (Ed.),
Darwinism and the Study of Society. London: Tavistock.
• Honeywill, Ross (2008). "Lamarck's Evolution: two centuries of genius and jealousy".
Murdoch Books, Sydney See website
• Cairns, J., J. Overbaugh, and S. Miller. 1988. Nature 335: 142-145
• Culotta, Elizabeth; "A Boost for 'Adaptive' Mutation", Science, 265:318, 1994.
• Vetsigian K, Woese C, Goldenfeld N. 2006. "Collective Evolution and the Genetic Code."
PNAS 103: 10696-10701.
• Hall Barry G., Adaptive Evolution That Requires Multiple Spontaneous Mutations. I.
Mutations Involving an Insertion Sequence
• Nonsense in Schoolbooks - The Imaginary Lamarck :Michael T. Ghiselin recounts Lamarck's
times and writings.
• Jean-Baptiste Lamarck : works and heritage: an English/French web site edited by Pietro
Corsi (Oxford Univ.) and realised by CNRS (France - IT team of CRHST). This web site contents all
books, texts, manuscripts and the lamarck's herbarium.
• Guralnick, Rob, et. al (2006). "Jean-Baptiste Lamarck (1744-1829)". A History of
Evolutionary Thought. University of California Museum of Paleontology.
http://www.ucmp.berkeley.edu/history/lamarck.html. Retrieved 3 July 2010.
• The Sins of the Fathers, Take 2: "At tributes to Darwin, Lamarckism — inheritance of acquired
traits — will be the skunk at the party." By Sharon Begley, Newsweek. From the magazine issue dated
January 26, 2009.
• Essay on Meta-Lamarckism


phenotype
Non-genetic
Developmental
[hide]v · d · eLysenkoism & Trofim Lysenko
Lysenkoists John Desmond Bernal · Nikita Khrushchev · Ivan Vladimirovich Michurin ·

Joseph Stalin · VASKhNIL
Dissidents Wacław Gajewski · Tan Jiazhen · Georgii Karpechenko · Roy Medvedev ·
Georgii Nadson · Nikolai Vavilov
Concepts Heredity · Heritability · Hybridization · Inheritance of acquired characteristics

· Lamarckism · Mendelian inheritance · Vernalization
Soviet Bourgeois pseudoscience · Collectivization in the Soviet Union · Pavlovian

policies session · Socialist realism · Suppressed research in the Soviet Union · Wrecking
Related
articles Leninism · Marxism · Politicization of science
Book:Lysenkoism
Retrieved from "http://en.wikipedia.org/wiki/Lamarckism"
Categories: History of evolutionary biology | Biology theories

W000
Evolution of color vision


Color vision, a proximate adaptation of the vision sensory modality, allows for the discrimination of
light based on its wavelength components.
Contents
[hide]
• 1 Invertebrates
• 2 Vertebrates
• 3 See also
• 4 References
[edit] Invertebrates
Color vision requires a number of opsin molecules with different absorbance peaks, and at least
three opsins were present in the ancestor of chelicerates and pancrustaceans; members of both these
groups today possess color vision.[1]
[edit] Vertebrates
Researchers studying the genes responsible for color vision pigments (opsin genes) have long
known that there exist four photopigment opsins in birds, reptiles and teleost fish[2]. This indicates that the
common ancestor of tetrapods and amniotes (~360 million years ago) had tetrachromatic vision, or the ability
to discern four different wavelengths of light, and presumably at least this many colors. [3]
Today most mammals possess dichromatic vision (probably a feature of the first mammalian
ancestors, which were probably small, nocturnal, and burrowing), and are only able to discern between short
and long wavelengths. This means they can differentiate at least two colors.
Most primates, however, have re-developed trichromatic color vision, and are able to discern
between violet [short wave (SW)], green [medium wave (MW)], and yellow-green [long wave (LW)] [4]. They
are able to discern all of the shades of colors that humans do, including reds.
Within the primate sub-order, the catarrhines (Old World monkeys and apes, including humans) are
routinely trichromatic, meaning that both males and females possess three opsins sensitive to SW, MW, and
LW [3]. Platyrrhines (New World monkeys), on the other hand, are non-routinely trichromatic; only a small
fraction of platyrrhines are trichromats [5].
[edit] See also

• Evolution of color vision in primates
• Evolution of the eye
[edit] References
1. ^ Koyanagi, M.; Nagata, T.; Katoh, K.; Yamashita, S.; Tokunaga, F. (2008). "Molecular
Evolution of Arthropod Color Vision Deduced from Multiple Opsin Genes of Jumping Spiders".
Journal of Molecular Evolution 66 (2): 130. doi:10.1007/s00239-008-9065-9. PMID 18217181. edit
2. ^ Yokoyama, S., and B. F. Radlwimmer. 2001. The molecular genetics and evolution of red
and green color vision in vertebrates. Genetics Society of America. 158: 1697-1710.
3. ^ a b Bowmaker, JK (1998). "Evolution of colour vision in vertebrates". Eye (London,
England) 12 ( Pt 3b): 541–7. PMID 9775215. edit
4. ^ Dulai, KS; von Dornum, M; Mollon, JD; Hunt, DM (1999). "The evolution of trichromatic
color vision by opsin gene duplication in New World and Old World primates". Genome research 9
(7): 629–38. PMID 10413401. edit
5. ^ Surridge, A. K., and D. Osorio. 2003. Evolution and selection of trichromatic vision in
primates. Trends in Ecol. and Evol. 18: 198-205.
Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_color_vision"
Categories: Vision | Color | Evolution by phenotype

W000
Neutral theory of molecular evolution


The neutral theory of molecular evolution states that the vast majority of evolutionary change at the
molecular level is caused by random drift of selectively neutral mutants.[1] The theory was introduced by
Motoo Kimura in the late 1960s and early 1970s, and although it was received by some as an argument
against Darwin's theory of evolution by natural selection, Kimura maintained (and most evolutionary
biologists agree) that the two theories are compatible: "The theory does not deny the role of natural selection
in determining the course of adaptive evolution" (Kimura, 1986). However, the theory attributes a large role to
genetic drift.
Contents
[hide]
• 1 Overview
• 2 The "neutralist–selectionist" debate
• 3 See also
• 4 References
[edit] Overview
While some scientists had hinted that maybe neutral mutations were widespread, like Sueoka (1962),
a coherent theory of neutral evolution was first formalized by Motoo Kimura in 1968, followed quickly by Jack
L. King and Thomas H. Jukes' provocative article, "Non-Darwinian Evolution" (1969).
According to Kimura, when one compares the genomes of existing species, the vast majority of
molecular differences are selectively "neutral." That is, the molecular changes represented by these
differences do not influence the fitness of the individual organism. As a result, the theory regards these
genomic features as neither subject to, nor explicable by, natural selection. This view is based in part on the
degenerate genetic code, in which sequences of three nucleotides (codons) may differ and yet encode the
same amino acid (GCC and GCA both encode alanine, for example). Consequently, many potential single-
nucleotide changes are in effect "silent" or "unexpressed" (see synonymous or silent substitution). Such
changes are presumed to have little or no biological effect. However, it should be noted that the original
theory was based on the consistency in rates of amino acid changes, and hypothesized that the majority of
those changes too were neutral.
A second assertion or hypothesis of the neutral theory is that most evolutionary change is the result
of genetic drift acting on neutral alleles. A new allele arises typically through the spontaneous mutation of a
single nucleotide within the sequence of a gene. In single-celled organisms, such an event immediately
contributes a new allele to the population, and this allele is subject to drift. In sexually reproducing
multicellular organisms, the nucleotide substitution must arise within one of the many sex cells that an
individual carries. Then only if that sex cell participates in the genesis of an embryo and offspring does the
mutation contribute a new allele to the population. Neutral substitutions create new neutral alleles.
Through drift, these new alleles may become more common within the population. They may
subsequently be lost, or in rare cases they may become fixed, meaning that the new allele becomes
standard in the population.
According to the mathematics of drift, when looking between divergent populations, most of the
single-nucleotide differences can be assumed to have accumulated at the same rate as individuals with
mutations are born. This latter rate, it has been argued, is predictable from the error rate of the enzymes that
carry out DNA replication: these enzymes have been well studied and are highly conserved across all
species. Thus, the neutral theory is the foundation of the molecular clock technique, which evolutionary
molecular biologists use to measure how much time has passed since species diverged from a common
ancestor. Diverse and more sophisticated clock techniques have emerged to account for variable mutation
rate.
Many molecular biologists and population geneticists also contributed to the development of the
neutral theory, which may be viewed as an offshoot of the modern evolutionary synthesis.
Neutral theory does not contradict natural selection, nor does it deny that selection occurs. Austin
Hughes writes: "Evolutionary biologists typically distinguish two main types of natural selection: (1) purifying
selection, which acts to eliminate deleterious mutations and (2) positive (Darwinian) selection, which favors
advantageous mutations. Positive selection can, in turn, be further subdivided into directional selection,
which tends toward fixation of an advantageous allele, and balancing selection, which maintains a
polymorphism. The neutral theory of molecular evolution predicts that purifying selection is ubiquitous, but
that both forms of positive selection are rare, whereas not denying the importance of positive selection in the
origin of adaptations."[2] In another essay, Hughes writes: "Purifiying selection is the norm in the evolution of
protein coding genes. Positive selection is a relative rarity — but of great interest, precisely because it
represents a departure from the norm."[3]
[edit] The "neutralist–selectionist" debate

See also: History of evolutionary thought and History of molecular evolution
A heated debate arose on the initial publication of Kimura's theory, in which discussion largely
revolved around the relative percentages of alleles that are "neutral" versus "non-neutral" in any given
genome. Contrary to the perception of many onlookers, the debate was not about whether or not natural
selection acts at all. Kimura argued that molecular evolution is dominated by selectively neutral evolution, but
at the phenotypic level changes in characters were probably dominated by natural selection rather than
sampling drift (Provine 1991).
After flirting with the idea that slightly deleterious mutations might be quite common (Ohta, 1973),
Tomoko Ohta, Kimura's student, made an important generalisation of the neutral theory by including the
concept of "near-neutrality",[4][5] that is, genes that are affected mostly by drift or mostly by selection
depending on the effective size of a breeding population. The neutralist-selectionist quarrel has since cooled,
yet the question of the relative percentages of neutral and non-neutral alleles remains. Graur & Li (2000), go
as far as to say;
"There are only two predictions we are willing to make about the future of molecular evolution.
The first concerns old controversies. Issues such as the neutralist-selectionist controversy or the
antiquity of introns, will continue to be debated with varying degrees of ferocity, and roars of "The
Neutral Theory Is Dead" and "Long Live the Neutral Theory" will continue to reverberate, sometimes in
the title of a single article."
As of the early 2000s, the neutral theory is widely used as a "null model" for so-called null hypothesis
testing. Researchers typically apply such a test when they already have an estimate of the amount of time
that has passed since two species or lineages diverged—for example, from radiocarbon dating at fossil
excavation sites, or from historical records in the case of human families. The test compares the actual
number of differences between two sequences and the number that the neutral theory predicts given the
independently estimated divergence time. If the actual number of differences is much less than the
prediction, the null hypothesis has failed, and researchers may reasonably assume that selection has acted
on the sequences in question. Thus such tests contribute to the ongoing investigation into the extent to which
molecular evolution is neutral.[6]
In a series of recent papers, Swiss researcher Andreas Wagner proposed a reconciliation between
selectionism and neutralism. Wagner's proposal demonstrates how evolutionary change involving several
independent stepwise mutations might take place. In pure selectionism, such change would be impossible,
because each step must occur independently. Each step must be favored by positive selection to become
established in the genome, so that the next step can occur. In Wagner's model, "innovation occurs via cycles
of exploration of nearly neutral spaces," which Wagner refers to as a neutralist regime. During a neutralist
regime, neutral mutations accumulate, and so genetic diversity increases. When a new phenotype with
higher fitness occurs, its genotype sweeps through the population to fixation, and genetic diversity is reduced
during a selectionist regime.[7]
Wagner's model for his ideas uses RNA sequences as genotype, and the final folded structure of
RNA as the phenotype. The work is made possible by the existence of a computationally efficient algorithm
which predicts RNA structure from an RNA sequence. The work shows that RNA phenotype is robust enough
to hold considerable variation in the underlying genotypes. This phenotype robustness promotes structure
evolvability. The likelihood that a mutation is deleterious is smaller in populations with more robust
phenotypes. As genetic diversity increases under such a neutralist regime, opportunities for an advantageous
mutation increase. Wagner writes: "Populations evolving on large neutral networks can access greater
amounts of variation." Wagner's summary explains the limitations of his work:
"This work leaves three important open questions. First, how robust and evolvable are
biologically important phenotypes, such as RNA structures? To answer this question is currently
impossible... no reliable and tractable method to do this is currently available. Second, how
general is the positive association between phenotypic robustness and evolvability?... Does it
occur in many other biological systems? Third, this work does not ask about the evolutionary
forces that might cause high evolvability, of which there may be many".[8]
[edit] See also

• Adaptive Evolution in the Human Genome
• Evolution
• Ewens's sampling formula
• John H. Gillespie
• Molecular evolution
• Nearly neutral theory of molecular evolution
• Tomoko Ohta
• Unified neutral theory of biodiversity
• Warren Ewens
[edit] References
1. ^ Kimura, Motoo. 1983. The neutral theory of molecular evolution. Cambridge (page xi).
2. ^ Hughes, Austin L. (2007-07-11). "Looking for Darwin in all the wrong places: the misguided
quest for positive selection at the nucleotide sequence level". Heredity 99 (4): 364–373.
doi:10.1038/sj.hdy.6801031. PMID 17622265.
3. ^ Hughes, Austin L.. Adaptive Evolution of Genes and Genomes. Oxford University Press.
pp. 53. ISBN 0195116267.
4. ^ Ohta, T (1992). "The nearly neutral theory of molecular evolution". Annual Review of
Ecology and Systematics 23: 263–286. doi:10.1146/annurev.es.23.110192.001403.
5. ^ Ohta, T. (2002). "Near-neutrality in evolution of genes and gene regulation". Proceedings
of the National Academy of Sciences 99 (25): 16134–16137. doi:10.1073/pnas.252626899.
PMID 12461171. PMC 138577. http://www.pnas.org/cgi/content/full/99/25/16134.
6. ^ Leigh E.G. (Jr) (2007). "Neutral theory: a historical perspective.". Journal of Evolutionary
Biology 20 (6): 2075–2091. doi:10.1111/j.1420-9101.2007.01410.x. PMID 17956380.
7. ^ Wagner A (dec 2008). "Neutralism and selectionism: a network-based reconciliation".
8. ^ Wagner A (2007-10-31). "Robustness and evolvability: a paradox resolved". Proceedings
of the Royal Society 275 (1630): 91–100. doi:10.1098/rspb.2007.1137. PMID 17971325.
• Gillespie, J. H (1991). The Causes of Molecular Evolution. Oxford University Press, New
York. ISBN 0-19-506883-1.
• Graur, D. and Li, W-H (2000). Fundamentals of Molecular Evolution, 2nd edition. Sinauer
Associates. ISBN 0-87893-266-6.
• Kimura, M. (1968). "Evolutionary rate at the molecular level". Nature 217 (5129): 624–626.
doi:10.1038/217624a0. PMID 5637732. [1]
• Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press,
Cambridge. ISBN 0-521-23109-4.
• King, J.L. and Jukes, T.H (1969). "Non-Darwinian Evolution". Science 164 (881): 788–798.
doi:10.1126/science.164.3881.788. PMID 5767777. [2]
• Lewontin, R (1974). The Genetic Basis of Evolutionary Change. Columbia University Press.
ISBN 0-231-03392-3.
• Ohta, T (1973). "Slightly deleterious mutant substitutions in evolution". Nature 246 (5428):
96–98. doi:10.1038/246096a0. PMID 4585855.
• Ohta, T. and Gillespie, J.H (1996). "Development of Neutral and Nearly Neutral Theories".
Theoretical Population Biology 49 (2): 128–142. doi:10.1006/tpbi.1996.0007. PMID 8813019.
• Sueoka, N. (1962). "On the genetic basis of variation and heterogeneity of DNA base
composition". PNAS USA 48: 582–592. doi:10.1073/pnas.48.4.582. [3]
• Kimura, M. (1986). "DNA and the Neutral Theory". Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences 312 (1154): 343–354. doi:10.1098/rstb.1986.0012.
• Provine W.B. Rise of the null selection hypothesis. In Cain A.J. and Provine W.B. 1991.
Genes and ecology in history. In Berry R.J. et al. (eds) Genes in ecology: the 33rd Symposium of the
British Ecological Society. Blackwell, Oxford, p15-23.
• Duret, L. (2008). "Neutral Theory: The Null Hypothesis of Molecular Evolution". Nature
Education 1 (1). [4]
• Nei M (2005-08-24). "Selectionism and neutralism in molecular evolution". Molecular Biology
and Evolution 22 (12): 2318–2342. doi:10.1093/molbev/msi242. PMID 16120807.

Effects of


Genetic genealogy
Retrieved from "http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution"
Categories: Population genetics | Molecular evolution

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History of molecular evolution


The history of molecular evolution starts in the early 20th century with "comparative biochemistry",
but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular
biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based
sequence comparison, and to use the differences between homologous sequences as a molecular clock to
estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution
provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were
controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as
the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular
evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a
reconceptualization of the early history of life.
Contents
[hide]
• 1 Early history
• 1.1 Genetic load, the classical/balance controversy,
and the measurement of heterozygosity
• 1.2 Protein sequences and the molecular clock
• 2 The "molecular wars"
• 2.1 Gene-centered view of evolution
• 3 The neutral theory of molecular evolution
• 3.1 The neutralist-selectionist debate and near-
neutrality
• 4 Microbial phylogeny
• 5 Notes
• 6 References
[edit] Early history
Before the rise of molecular biology in the 1950s and 1960s, a small number of biologists had
explored the possibilities of using biochemical differences between species to study evolution. Ernest
Baldwin worked extensively on comparative biochemistry beginning in the 1930s, and Marcel Florkin
pioneered techniques for constructing phylogenies based on molecular and biochemical characters in the
1940s. However, it was not until the 1950s that biologists developed techniques for producing biochemical
data for the quantitative study of molecular evolution.[1]
The first molecular systematics research was based on immunological assays and protein
"fingerprinting" methods. Alan Boyden—building on immunological methods of G. H. F. Nuttall—developed
new techniques beginning in 1954, and in the early 1960s Curtis Williams and Morris Goodman used
immunological comparisons to study primate phylogeny. Others, such as Linus Pauling and his students,
applied newly developed combinations of electrophoresis and paper chromatography to proteins subject to
partial digestion by digestive enzymes to create unique two-dimensional patterns, allowing fine-grained
comparisons of homologous proteins.[2]
Beginning in the 1950s, a few naturalists also experimented with molecular approaches—notably
Ernst Mayr and Charles Sibley. While Mayr quickly soured on paper chromatography, Sibley successfully
applied electrophoresis to egg-white proteins to sort out problems in bird taxonomy, soon supplemented that
with DNA hybridization techniques—the beginning of a long career built on molecular systematics.[3]
While such early biochemical techniques found grudging acceptance in the evolutionary biology
community, for the most part they did not impact the main theoretical problems of evolution and population
genetics. This would change as molecular biology shed more light on the physical and chemical nature of
genes.
[edit] Genetic load, the classical/balance controversy, and the measurement
of heterozygosity
At the time that molecular biology was coming into its own in the 1950s, there was a long-running
debate—the classical/balance controversy—over the causes of heterosis, the increase in fitness observed
when inbred lines are crossed. In 1950, James F. Crow offered two different explanations (later dubbed the
classical and balance positions) based the paradox first articulated by J. B. S. Haldane in 1937: the effect of
deleterious mutations on the average fitness of a population depends only on the rate of mutations (not the
degree of harm caused by each mutation) because more-harmful mutations are eliminated more quickly by
natural selection, while less-harmful mutations remain in the population longer. H. J. Muller dubbed this
"genetic load".[4]
Muller, motivated by his concern about the effects of radiation on human populations, argued that
heterosis is primarily the result of deleterious homozygous recessive alleles, the effects of which are masked
when separate lines are crossed—this was the dominance hypothesis, part of what Dobzhansky labeled the
classical position. Thus, ionizing radiation and the resulting mutations produce considerable genetic load
even if death or disease does not occur in the exposed generation, and in the absence of mutation natural
selection will gradually increase the level of homozygosity. Bruce Wallace, working with J. C. King, used the
overdominance hypothesis to develop the balance position, which left a larger place for overdominance
(where the heterozygous state of a gene is more fit than the homozygous states). In that case, heterosis is
simply the result of the increased expression of heterozygote advantage. If overdominant loci are common,
then a high level of heterozygosity would result from natural selection, and mutation-induced radiation may in
fact facilitate an increase in fitness due to overdominance. (This was also the view of Dobzhansky.)[5]
Debate continued through 1950s, gradually becoming a central focus of population genetics. A 1958
study of Drosophila by Wallace suggested that radiation-induced mutations increased the viability of
previously homozygous flies, providing evidence for heterozygote advantage and the balance position;
Wallace estimated that 50% of loci in natural Drosophila populations were heterozygous. Motoo Kimura's
subsequent mathematical analyses reinforced what Crow had suggested in 1950: that even if overdominant
loci are rare, they could be responsible for a disproportionate amount of genetic variability. Accordingly,
Kimura and his mentor Crow came down on the side of the classical position. Further collaboration between
Crow and Kimura led to the infinite alleles model, which could be used to calculate the number of different
alleles expected in a population, based on population size, mutation rate, and whether the mutant alleles
were neutral, overdominant, or deleterious. Thus, the infinite alleles model offered a potential way to decide
between the classical and balance positions, if accurate values for the level of heterozygosity could be found.
[6]
By the mid-1960s, the techniques of biochemistry and molecular biology—in particular,
electrophoresis—provided a way to measure the level of heterozygosity in natural populations: a possible
means to resolve the classical/balance controversy. In 1963, Jack L. Hubby published an electrophoresis
study of protein variation in Drosophila[7]; soon after, Hubby began collaborating with Richard Lewontin to
apply Hubby's method to the classical/balance controversy by measuring the proportion of heterozygous loci
in natural populations. Their two landmark papers, published in 1966, established a significant level of
heterozygosity for Drosophila (12%, on average).[8] However, these findings proved difficult to interpret. Most
population geneticists (including Hubby and Lewontin) rejected the possibility of widespread neutral
mutations; explanations that did not involve selection were anathema to mainstream evolutionary biology.
Hubby and Lewontin also ruled out heterozygote advantage as the main cause because of the segregation
load it would entail, though critics argued that the findings actually fit well with overdominance hypothesis.[9]
[edit] Protein sequences and the molecular clock
While evolutionary biologists were tentatively branching out into molecular biology, molecular
biologists were rapidly turning their attention toward evolution.
After developing the fundamentals of protein sequencing with insulin between 1951 and 1955,
Frederick Sanger and his colleagues had published a limited interspecies comparison of the insulin
sequence in 1956. Francis Crick, Charles Sibley and others recognized the potential for using biological
sequences to construct phylogenies, though few such sequences were yet available. By the early 1960s,
techniques for protein sequencing had advanced to the point that direct comparison of homologous amino
acid sequences was feasible.[10] In 1961, Emanuel Margoliash and his collaborators completed the
sequence for horse cytochrome c (a longer and more widely distributed protein than insulin), followed in short
order by a number of other species.
In 1962, Linus Pauling and Emile Zuckerkandl proposed using the number of differences between
homologous protein sequences to estimate the time since divergence, an idea Zuckerkandl had conceived
around 1960 or 1961. This began with Pauling's long-time research focus, hemoglobin, which was being
sequenced by Walter Schroeder; the sequences not only supported the accepted vertebrate phylogeny, but
also the hypothesis (first proposed in 1957) that the different globin chains within a single organism could
also be traced to a common ancestral protein.[11] Between 1962 and 1965, Pauling and Zuckerkandl refined
and elaborated this idea, which they dubbed the molecular clock, and Emil L. Smith and Emanuel Margoliash
expanded the analysis to cytochrome c. Early molecular clock calculations agreed fairly well with established
divergence times based on paleontological evidence. However, the essential idea of the molecular clock—that
individual proteins evolve at a regular rate independent of a species' morphological evolution—was extremely
provocative (as Pauling and Zuckerkandl intended it to be).[12]
[edit] The "molecular wars"
From the early 1960s, molecular biology was increasingly seen as a threat to the traditional core of
evolutionary biology. Established evolutionary biologists—particularly Ernst Mayr, Theodosius Dobzhansky
and G. G. Simpson, three of the founders of the modern evolutionary synthesis of the 1930s and 1940s—were
extremely skeptical of molecular approaches, especially when it came to the connection (or lack thereof) to
natural selection. Molecular evolution in general—and the molecular clock in particular—offered little basis for
exploring evolutionary causation. According to the molecular clock hypothesis, proteins evolved essentially
independently of the environmentally determined forces of selection; this was sharply at odds with the
panselectionism prevalent at the time. Moreover, Pauling, Zuckerkandl, and other molecular biologists were
increasingly bold in asserting the significance of "informational macromolecules" (DNA, RNA and proteins)
for all biological processes, including evolution.[13] The struggle between evolutionary biologists and
molecular biologists—with each group holding up their discipline as the center of biology as a whole—was later
dubbed the "molecular wars" by Edward O. Wilson, who experienced firsthand the domination of his biology
department by young molecular biologists in the late 1950s and the 1960s.[14]
In 1961, Mayr began arguing for a clear distinction between functional biology (which considered
proximate causes and asked "how" questions) and evolutionary biology (which considered ultimate causes
and asked "why" questions)[15] He argued that both disciplines and individual scientists could be classified
on either the functional or evolutionary side, and that the two approaches to biology were complementary.
Mayr, Dobzhansky, Simpson and others used this distinction to argue for the continued relevance of
organismal biology, which was rapidly losing ground to molecular biology and related disciplines in the
competition for funding and university support.[16] It was in that context that Dobzhansky first published his
famous statement, "nothing in biology makes sense except in the light of evolution", in a 1964 paper affirming
the importance of organismal biology in the face of the molecular threat; Dobzhansky characterized the
molecular disciplines as "Cartesian" (reductionist) and organismal disciplines as "Darwinian".[17]
Mayr and Simpson attended many of the early conferences where molecular evolution was
discussed, critiquing what they saw as the overly simplistic approaches of the molecular clock. The molecular
clock, based on uniform rates of genetic change driven by random mutations and drift, seemed incompatible
with the varying rates of evolution and environmentally-driven adaptive processes (such as adaptive
radiation) that were among the key developments of the evolutionary synthesis. At the 1962 Wenner-Gren
conference, the 1964 Colloquium on the Evolution of Blood Proteins in Bruges, Belgium, and the 1964
Conference on Evolving Genes and Proteins at Rutgers University, they engaged directly with the molecular
biologists and biochemists, hoping to maintain the central place of Darwinian explanations in evolution as its
study spread to new fields.[18]
[edit] Gene-centered view of evolution

Though not directly related to molecular evolution, the mid-1960s also saw the rise of the gene-
centered view of evolution, spurred by George C. Williams's Adaptation and Natural Selection (1966). Debate
over units of selection, particularly the controversy over group selection, led to increased focus on individual
genes (rather than whole organisms or populations) as the theoretical basis for evolution. However, the
increased focus on genes did not mean a focus on molecular evolution; in fact, the adaptationism promoted
by Williams and other evolutionary theories further marginalized the apparently non-adaptive changes
studied by molecular evolutionists.
[edit] The neutral theory of molecular evolution

Further information: Neutral theory of molecular evolution
The intellectual threat of molecular evolution became more explicit in 1968, when Motoo Kimura
introduced the neutral theory of molecular evolution.[19] Based on the available molecular clock studies (of
hemoglobin from a wide variety of mammals, cytochrome c from mammals and birds, and triosephosphate
dehydrogenase from rabbits and cows), Kimura (assisted by Tomoko Ohta) calculated an average rate of
DNA substitution of one base pair change per 300 base pairs (encoding 100 amino acids) per 28 million
years. For mammal genomes, this indicated a substitution rate of one every 1.8 years, which would produce
an unsustainably high genetic load unless the preponderance of substitutions was selectively neutral. Kimura
argued that neutral mutations occur very frequently, a conclusion compatible with the results of the
electrophoretic studies of protein heterozygosity. Kimura also applied his earlier mathematical work on
genetic drift to explain how neutral mutations could come to fixation, even in the absence of natural selection;
he soon convinced James F. Crow of the potential power of neutral alleles and genetic drift as well.[20]
Kimura's theory—described only briefly in a letter to Nature—was followed shortly after with a more
substantial analysis by Jack L. King and Thomas H. Jukes—who titled their first paper on the subject "non-
Darwinian evolution".[21] Though King and Jukes produced much lower estimates of substitution rates and
the resulting genetic load in the case of non-neutral changes, they agreed that neutral mutations driven by
genetic drift were both real and significant. The fairly constant rates of evolution observed for individual
proteins was not easily explained without invoking neutral substitutions (though G. G. Simpson and Emil
Smith had tried). Jukes and King also found a strong correlation between the frequency of amino acids and
the number different of codons for each; this pointed to amino acid sequences as largely the product of
random genetic drift.[22]
King and Jukes' paper, especially with the provocative title, was seen as a direct challenge to
mainstream neo-Darwinism, and it brought molecular evolution and the neutral theory to the center of
evolutionary biology. It provided a mechanism for the molecular clock and a theoretical basis for exploring
deeper issues of molecular evolution, such as the relationship between rate of evolution and functional
importance. The rise of the neutral theory marked synthesis of evolutionary biology and molecular biology—
though an incomplete one.[23]
With their work on firmer theoretical footing, in 1971 Emile Zuckerkandl and other molecular
evolutionists founded the Journal of Molecular Evolution .
[edit] The neutralist-selectionist debate and near-neutrality

The critical responses to the neutral theory that soon appeared marked the beginning of the
neutralist-selectionist debate. In short, selectionists viewed natural selection as the primary or only cause of
evolution, even at the molecular level, while neutralists held that neutral mutations were widespread and that
genetic drift was a crucial factor in the evolution of proteins. Kimura became the most prominent defender of
the neutral theory—which would be his main focus for the rest of his career. With Ohta, he refocused his
arguments on the rate at which drift could fix new mutations in finite populations, the significance of constant
protein evolution rates, and the functional constraints on protein evolution that biochemists and molecular
biologists had described. Though Kimura had initially developed the neutral theory partly as an outgrowth of
the classical position within the classical/balance controversy (predicting high genetic load as a consequence
of non-neutral mutations), he gradually deemphasized his original argument that segregational load would be
impossibly high without neutral mutations (which many selectionists, and even fellow neutralists King and
Jukes, rejected).[24]
From the 1970s through the early 1980s, both selectionists and neutralists could explain the
observed high levels of heterozygosity in natural populations, by assuming different values for unknown
parameters. Early in the debate, Kimura's student Tomoko Ohta focused on the interaction between natural
selection and genetic drift, which was significant for mutations that were not strictly neutral, but nearly so. In
such cases, selection would compete with drift: most slightly deleterious mutations would be eliminated by
natural selection or chance; some would move to fixation through drift. The behavior of this type of mutation,
described by an equation that combined the mathematics of the neutral theory with classical models, became
the basis of Ohta's nearly neutral theory of molecular evolution.[25]
In 1973, Ohta published a short letter in Nature[26] suggesting that a wide variety of molecular
evidence supported the theory that most mutation events at the molecular level are slightly deleterious rather
than strictly neutral. Molecular evolutionists were finding that while rates of protein evolution (consistent with
the molecular clock) were fairly independent of generation time, rates of noncoding DNA divergence were
inversely proportional to generation time. Noting that population size is generally inversely proportional to
generation time, Tomoko Ohta proposed that most amino acid substitutions are slightly deleterious while
noncoding DNA substitutions are more neutral. In this case, the faster rate of neutral evolution in proteins
expected in small populations (due to genetic drift) is offset by longer generation times (and vice versa), but
in large populations with short generation times, noncoding DNA evolves faster while protein evolution is
retarded by selection (which is more significant than drift for large populations).[27]
Between then and the early 1990s, many studies of molecular evolution used a "shift model" in which
the negative effect on the fitness of a population due to deleterious mutations shifts back to an original value
when a mutation reaches fixation. In the early 1990s, Ohta developed a "fixed model" that included both
beneficial and deleterious mutations, so that no artificial "shift" of overall population fitness was necessary.
[28] According to Ohta, however, the nearly neutral theory largely fell out of favor in the late 1980s, because
the mathematically simpler neutral theory for the widespread molecular systematics research that flourished
after the advent of rapid DNA sequencing. As more detailed systematics studies started to compare the
evolution of genome regions subject to strong selection versus weaker selection in the 1990s, the nearly
neutral theory and the interaction between selection and drift have once again become an important focus of
research.[29]
[edit] Microbial phylogeny

While early work in molecular evolution focused on readily sequenced proteins and relatively recent
evolutionary history, by the late 1960s some molecular biologists were pushing further toward the base of the
tree of life by studying highly conserved nucleic acid sequences. Carl Woese, a molecular biologist whose
earlier work was on the genetic code and its origin, began using small subunit ribosomal RNA to reclassify
bacteria by genetic (rather than morphological) similarity. Work proceeded slowly at first, but accelerated as
new sequencing methods were developed in the 1970s and 1980s. By 1977, Woese and George Fox
announced that some bacteria, such as methanogens, lacked the rRNA units that Woese's phylogenetic
studies were based on; they argued that these organisms were actually distinct enough from conventional
bacteria and the so-called higher organisms to form their own kingdom, which they called archaebacteria.
Though controversial at first (and challenged again in the late 1990s), Woese's work became the basis of the
modern three-domain system of Archaea, Bacteria, and Eukarya (replacing the five-domain system that had
emerged in the 1960s).[30]
Work on microbial phylogeny also brought molecular evolution closer to cell biology and origin of life
research. The differences between archaea pointed to the importance of RNA in the early history of life. In his
work with the genetic code, Woese had suggested RNA-based life had preceded the current forms of DNA-
based life, as had several others before him—an idea that Walter Gilbert would later call the "RNA world". In
many cases, genomics research in the 1990s produced phylogenies contradicting the rRNA-based results,
leading to the recognition of widespread lateral gene transfer across distinct taxa. Combined with the
probable endosymbiotic origin of organelle-filled eukarya, this pointed to a far more complex picture of the
origin and early history of life, one which might not be describable in the traditional terms of common
ancestry.[31]
[edit] Notes
1. ^ Dietrich, "Paradox and Persuasion", pp. 90-91; Zuckerkandl, "On the Molecular
Evolutionary Clock", p. 34
2. ^ Dietrich, "Paradox and Persuasion", pp. 90-91; Morgan, "Emile Zuckerkandl, Linus Pauling,
and the Molecular Evolutionary Clock", pp. 161-162.
3. ^ Hagen, "Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution", pp.
335-339
7. ^ Hubby J. L. (1963). "Protein Differences in Drosophila. I. Drosophila melanogaster".
Genetics 48 (6): 871–879. PMID 17248176.
8. ^ Hubby, J. L.; Lewontin, R. C. (1966). "A Molecular Approach to the Study of Genic
Heterozygosity in Natural Populations. I. The Number of Alleles at Different Loci in Drosophila
pseudoobscura". Genetics 54: 546–595. ; and Lewontin, R. C.; Hubby, J. L. (1966). "A Molecular
Approach to the Study of Genic Heterozygosity in Natural Populations. II. Amount of Variation and
Degree of Heterozygosity in Natural Populations of Drosophila pseudoobscura". Genetics 54 (2):
595–609. PMID 5968643.
10.^ Hagen, "Naturalists, Molecular Biologists, and the Challenge of Molecular Evolution", pp.
323-325
11.^ Zuckerkandl, "On the Molecular Evolutionary Clock", pp. 34-35
14.^ Wilson, Naturalist, pp. 219-237
15.^ Mayr's first published argument for the proximate/ultimate distinction was: Mayr Ernst
(1961). "Cause and Effect in Biology". Science 134: 1501–1506. PMID 14471768.
16.^ Hagen, "Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution", pp.
333-335
17.^ Dietrich, "Paradox and Persuation", pp. 100-103. Dobzhansky's famous phrase appears in
the first page of: Theodosius Dobzhansky, "Biology, Molecular and Organismic", American Zoologist,
volume 4 (1964), pp 443-452.
18.^ Dietrich, "Paradox and Persuation", pp. 95-98; Hagen, "Naturalists, Molecular Biologists,
and the Challenges of Molecular Evolution", pp. 330-332
19.^ Motoo Kimura, [Evolutionary Rate at the Molecular Level", Nature, Vol. 217 (1968), pp.
624-626
21.^ King, Jack L.; Jukes, Thomas (1969). "Non-Darwinian Evolution". Science 164 (881): 788–
798. doi:10.1126/science.164.3881.788. PMID 5767777.
23.^ Dietrich, "The Origins of the Neutral Theory of Molecular Evolution", pp. 54, 57-58
25.^ Ohta, "The current significance and standing of neutral and nearly neutral theories", pp.
673-674
26.^ Ohta, Tomoko (1973-11-09). "Slightly Deleterious Mutant Substitutions in Evolution".
Nature 246 (5428): 96–98. doi:10.1038/246096a0. PMID 4585855.
27.^ Ohta, Tomoko; John H. Gillespie (1996-04). "Development of Neutral and Nearly Neutral
Theories". Theoretical Population Biology 49 (2): 128–42. doi:10.1006/tpbi.1996.0007.
PMID 8813019. , pp 130-131
28.^ Ohta and Gillispie, "Development of Neutral and Nearly Neutral Theories", pp. 135-136
29.^ Ohta, "The current significance and standing of neutral and nearly neutral theories", p. 674
[edit] References
• Dietrich, Michael R. "The Origins of the Neutral Theory of Molecular Evolution." Journal of
the History of Biology, Vol. 27, No. 1 (Spring 1994), pp 21–59
• Dietrich, Michael R. (1998). "Paradox and Persuasion: Negotiating the Place of Molecular
Evolution within Evolutionary Biology". Journal of the History of Biology 31 (1): 85–111.
doi:10.1023/A:1004257523100. PMID 11619919.
• Crow, James F. "Motoo Kimura, 13 November 1924 - 13 November 1994." Biographical
Memoirs of Fellows of the Royal Society, Vol. 43 (November 1997), pp 254–265
• Hagen, Joel B. (1999). "Naturalists, Molecular Biologists, and the Challenge of Molecular
Evolution". Journal of the History of Biology 32 (2): 321–341. doi:10.1023/A:1004660202226.
PMID 11624208.
• Kreitman, Martin. "The neutralist-selectionist debate: The neutral theory is dead. Long live
the neutral theory", BioEssays, Vol. 18, No. 8 (1996), pp. 678–684
• Morgan, Gregory J. (1998). "Emile Zuckerkandl, Linus Pauling, and the Molecular
Evolutionary Clock, 1959-1965". Journal of the History of Biology 31 (2): 155–178.
doi:10.1023/A:1004394418084. PMID 11620303.
• Ohta, Tomoko. "The neutralist-selectionist debate: The current significance and standing of
neutral and nearly neutral theories", BioEssays, Vol. 18, No. 8 (1996), pp. 673–677
• Sapp, Jan. Genesis: The Evolution of Biology. New York: Oxford University Press, 2003.
ISBN 0-19-515618-8
• Wilson, Edward O. Naturalist. Warner Books, 1994. ISBN 0-446-67199-1
• Zuckerkandl, Emile (1987). "On the Molecular Evolutionary Clock". Journal of Molecular
Evolution 26 (1-2): 34–46. doi:10.1007/BF02111280. PMID 3125336.

• Perspectives on Molecular Evolution - maintained by historian of science Michael R. Dietrich
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W000
Orthogenesis

Orthogenesis, orthogenetic evolution, progressive evolution or autogenesis, is the hypothesis that life
has an innate tendency to move in an unilinear fashion due to some internal or external "driving force". The
hypothesis is based on essentialism and cosmic teleology and proposes an intrinsic drive which slowly
transforms species. George Gaylord Simpson (1953) in an attack on orthogenesis called this mechanism
"the mysterious inner force".[1] Classic proponents of orthogenesis have rejected the theory of natural
selection as the organising mechanism in evolution, and theories of speciation for a rectilinear model of
guided evolution acting on discrete species with "essences". The term orthogenesis was popularised by
Theodor Eimer, though many of the ideas are much older (Bateson 1909).[2]
Contents
[hide]
• 1 No Goal
• 2 Origins
• 3 Comparison of Theories
• 4 Collapse of the hypothesis
• 5 Modern co-opted usage
• 6 See also
• 7 References
• 8 Sources
[edit] No Goal
This section may contain original research. Please improve it by verifying the claims
removed. More details may be available on the talk page. (December 2008)
Orthogenesis does not postulate a "goal" for evolution. Though it proceeds in a linear fashion driven
by some internal mechanism, it does not have a goal.
Many sources mix this heterodox view of evolution with another—- that evolution is proceeding to
some long term or ultimate goal; the result are definitions that state "orthogenesis proposes that evolution
moves in a unilinear fashion towards a perfect goal". While it is true that early and famous examples of
orthogenesis often conflated these two ideas (e.g. Jean-Baptiste Lamarck's theory of evolution), it is
important to recognize that these are in fact two separate ideas that are rejected by mainstream science; the
latter idea of goal-oriented evolution is better understood as a form of teleology.
The distinction can be seen when we recognize that orthogenesis is inherent in the theories of
German biologist Ernst Haeckel and American paleontologist Richard Swann Lull. Both scientists proposed
mechanisms whereby evolution proceeded in unilinear fashion, but neither saw goals (instead they made
pseudo-scientific appeals to unknown genetic driving processes).
This is important because similar flaws occur recurrently at the fringes of science, typically taking the
form of mysterious molecular drives that supposedly are pushing phenotypic evolution in certain directions or
forcing the formation of new species.
[edit] Origins
The orthogenesis hypothesis had a significant following in the 19th century when a number of
evolutionary mechanisms, such as Lamarckism, were being proposed. Jean-Baptiste Lamarck himself
accepted the idea, and it had a central role in his theory of inheritance of acquired characteristics, the
hypothesised mechanism of which resembled the "mysterious inner force" of orthogenesis. Other proponents
of orthogenesis included Leo Berg, philosopher Henri Bergson and, for a time, the paleontologist Henry
Fairfield Osborn. Orthogenesis was particularly accepted by paleontologists who saw in their fossils a
directional change, and in invertebrate paleontology thought there was a gradual and constant directional
change. Those who accepted orthogenesis in this way, however, did not necessarily accept that the
mechanism that drove orthogenesis was teleological. In fact, Darwin himself rarely used the term "evolution"
now so commonly used to describe his theory, because in Darwin's time, evolution usually was associated
with some sort of progressive process like orthogenesis, and this had been common usage since at least
1647.[3]
[edit] Comparison of Theories

Theories of Evolution
• Based on Essentialism:
• Transmutationism
(saltationism)
• Transformationism
• Orthogenesis
• Lamarcki
sm
• Based on population biology:
• Darwinian evolution
Comparison of different theories of evolution
Darwinism Orthogenesis Lamarckism
Mechanism Short-sighted Intrinsic drive Intrinsic drive

Natural Selection sorting towards perfection; natural towards perfection and
random genetic variation, selection unimportant. inheritance of acquired
no other guidance or aim. Characters produced may characteristics (both are
Selected traits are Lamarckian principles);
be totally non-adaptive,
adaptive, i.e. have some natural selection adopted by
i.e. have no survival value.
survival value. some in latter years.
No, speciation Depends upon

rejected or considered source quoted. Signs that
Yes, new species unimportant in long term species shared a common
Common
coming into existence by trends; spontaneous ancestor were detected
descent
speciation events. generation of new species before Darwin, but in
resulting in parallel absence of a mechanism
evolution. some still rejected the idea.
Declined after the

Origin, though the
Refuted by mechanism was not refuted
Prevailing in
Charles Darwin's Origin of until the modern
Status modified form as modern
Species and the modern evolutionary synthesis in
evolutionary synthesis.
evolutionary synthesis. which it was established that
the mechanism does not
exist.
[edit] Collapse of the hypothesis
The orthogenesis hypothesis began to collapse when it became clear that it could not explain the
patterns found by paleontologists in the fossil record, which was non-linear with many complications. The
hypothesis was generally abandoned when no mechanism could be found that would account for the
process, and the theory of evolution by natural selection became the prevailing theory of evolution. The
modern evolutionary synthesis, in which the genetic mechanisms of evolution were discovered, refuted the
hypothesis for good. As more was understood about these mechanisms it became obvious that there was no
possible naturalistic way in which the newly discovered mechanism of heredity could be far-sighted or have a
memory of past trends.
The orthogenetic hypothesis, however, died hard. Even Darwin was at first not opposed to orthogenic
thinking, as this quote from the 1911 Encyclopedia Britannica demonstrates:
Darwin and his generation were deeply imbued with the Butlerian tradition, and regarded the
organic world as almost a miracle of adaptation, of the minute dovetailing of structure, function
and environment. Darwin certainly was impressed with the view that natural selection and
variation together formed a mechanism, the central product of which was adaptation. From the
Butlerian side, too, came the most urgent opposition to Darwinism. How is it possible, it was
said, that fortuitous variations can furnish the material for the precise and balanced adaptations
that all nature reveals? Selection cannot create the materials on which it is supposed to operate;
the beginnings of new organs, the initial stages of new functions cannot be supposed to have
been useful. Moreover, many naturalists, especially those concerned with palaeontology,
pointed to the existence of orthogenetic series, of long lines of ancestry, which displayed not a
sporadic differentiation. in every direction, but apparently a steady and progressive march in one
direction.[4]
Edward Drinker Cope put such a line of argument in the most cogent fashion; the course of
evolution, both in the production of variations and their selection, seemed to him to imply the
existence of an originative, conscious and directive force, for which he invented the term
bathmism (Gr. βαθμ, a step or beginning). On the other hand, dislike of mystical interpretations
of natural facts has driven many capable naturalists to another extreme and has led them to
insist on the all-powerfulness of natural selection and on the complete indefiniteness of
variation. The apparent opposition between the conflicting schools is more acute than the facts
justify.... there is no connection between the appearance of the variation and the use to which it
may be put... in one sense it is a mere coincidence if a particular variation turn out to be useful.
But there are several directions in which the field of variation appears to be not only limited but
defined in a certain direction. Obviously variations depend on the constitution of the varying
organism; a modification, whether it be large or small, is a modification of an already definite
and limited structure.... A continuous environment both from the point of view of production of
variation and selection of variation would appear necessarily to result in a series with the
appearance of orthogenesis. The past history of the organic world displays many successful
series and these, as they have survived, must inevitably display orthogenesis to some extent;
but it also displays many failures which indeed may be regarded as showing that the limitation of
variation has been such that the organisms have lost the possibility of successful response to a
new environment.[4]
A few hung on to the orthogenesis hypothesis as late as the 1950s by claiming that the processes of
macroevolution, the long term trends in evolution, were distinct from the processes of microevolution (genetic
variation and natural selection) which were by then well understood and it was known they could not behave
in an orthogenetic manner. Teilhard de Chardin, a Jesuit paleontologist, in The Phenomenon of Man (a book
influential among non-scientists that was published four years after his death in 1959) argued for evolution
aiming for the "Omega Point", while putting man at the center of the universe and accounting for original sin
(Dennett 1995, von Kitzing 1998). The term Chardin used for this was "directed additivity". This form of
orthogenesis has now also been abandoned as more about evolutionary processes has been discovered
(Wilkins 1997).
The refutation of orthogenesis had some ramifications in the field of philosophy, as it refuted the idea
of teleology as first postulated by Aristotle and accepted by Immanuel Kant, who had greatly influenced many
scientists. Before the scientific and philosophical revolution that began with Charles Darwin's ideas, the
prevailing philosophy was that the world was teleological and purposeful, and that science was the study of
God's creation. The refutation of these concepts have led to a shift in what science and scientists are
perceived to be.
[edit] Modern co-opted usage

Though linear teleological evolution has been refuted, it is not true that evolution never proceeds in a
linear way, reinforcing characteristics, in certain lineages at times, for example, during a period of slow,
sustained environmental change, but such examples are entirely consistent with the modern neo-Darwinian
theory of evolution. These examples have sometimes been referred to as orthogenetic (e.g. by Jacobs et al.
1995 & Woodley 2006) but are not strictly orthogenetic, and simply appear as linear and constant changes
because of environmental and molecular constraints on the direction of change.
[edit] See also

• Facilitated variation
• Evolution of complexity
• Eclipse of Darwinism
• Law of Complexity/Consciousness
[edit] References
1. ^ George Gaylord Simpson, Life of the Past: An Introduction to Paleontology, Yale University
Press, New Haven, 1953, p. 125.
2. ^ The evolutionary future of man: A biological view of progress
3. ^ Darwin's Dilemma: The Odyssey of Evolution, Stephen Jay Gould, an essay in Ever Since
Darwin: Reflections in Natural History, W. W. Norton, 1977, ISBN 0-393-06425-5
4. ^ a b The Encyclopaedia Britannica: A Dictionary of Arts, Sciences, Literature and General
Information, Eleventh Edition, Copyright in all countries subscribing the Berne Convention by the
Chancellor, Masters and Scholars of the University of Cambridge, Copyright in the United States of
America by the Encyclopaedia Britannica Company, London, May 31, 1911.
[edit] Sources
1. Bateson, William, 1909. Heredity and variation in modern lights, in Darwin and Modern
Science (A.C. Seward ed.). Cambridge University Press. Chapter V. E-book.
2. Dennett, Daniel, 1995. Darwin's Dangerous Idea. Simon & Schuster.
3. Huxley, Julian, 1942. The Modern Evolutionary Synthesis, London: George Allen and Unwin.
4. Jacobs, Susan C., Allan Larson & James M. Cheverud, 1995. Phylogenetic Relationships
and Orthogenetic Evolution of Coat Color Among Tamarins (Genus Saguinus). Syst. Biol. 44(4):515—
532, Abstract.
5. Mayr, Ernst, 2002. What Evolution Is, London: Weidenfeld and Nicolson.
6. Simpson, George G., 1957. Life Of The Past: Introduction to Paleontology. Yale University
Press, p.119.
7. Wilkins, John, 1997. What is macroevolution?. TalkOrigins Archive [1] (14:08 UTC, Oct 13
2004)
8. Woodley, Michael A., 2006. The Limits of Ecology: New Perspectives from a Theoretical
Borderland. Abramis Academic Press.
This article incorporates text from a publication now in the public domain: Chisholm, Hugh, ed
(1911). Encyclopædia Britannica (Eleventh ed.). Cambridge University Press.
Retrieved from "http://en.wikipedia.org/wiki/Orthogenesis"
Categories: History of evolutionary biology | Teleology | Essentialism | Obsolete biological theories

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E. coli long-term evolution experiment


The 12 evolving E. coli populations on June 25, 2008.
The E. coli long-term evolution experiment is an ongoing study in experimental evolution led by
Richard Lenski that has been tracking genetic changes in 12 initially nearly identical populations of asexual
Escherichia coli bacteria since 24 February 1988.[1] The populations reached the milestone of 50,000
generations in February 2010.
Since the experiment's inception, Lenski and his colleagues have reported a wide array of genetic
changes; some evolutionary adaptations have occurred in all 12 populations, while others have only
appeared in one or a few populations. One particularly striking adaption was the evolution of a strain of E.
coli that was able to grow on citric acid in the growth media.
Contents
[hide]
• 1 Experimental approach
• 1.1 Methods
• 2 Results
• 3 References
[edit] Experimental approach
The long-term evolution experiment was intended to provide experimental evidence for several of the
central problems of evolutionary biology: how rates of evolution vary over time; the extent to which
evolutionary changes are repeatable in separate populations with identical environments; and the
relationship between evolution at the phenotypic and genomic levels.[2]
The use of E. coli as the experimental organism has allowed many generations and large populations
to be studied in a relatively short period of time, and has made experimental procedures (refined over
decades of E. coli use in molecular biology) fairly simple. The bacteria can also be frozen and preserved,
creating what Lenski has described as a "frozen fossil record" that can be revived at any time (and can be
used to restart recent populations in cases of contamination or other disruption of the experiment). Lenski
chose an E. coli strain that reproduces only asexually, without bacterial conjugation; this limits the study to
evolution based on new mutations and also allows genetic markers to persist without spreading except by
common descent.[2]
[edit] Methods
Each of the 12 populations is kept in an incubator in Lenski's laboratory at Michigan State University
in a minimal growth medium. Each day, 1% of each population is transferred to a flask of fresh growth
medium. Large, representative samples of each population are frozen with glycerol as a cryoprotectant at
500-generation (75 day) intervals. The populations are also regularly screened for changes in mean fitness,
and supplemental experiments are regularly performed to study interesting developments in the populations.
[3] As of February 2010[update], the E. coli populations have been under study for over 50,000 generations,
and are thought to have undergone enough spontaneous mutations that every possible single point mutation
in the E. coli genome should have occurred multiple times.[4]
The initial strain of E. coli for Lenski's long-term evolution experiment came from "strain Bc251", as
described in a 1966 paper by Seymour Lederberg, via Bruce Levin (who used it in a bacterial ecology
experiment in 1972). The defining genetics traits of this strain were: T6 r, Strr, r−m−, Ara− (unable to grow on
arabinose).[1] Before the beginning of the experiment Lenski prepared a Ara+ variant (a point mutation in the
ara operon that enables growth on arabinose) of the strain; the initial populations consisted of 6 Ara − colonies
and 6 Ara+ colonies, which allowed the two sets of strains to be differentiated and tested for fitness against
each other. Unique genetic markers have since evolved to allow identification of each strain.
[edit] Results
Growth in cell size of bacteria in the Lenski experiment

In the early years of the experiment, there were several common evolutionary developments shared
by the populations. The mean fitness of each population, as measured against the ancestor strain, increased
—rapidly at first, but leveling off after close to 20,000 generations (at which point they grew about 70% faster
than the ancestor strain). All populations evolved larger cell volumes and lower maximum population
densities, and all became specialized for living on glucose (with declines in fitness relative to the ancestor
strain when grown in dissimilar nutrients). 4 of the 12 populations developed defects in their ability to repair
DNA, greatly increasing the rate of additional mutations in those strains. Although the bacteria in each
population are thought to have generated hundreds of millions of mutations over the first 20,000 generations,
Lenski has estimated that only 10 to 20 beneficial mutations achieved fixation in each population, with less
than 100 total point mutations (including neutral mutations) reaching fixation in each population.[2]
The population designated Ara-3 (center) is more turbid because that population evolved to use the
citrate present in the growth medium.
In 2008, Lenski and his collaborators reported on a particularly important adaptation that occurred in
one of the twelve populations: the bacteria evolved the ability to utilize citrate as a source of energy. Wild
type E. coli cannot transport citrate across the cell membrane to the cell interior (where it could be
incorporated into the citric acid cycle) when oxygen is present. The consequent lack of growth on citrate
under oxic conditions is considered a defining characteristic of the species that has been a valuable means
of differentiating E. coli from pathogenic Salmonella. Around generation 33,127, the experimenters noticed a
dramatically expanded population-size in one of the samples; they found that there were clones in this
population that could grow on the citrate included in the growth medium to permit iron acquisition.
Examination of samples of the population frozen at earlier time points led to the discovery that a citrate-using
variant had evolved in the population at some point between generations 31,000 and 31,500. They used a
number of genetic markers unique to this population to exclude the possibility that the citrate-using E. coli
were contaminants. They also found that the ability to use citrate could spontaneously re-evolve in
populations of genetically pure clones isolated from earlier time points in the population's history. Such re-
evolution of citrate utilization was never observed in clones isolated from before generation 20,000. Even in
those clones that were able to re-evolve citrate utilization, the function showed a rate of occurrence on the
order of once per trillion cells. The authors interpret these results as indicating that the evolution of citrate
utilization in this one population depended on an earlier, perhaps non-adaptive "potentiating" mutation that
had the effect of increasing the rate of mutation to citrate utilization to an accessible level (with the data they
present further suggesting that citrate utilization required at least two mutations subsequent to this
"potentiating" mutation). More generally the authors suggest that these results indicate (following the
argument of Stephen Jay Gould) "that historical contingency can have a profound and lasting impact" on the
course of evolution.[4]
Another adaptation that occurred in all these bacteria was an increase in cell size and in many
cultures, a more rounded cell shape.[5] This change was partly the result of a mutation that changed the
expression of a gene for a penicillin binding protein, which allowed the mutant bacteria to out-compete
ancestral bacteria under the conditions in the long-term evolution experiment. However, although this
mutation increased fitness under these conditions, it also increased the bacteria's sensitivity to osmotic
stress and decreased their ability to survive long periods in stationary phase cultures, so the phenotype of
this adaptation depends on the environment of the cells.[5]
[edit] References
1. ^ a b Richard E. Lenski, Source of founding strain, 2000. Accessed June 18, 2008.
2. ^ a b c Lenski, Richard E. (2004). "Phenotypic and genomic evolution during a 20,000-
generation experiment with the bacterium Escherichia coli" (PDF). Plant Breeding Reviews 24 (2):
225–265. http://myxo.css.msu.edu/lenski/pdf/2004,%20Plant%20Breeding%20Reviews,
%20Lenski.pdf. Retrieved 2008-06-18.
3. ^ Richard E. Lenski, Overview of the E. coli long-term evolution experiment, 2000. Accessed
June 18, 2008.
4. ^ a b Blount, Zachary D.; Christina Z. Borland, Richard E. Lenski (2008-06-10). "Inaugural
Article: Historical contingency and the evolution of a key innovation in an experimental population of
Escherichia coli". Proceedings of the National Academy of Sciences 105 (23): 7899–7906.
doi:10.1073/pnas.0803151105. PMID 18524956. PMC 2430337.
http://www.pnas.org/cgi/content/abstract/105/23/7899. Retrieved 2008-06-18. .
This article is available in PDF formPDF (571 KB) from Richard Lenski's website.
5. ^ a b Philippe N, Pelosi L, Lenski RE, Schneider D (February 2009). "Evolution of penicillin-
binding protein 2 concentration and cell shape during a long-term experiment with Escherichia coli".
J. Bacteriol. 191 (3): 909–21. doi:10.1128/JB.01419-08. PMID 19047356.

• E. coli Long-term Experimental Evolution Project Site
• Bacteria make major evolutionary shift in the lab Bob Holmes New Scientist 09 June 2008
• Evolution: Past, Present and Future Richard Lenski
• List of publications on the experiment
Retrieved from "http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment"
Categories: Biology experiments | Molecular evolution | Evolutionary biology | Escherichia coli

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Darwinism

This article is about concepts called Darwinism. For biological evolution, see evolution. For modern
evolutionary theory, see modern evolutionary synthesis.
Charles Darwin in 1868
Darwinism is a set of movements and concepts related to ideas of transmutation of species or
evolution, including ideas with no connection to the work of Charles Darwin.[1][2][3] The meaning of
"Darwinism" has changed over time, and varies depending on who is using the term.[4] In the United States,
the term "Darwinism" is often used by creationists as a pejorative term, but in the United Kingdom the term
has no negative connotations, being freely used as a short hand for evolutionary theory.[5]
The term was coined by Thomas Henry Huxley in April 1860,[6] and was used to describe
evolutionary concepts, including earlier concepts such as Malthusianism and Spencerism. In the late 19th
century it came to mean the concept that natural selection was the sole mechanism of evolution, in contrast
to Lamarckism, then around 1900 it was eclipsed by Mendelism until the modern evolutionary synthesis
unified Darwin's and Gregor Mendel's ideas. As modern evolutionary theory has developed, the term has
been associated at times with specific ideas.[4]
While the term has remained in use amongst scientific authors, it is increasingly regarded as an
inappropriate description of modern evolutionary theory.[7][8][9] For example, Darwin was unfamiliar with the
work of Gregor Mendel,[10] having as a result only a vague and inaccurate understanding of heredity, and
knew nothing of genetic drift.[11]
Contents
[hide]
• 1 Conceptions of Darwinism
• 2 19th Century usage
• 3 Other uses
• 4 See also
• 5 Notes
• 6 References
[edit] Conceptions of Darwinism

As "Darwinism" became widely accepted in the 1870s, caricatures of Charles Darwin with an ape or
monkey body symbolised evolution.[12]
While the term Darwinism had been used previously to refer to the work of Erasmus Darwin in the
late 18th century, the term as understood today was introduced when Charles Darwin's 1859 book On the
Origin of Species was reviewed by Thomas Henry Huxley in the April 1860 issue of the Westminster Review.
[13] Having hailed the book as, "a veritable Whitworth gun in the armoury of liberalism" promoting scientific
naturalism over theology, and praising the usefulness of Darwin's ideas while expressing professional
reservations about Darwin's gradualism and doubting if it could be proved that natural selection could form
new species,[14] Huxley compared Darwin's achievement to that of Copernicus in explaining planetary
motion:
What if the orbit of Darwinism should be a little too circular? What if species should offer residual
phenomena, here and there, not explicable by natural selection? Twenty years hence naturalists
may be in a position to say whether this is, or is not, the case; but in either event they will owe
the author of "The Origin of Species" an immense debt of gratitude...... And viewed as a whole,
we do not believe that, since the publication of Von Baer's "Researches on Development," thirty
years ago, any work has appeared calculated to exert so large an influence, not only on the
future of Biology, but in extending the domination of Science over regions of thought into which
she has, as yet, hardly penetrated.[6]
Another important evolutionariy theorist of the same period was Peter Kropotkin who, in his book
Mutual Aid: A Factor of Evolution, advocated a conception of Darwinism counter to that of Huxley. His
conception was centred around what he saw as the widespread use of cooperation as a survival mechanism
in human societies and animals. He used biological and sociological arguments in an attempt to show that
the main factor in facilitating evolution is cooperation between individuals in free-associated societies and
groups. This was in order to counteract the conception of fierce competition as the core of evolution, which
provided a rationalisation for the dominant political, economic and social theories of the time; and the
prevalent interpretations of Darwinism, such as those by Huxley, who is targeted as an opponent by
Kropotkin. Kropotkin's conception of Darwinism could be summed up by the following quote:
In the animal world we have seen that the vast majority of species live in societies, and that they
find in association the best arms for the struggle for life: understood, of course, in its wide
Darwinian sense – not as a struggle for the sheer means of existence, but as a struggle against
all natural conditions unfavourable to the species. The animal species, in which individual
struggle has been reduced to its narrowest limits, and the practice of mutual aid has attained the
greatest development, are invariably the most numerous, the most prosperous, and the most
open to further progress. The mutual protection which is obtained in this case, the possibility of
attaining old age and of accumulating experience, the higher intellectual development, and the
further growth of sociable habits, secure the maintenance of the species, its extension, and its
further progressive evolution. The unsociable species, on the contrary, are doomed to decay.
– Peter Kropotkin, Mutual Aid: A Factor of Evolution (1902), Conclusion.
[edit] 19th Century usage

"Darwinism" soon came to stand for an entire range of evolutionary (and often revolutionary)
philosophies about both biology and society. One of the more prominent approaches was that summed in the
phrase "survival of the fittest" by the philosopher Herbert Spencer, which was later taken to be emblematic of
Darwinism even though Spencer's own understanding of evolution was more similar to that of Jean-Baptiste
Lamarck than to that of Darwin, and predated the publication of Darwin's theory. What is now called "Social
Darwinism" was, in its day, synonymous with "Darwinism" — the application of Darwinian principles of
"struggle" to society, usually in support of anti-philanthropic political agendas. Another interpretation, one
notably favoured by Darwin's half-cousin Francis Galton, was that Darwinism implied that because natural
selection was apparently no longer working on "civilised" people it was possible for "inferior" strains of people
(who would normally be filtered out of the gene pool) to overwhelm the "superior" strains, and voluntary
corrective measures would be desirable—the foundation of eugenics.
[Both] a Darwinian 'left' and a Darwinian 'right' were in place before most people
“ ”
had grasped the Darwinian middle, which was where the maker was.[15]
In Darwin's day there was no rigid definition of the term "Darwinism", and it was used by opponents
and proponents of Darwin's biological theory alike to mean whatever they wanted it to in a larger context. The
ideas had international influence, and Ernst Haeckel developed what was known as Darwinismus in
Germany, although, like Spencer Haeckel's "Darwinism" had only a rough resemblance to the theory of
Charles Darwin, and was not centred on natural selection at all.
While the reaction against Darwin's ideas is nowadays often thought to have been widespread
immediately, in 1886 Alfred Russel Wallace went on a lecture tour across the United States, starting in New
York and going via Boston, Washington, Kansas, Iowa and Nebraska to California, lecturing on what he
called Darwinism without any problems.[16]
[edit] Other uses

The term Darwinism is often used in the United States by promoters of creationism, notably by
leading members of the intelligent design movement, as an epithet to attack evolution as though it were an
ideology (an "ism") of philosophical naturalism, or atheism.[17] For example, Phillip E. Johnson makes this
accusation of atheism with reference to Charles Hodge's book What Is Darwinism?.[18] However, unlike
Johnson, Hodge confined the term to exclude those like Asa Gray who combined Christian faith with support
for Darwin's natural selection theory, before answering the question posed in the book's title by concluding:
"It is Atheism."[19][20][21] Creationists use the term Darwinism, often pejoratively, to imply that the theory
has been held as true only by Darwin and a core group of his followers, whom they cast as dogmatic and
inflexible in their belief.[22] Casting evolution as a doctrine or belief, as well as a pseudo-religious ideology
like Marxism,[23] bolsters religiously motivated political arguments to mandate equal time for the teaching of
creationism in public schools.
However, Darwinism is also used neutrally within the scientific community to distinguish modern
evolutionary theories from those first proposed by Darwin, as well as by historians to differentiate it from
other evolutionary theories from around the same period. For example, Darwinism may be used to refer to
Darwin's proposed mechanism of natural selection, in comparison to more recent mechanisms such as
genetic drift and gene flow. It may also refer specifically to the role of Charles Darwin as opposed to others in
the history of evolutionary thought — particularly contrasting Darwin's results with those of earlier theories
such as Lamarckism or later ones such as the modern synthesis.
In the United Kingdom the term retains its positive sense as a reference to natural selection, and for
example Richard Dawkins wrote in his collection of essays A Devil's Chaplain, published in 2003, that as a
scientist he is a Darwinist.[24]
[edit] See also

Book:Evolution

• Darwinism (book)
• Modern evolutionary synthesis
• Neo-Darwinism
• Neural Darwinism
• Social Darwinism
• Darwin Awards
• Pangenesis - Charles Darwin's hypothetical mechanism for heredity
• Universal Darwinism
[edit] Notes
1. ^ John Wilkins (1998). "How to be Anti-Darwinian". TalkOrigins Archive.
http://www.talkorigins.org/faqs/anti-darwin.html. Retrieved 19 June 2008.
2. ^ "Expelled Exposed: Why Expelled Flunks » …on what evolution explains" . National Center
for Science Education. http://www.expelledexposed.com/index.php/contest/on-what-evolution-
explains. Retrieved 22 December 2008.
3. ^ based on an European Southern Observatory release (9 December 2006). "Galactic
Darwinism :: Astrobiology Magazine - earth science - evolution distribution Origin of life universe - life
beyond :: Astrobiology is study of earth science evolution distribution Origin of life in universe
terrestrial". http://www.astrobio.net/news/index.php?
name=News&file=article&sid=2169&theme=Printer. Retrieved 22 December 2008.
4. ^ a b Joel Hanes. "What is Darwinism?". TalkOrigins Archive.
http://www.talkorigins.org/faqs/darwinism.html. Retrieved 19 June 2008.
5. ^ Scott, Eugenie C.; Branch, Glenn (16 January 2009). "Don’t Call it “Darwinism”". Evolution:
Education and Outreach (New York: Springer) 2 (1): 90. doi:10.1007/s12052-008-0111-2.
ISSN 1936-6434. http://www.springerlink.com/content/n47h34357743w4p0/?
p=e3b030036a4d442a8ce393291fe0688f&pi=9. Retrieved 17 November 2009.
6. ^ a b Huxley, T.H. (April 1860). "ART. VIII.- Darwin on the origin of Species". Westminster
Review. pp. 541–70. http://darwin-online.org.uk/content/frameset?
viewtype=side&itemID=A32&pageseq=29. Retrieved 19 June 2008. "What if the orbit of Darwinism
should be a little too circular?"
7. ^ John Wilkins (1998). "How to be Anti-Darwinian". TalkOrigins Archive.
http://www.talkorigins.org/faqs/anti-darwin.html. Retrieved 27 June 2008.
8. ^ Ruse, Michael (2003). Darwin and Design: Does Evolution Have a Purpose? . Cambridge,
MA: Harvard University Press. pp. 293. ISBN 0674016319. http://books.google.com/?
id=SHWaeRiRD-cC&printsec=frontcover&dq=%22michael+ruse%22+darwinism. Retrieved 18 July
2008.
9. ^ Olivia Judson (15 July 2008). "Let’s Get Rid of Darwinism". New York Times.
http://judson.blogs.nytimes.com/2008/07/15/lets-get-rid-of-darwinism/.
10.^ Sclater, Andrew (June 2006). "The extent of Charles Darwin’s knowledge of Mendel".
Journal of Biosciences (Bangalore, India: Springer India / Indian Academy of Sciences) 31 (2): 191–
193. doi:10.1007/BF02703910. PMID 16809850.
http://www.springerlink.com/content/w112307246x77t37/. Retrieved 3 January 2009.
11.^ Laurence Moran (1993). "Random Genetic Drift". TalkOrigins Archive.
http://www.talkorigins.org/faqs/genetic-drift.html. Retrieved 27 June 2008.
12.^ Browne 2002, pp. 376–379
13.^ "The Huxley File § 4 Darwin's Bulldog". http://aleph0.clarku.edu/huxley/guide4.html.
Retrieved 29 June 2008.
14.^ Browne 2002, pp. 105–106
15.^ Gopnik 2009, p. 152.
16.^ "Evolution and Wonder - Understanding Charles Darwin - Speaking of Faith from American
Public Media". http://speakingoffaith.publicradio.org/programs/darwin/transcript.shtml. Retrieved 27
July 2007.
17.^ Scott, Eugenie C. (2008). "Creation Science Lite: "Intelligent Design" as the New Anti-
Evolutionism". In Godfrey, Laurie R.; Petto, Andrew J.. Scientists Confront Creationism: Intelligent
Design and Beyond. New York: W. W. Norton. pp. 72. ISBN 0-393-33073-7.
http://biology.ucf.edu/~clp/Courses/seminar/papers/07-Scott-scientists_confront-cs_lite.pdf
18.^ Johnson, Phillip E.. "What is Darwinism?". http://www.arn.org/docs/johnson/wid.htm.
Retrieved 4 January 2007.
19.^ Matthew, Ropp. "Charles Hodge and His Objection to Darwinism".
http://www.theropps.com/papers/Winter1997/CharlesHodge.htm. Retrieved 4 January 2007.
20.^ Hodge, Charles. "What is Darwinism?". http://www.gutenberg.org/files/19192/19192-8.txt.
21.^ Hodge, Charles (1874). What is Darwinism?. Scribner, Armstrong, and Company.
OCLC 11489956.
22.^ Sullivan, M (2005). "From the Beagle to the School Board: God Goes Back to School".
Impact Press. http://www.impactpress.com/articles/spring05/sullivanspring05.html. Retrieved 18
September 2008.
23.^ "Darwinism should be allowed to collapse and end up on the ash heap of history".
http://www.docstoc.com/docs/20835072/Darwinism-should-be-allowed-to-collapse-and-end-up-on-
the-ash-heap-of-history.
24.^ Sheahen, Laura. Religion: For Dummies. BeliefNet.com, interview about 2003 book.
[edit] References
• Browne, E. Janet (2002). Charles Darwin: Vol. 2 The Power of Place. London: Jonathan
Cape. ISBN 0712668373.
• Gopnik, Adam (2009). Angels and Ages: A Short Book About Darwin, Lincoln, and Modern
Life. London: Quercus. ISBN 9781847249296.

Look up darwinism in Wiktionary, the free dictionary.
• Universal Darwinism
• (Russian) Nikolai Danilevsky. 1885-1889 Darwinism. A Critical Study (Дарвинизм.
Критическое исследование) at Runivers.ru in DjVu format
• What is Darwinism
• The Darwinian Revolution
Retrieved from "http://en.wikipedia.org/wiki/Darwinism"
Categories: Evolution | History of evolutionary biology

W000
Peppered moth

Peppered moth
The melanic carbonaria (left) and the more common light-colored typica (right).
Conservation status
Not evaluated (IUCN 3.1)

Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Lepidoptera
Family: Geometridae
Genus: Biston
Species: B. betularia
Binomial name
Biston betularia
Linnaeus, 1758
Subspecies
B. b. betularia
B. b. cognataria
B. b. parva
The peppered moth (Biston betularia) is a temperate species of night-flying moth.[1] Peppered moth
evolution is often used by educators as an example of natural selection.[2]
Contents
[hide]
• 1 Ecology and life cycle
• 1.1 Resting behaviour
• 2 Morphs
• 3 Evolution
• 4 References
[edit] Ecology and life cycle

Biston betularia caterpillars on birch (left) and willow (right), demonstrating twig mimicry. [3]
In Britain and Ireland, the peppered moth is univoltine (i.e., it has one generation per year), whilst in
south-eastern North America it is bivoltine (two generations per year). The lepidopteran life cycle consists of
four stages: ova (eggs), several larval instars (caterpillars), pupae, which overwinter live in the soil, and
imagines (adults). During the day, the moths typically rest on trees, where they are preyed on by birds.
The caterpillar is a twig mimic, varying in colour between green and brown. It goes into the soil late in
the season, where it pupates in order to spend the winter. The imagines emerge from the pupae between late
May and August, the males slightly before the females (this is common and expected from sexual selection).
They emerge late in the day and dry their wings before flying that night.
The males fly every night of their lives in search of females, whereas the females only fly on the first
night. Thereafter, the females release pheromones to attract males. Since the pheromone is carried by the
wind, males tend to travel up the concentration gradient, i.e., toward the source. During flight, they are
subject to predation by bats. The males guard the female from other males until she lays the eggs. The
female lays about 2,000 pale-green ovoid eggs about 1 mm in length into crevices in bark with her ovipositor.
[edit] Resting behaviour
Figure 2a. Total number of observed moths = 59: Exposed trunk = 7; unexposed trunk = 7; trunk-
branch joint = 23; branches = 22
Figure 2b. Total number of observed moths = 23: Exposed trunk =1; unexposed trunk =1; trunk
branch join = 3; branches thicker than 5 centimetres diameter = 10; branches and twigs less thick than 5
centimetres = 8
A mating pair or a lone individual will spend the day hiding from predators, particularly birds. In the
case of the former, the male stays with the female to ensure paternity. The best evidence for resting positions
is given by data collected by the peppered moth researcher Michael Majerus, and it is given in the
accompanying charts. These data were originally published in Howlett and Majerus (1987), and an updated
version published in Majerus (1998), who concluded that the moths rest in the upper part of the trees.
Majerus notes:
Creationist critics of the peppered moth have often pointed to a statement made by Clarke et al.
(1985): "... In 25 years we have only found two betularia on the tree trunks or walls adjacent to
our traps, and none elsewhere". The reason now seems obvious. Few people spend their time
looking for moths up in the trees. That is where peppered moths rest by day.
From their original data, Howlett and Majerus (1987) concluded that peppered moths generally rest in
unexposed positions, using three main types of site. Firstly, a few inches below a branch-trunk joint on a tree
trunk where the moth is in shadow; secondly, on the underside of branches and thirdly on foliate twigs. The
above data would appear to support this.
Further support for these resting positions is given from experiments watching captive moths taking
up resting positions in both males (Mikkola, 1979; 1984) and females (Liebert and Brakefield, 1987).
Majerus, et al., (2000) have shown that peppered moths are cryptically camouflaged against their
backgrounds when they rest in the boughs of trees. It is clear that in human visible wavelengths, typica are
camouflaged against lichens and carbonaria against plain bark. However, birds are capable of seeing
ultraviolet light that humans cannot see. Using an ultraviolet-sensitive video camera, Majerus et al. showed
that typica reflect ultraviolet light in a speckled fashion and are camouflaged against crustose lichens
common on branches, both in ultraviolet and human-visible wavelengths. However, typica are not as well
camouflaged against foliose lichens common on tree trunks; though they are camouflaged in human
wavelengths, in ultraviolet wavelengths, foliose lichens do not reflect ultraviolet light.
During an experiment in Cambridge over the seven years 2001-2007 Majerus noted the natural
resting positions of peppered moths, and of the 135 moths examined over half were on tree branches, mostly
on the lower half of the branch, 37% were on tree trunks, mostly on the north side, and only 12.6% were
resting on or under twigs.[4][5]
[edit] Morphs
Further information: Polymorphism (biology)
There are several melanic and non-melanic morphs of the peppered moth. These are controlled
genetically. A particular morph can be indicated in a standard way by following the species name in the form
"morpha morph name".
It is a common mistake to confuse the name of the morph with that of the species or subspecies,
hence mistakes such as "Biston carbonaria" and "Biston betularia carbonaria". This might lead to the
erroneous belief that speciation was involved in the observed evolution of the peppered moth. This is not the
case; individuals of each morph interbreed and produce fertile offspring with individuals of all other morphs;
hence there is only one peppered moth species.
By contrast, different subspecies of the same species can theoretically interbreed with one another
and will produce fully fertile and healthy offspring but in practice do not, as they live in different regions or
reproduce in different seasons. Full-fledged species are either unable to produce fertile and healthy offspring,
or do not recognize each other's courtship signals, or both.
In continental Europe, there are three morphs: morpha typica, the typical white morph (also known as
"morpha betularia"), morpha carbonaria, the melanic black morph (also previously known as "morpha
doubledayaria"), and morpha medionigra, an intermediate semi-melanic morph. European breeding
experiments have shown that in Biston betularia betularia, the allele for melanism producing morpha
carbonaria is controlled by a single locus. The melanic allele is dominant to the non-melanic allele. This
situation is, however, somewhat complicated by the presence of three other alleles that produce
indistinguishable morphs of morpha medionigra. These are of intermediate dominance, but this is not
complete (Majerus, 1998).
In Britain, the typical white speckled morph is known as morpha typica, the melanic morph is morpha
carbonaria, and the intermediate phenotype is morpha insularia.
In North America, the melanic black morph is morpha swettaria. In Biston betularia cognataria, the
melanic allele (producing morpha swettaria) is similarly dominant to the non-melanic allele. There are also
some intermediate morphs. In Japan, no melanic morphs have been recorded; they are all morpha typica.
At present, the precise molecular genetics and biochemistry of the melanism in this species remains
unknown. True (2003) has reviewed this and suggests work based on candidate genes from other insects
such as the fruit fly Drosophila melanogaster. In any case, it is rather likely that the underlying mechanism is
not overly complex and, as indicated above, does not involve very many genes and alleles: Unlike for
example the variation seen in human skin color, Peppered Moth morphs are not clinal and can generally be
readily distinguished from another.
[edit] Evolution
Main article: Peppered moth evolution
Biston betularia betularia morpha typica, the white-bodied peppered moth.
Biston betularia betularia morpha carbonaria, the black-bodied peppered moth.
The evolution of the peppered moth over the last two hundred years has been studied in detail.
Originally, the vast majority of peppered moths had light colouration, which effectively camouflaged them
against the light-coloured trees and lichens upon which they rested. However, due to widespread pollution
during the Industrial Revolution in England, many of the lichens died out, and the trees which peppered
moths rested on became blackened by soot, causing most of the light-coloured moths, or typica, to die off
due to predation. At the same time, the dark-coloured, or melanic, moths, carbonaria, flourished because of
their ability to hide on the darkened trees.[6]
Since then, with improved environmental standards, light-colored peppered moths have again
become common, but the dramatic change in the peppered moth's population has remained a subject of
much interest and study. This has led to the coining of the term "industrial melanism" to refer to the genetic
darkening of species in response to pollutants. As a result of the relatively simple and easy-to-understand
circumstances of the adaptation, the peppered moth has become a common example used in explaining or
demonstrating natural selection to laypeople and classroom students.[7]
The first carbonaria morph was recorded by Edleston in Manchester in 1848, and over the
subsequent years it increased in frequency. Predation experiments, particularly by Bernard Kettlewell,
established that the agent of selection was birds who preyed on the morpha carbonaria morph.
Jonathan Wells is one of a number of creationists who have criticized the use of peppered moth
melanism as an example of evolution in action. In his book Icons of Evolution, Wells alleges that peppered
moth studies, and in particular Kettlewell's experiments, were erroneous.[8] Similarly, in 2002 Judith Hooper
repeatedly implied fraud and error in Kettlewell's experiments in her book titled Of moths and men.[9] Despite
some valid criticisms of the early experiments, there has been no evidence of fraud. Subsequent experiments
and observations have supported the initial explanation of the phenomenon.[8][10][11] But the problem,
according to the Young Earth creationist Dr. Tommy Mitchell of "Answers in Genesis", is this only represents
a case of natural selection, and not of evolution, as a population of a "kind" of moth turned into simply a
population of another "kind" of moth.[12] While it is true that this example shows natural selection causing
microevolution within a species, it demonstrates rapid and obvious adaptiveness with such change.[13]
[edit] References
1. ^ Grant, Bruce S (1999). "Fine tuning the peppered moth paradigm" (PDF). Evolution. pp. 53
980–984. http://bsgran.people.wm.edu/melanism.pdf. Retrieved 2009-12-19.
2. ^ Alan Gishlick (November 23, 2006). "Icon 6 — Peppered Moths". National Center for
Science Education. http://ncse.com/creationism/analysis/icon-6-peppered-moths. Retrieved 2009-12-
19.
3. ^ Noor MA, Parnell RS, Grant BS (2008). "A Reversible Color Polyphenism in American
Peppered Moth (Biston betularia cognataria) Caterpillars". PLoS ONE 3 (9): e3142.
4. ^ Michael E. N. Majerus (August 2007). "The Peppered Moth: The Proof of Darwinian
Evolution" (PDF). Archived from the original on 2008-02-21.
http://web.archive.org/web/20080221224640/http://www.gen.cam.ac.uk/Research/Majerus/Swedenta
lk220807.pdf. Retrieved 2007-09-09.
5. ^ Steve Connor, Science Editor (25 August 2007). "Moth study backs classic 'test case' for
Darwin's theory - Independent Online Edition > Sci_Tech". The Independent.
http://news.independent.co.uk/sci_tech/article2893896.ece. Retrieved 2007-09-09.
6. ^ Ken Miller (August 1999). "The peppered moth: an update". Brown University.
http://www.millerandlevine.com/km/evol/Moths/moths.html.
7. ^ "A modelling exercise for students using the peppered moth as its example".
http://www.globalchange.umich.edu/globalchange1/current/labs/peppered_moth/pepperedmoth.html.
8. ^ a b Marc Isaak (2005-05-02). "The peppered moth story". TalkOrigins Archive. Index to
Creationist Claims: CB601. http://www.talkorigins.org/indexcc/CB/CB601.html.
9. ^ Bryan Clarke (2003). "Heredity - The art of innuendo". Heredity. pp. 90, 279–280.
http://www.nature.com/hdy/journal/v90/n4/full/6800229a.html. Retrieved 2008-07-11.
10.^ Marc Isaak (2003-09-10). "Peppered moths affected by mutagens". Index to Creationist
Claims: CB601.2.3. http://www.talkorigins.org/indexcc/CB/CB601_2_3.html.
11.^ Marc Isaak (2003-09-10). "Dark peppered moths unexpectedly common in areas". Index to
Creationist Claims: CB601.2.2. http://www.talkorigins.org/indexcc/CB/CB601_2_2.html.
12.^ Dr. Tommy Mitchell (2005-05-02). "Much Ado About Moths". Answers in Genesis.
http://www.answersingenesis.org/articles/am/v3/n2/much-ado-about-moths.
13.^ "Icon of Obfuscation". TalkOrigins Archive.
http://www.talkorigins.org/faqs/wells/iconob.html#moths. Retrieved 2008-05-22.

Wikimedia Commons has media related to: Biston betularia
• Bruce Grant has written several papers on melanism in the peppered moth which are listed
on his home page.
• Online lecture: "The rise and fall of the melanic Peppered Moth" presented by Laurence
Cook.
• Matt Young. "Moonshine: Why the Peppered Moth remains an Icon of Evolution".
Department of Physics, Colorado School of Mines. http://www.talkreason.org/articles/moonshine.cfm.
• The Peppered Moth: Decline of a Darwinian Disciple . This is the transcript of Michael
Majerus' lecture delivered to the British Humanist Association on Darwin Day 2004.
• The Peppered Moth: The Proof of Darwinian Evolution . This is the transcript of Majerus'
lecture given at the European Society for Evolutionary Biology meeting on 23 August 2007. The
accompanying powerpoint presentation is also available.
• Michael E. N. Majerus (6 December 2008). "Industrial Melanism in the Peppered Moth,
Biston betularia: An Excellent Teaching Example of Darwinian Evolution in Action" . 10.1007/s12052-
008-0107-y. Springer Science+Business Media, LLC 2008.
http://www.springerlink.com/content/h7n4r6h026q1u6hk/fulltext.html. Retrieved 2009-01-13.
"Accusations of data fudging and scientific fraud in the case are found to be vacuous."
Retrieved from "http://en.wikipedia.org/wiki/Peppered_moth"
Categories: Butterflies and moths of North America | Peppered moth

W000
Peppered moth evolution


{{about|the peppered moth's significance in evolutionary biology|its evolutionary ancestry|Insect
evolug|thumb|260px|Biston betularia f. typica, the white-bodied peppered moth.]]
Biston betularia f. carbonaria, the black-bodied peppered moth.
se of their ability to hide on the darkened trees.[1]
Since then, with improved environmental standards, light-coloured peppered moths have again
become common, but the dramatic change in the peppered moth's population has remained a subject of
much interest and study, and has led to the coining of the term industrial melanism to refer to the genetic
darkening of species in response to pollutants. As a result of this relatively simple and easy-to-understand
circumstances of the adaptation, the peppered moth has become a common example used in explaining or
demonstrating natural selection.[2]
Contents
[hide]
• 1 Genetics
• 2 Environmental changes
• 3 Rise and fall of phenotype frequency
• 4 Predation experiments
• 5 Alternative hypotheses
• 5.1 Phenotypic induction
• 6 Criticism and controversy
• 7 References
• 8 See also
[edit] Genetics
Main articles: Peppered moth and genetics
Evolution is defined as "a change in the frequency of an allele within a gene pool",[3] an occurrence
that causes a population's genetically inherited traits to change over successive generations. Evolution in the
wild is chiefly caused by two mechanisms: natural selection, the process by which individual organisms with
beneficial traits are more likely to survive and reproduce, and genetic drift, the statistical drift over time of
allele frequencies in a population from random sampling effects in the formation of successive generations.
J.W. Tutt first proposed the "differential bird predation hypothesis" in 1896, as a mechanism of
natural selection. The melanic morphs were better camouflaged against the bark of trees without foliose
lichen, whereas the typica morphs were better camouflaged against trees with lichens. As a result, birds
would find and eat those morphs that were not camouflaged with increased frequency.
In 1924, J.B.S. Haldane calculated, using a simple general selection model, the selective advantage
necessary for the recorded evolution of peppered moths, based on the assumption that in 1848 the frequency
of dark-coloured moths was 2%, and by 1895 it was 95%. The dark-coloured, or melanic, form would have
had to be one and a half times as fit as the typical, light-coloured form. Even taking into consideration the
errors in the model, this reasonably excluded the stochastic process of genetic drift, because the changes
were too fast.[4]
In peppered moths, the allele for dark-bodied moths is dominant, while the allele for light-bodied
moths is recessive, meaning that the typica moths have a phenotype (visible or detectable characteristic) that
is only seen in a homozygous genotype (an organism that has two copies of the same allele), and never in a
heterozygous one. This helps explain how dramatically quickly the population changed when being selected
for dark colouration.
The peppered moth Biston betularia is also a model of parallel evolution in the incidence of melanism
in the British form (f. carbonaria) and the American form (f. swettaria) as they are indistinguishable in
appearance. Genetic analysis indicates that both phenotypes are inherited as autosomal dominants. Cross
hybridizations indicate the phenotypes are produced by isoalleles at a single locus. [5]
[edit] Environmental changes
Typica and carbonaria morphs resting on the same tree. The light-colored typica (below the bark's
scar) is nearly invisible on this pollution-free tree, camouflaging it from predators.
Before the Industrial Revolution, the peppered moth was mostly found in a light grey form with little
black speckled spots. The light-bodied moths were able to blend in with the light-coloured lichens and tree
bark, and the less common black moth was more likely to be eaten by birds. As a result of the common light-
coloured lichens and English trees, therefore, the light-coloured moths were much more effective at hiding
from predators, and the frequency of the dark allele was about 0.01%.
During the early decades of the Industrial Revolution in England, the countryside between London
and Manchester was blanketed with soot from the new coal-burning factories. Many of the light-bodied
lichens died from sulphur dioxide emissions, and the trees became covered with soot. This led to an increase
in bird predation for light-coloured moths, as they no longer blended in as well in their polluted ecosystem:
indeed, their bodies now dramatically contrasted with the colour of the bark. Dark-coloured moths, on the
other hand, were camouflaged very well by the blackened trees.[1]
Although a majority of light-coloured moths initially continued to be produced, most of them didn't
survive, while the dark-coloured moths flourished. As a result, over the course of many generations of moths,
the allele frequency gradually shifted towards the dominant allele, as more and more dark-bodied moths
survived to reproduce. By the mid-19th century, the number of dark-coloured moths had risen noticeably, and
by 1895, the percentage of dark-coloured moths in the Manchester peppered moth population was reported
at 98%, a dramatic change (by almost 1000%) from the original frequency.[1] This evolved darkening in
colour as a result of industrialization has come to be known as industrial melanism as a result.
While evidence of increasing frequency of melanic forms in the Lepidoptera was available during
Darwin’s lifetime — the first observations were made in 1848 [6] — current understanding is that it was not until
1896, 14 years after Darwin’s death, that Tutt explicitly linked melanism with natural selection. However, a
recent article [7] reports that melanism in the Lepidoptera had been linked to natural selection prior to Tutt.
Albert Brydges Farn (1841–1921), a British entomologist, wrote to Darwin on the 18th November 1878 to
discuss his observation of colour variations in the Annulet moth (then Gnophos obscurata, now Charissa
obscurata). In his letter, Farn [8] mentions the existence of different colour morphs, describing how each is
matched to the habitats in which they are found (dark morphs on peat, white morphs on chalk cliffs) and
refers explicitly to this variability as pointing to ‘survival of the fittest’.
In modern times, because of cleaner air standards in Europe and North America, the dark-bodied
moth is becoming less frequent, again demonstrating the adaptive shifts in the peppered moth population.[2]
[edit] Rise and fall of phenotype frequency

Melanism has appeared in the European and North American peppered moth populations.
Information about the rise in frequency is scarce. Much more is known about the subsequent fall in
phenotype frequency, as it has been measured by lepidopterists using moth traps.
Though a black peppered moth was found in 1811, this can be seen as an aberrant morph caused by
a recurrent mutation that was probably selected out of the population. The first carbonaria to be found was
caught in Manchester, England in 1848, but was only reported 16 years later in 1864 by Edleston. Edleston
notes that by 1864 it was the more common morph in his garden in Manchester. Steward compiled data for
the first recordings of the peppered moth by locality, and deduced that the carbonaria morph was the result of
a single mutation that subsequently spread. By 1895, it had reached a reported frequency of 98% in
Manchester.[9]
From around 1962 to the present, the phenotype frequency of carbonaria has steadily fallen. Its
decline has been measured more accurately than its rise, because of more rigorous scientific studies being
conducted. Notably, Bernard Kettlewell conducted a national survey in 1956, Bruce Grant conducted a
similar one in early 1996.[10] , and L.M. Cook in 2003.[11]
Similar results were found in America. Melanic forms have not been found in Japan. It is believed
that this is because peppered moths in Japan do not inhabit industrialised regions.
[edit] Predation experiments
The Great Tit, an insectivorous bird.

In 1896 J. W. Tutt hypothesised that the increased proportion of carbonaria resulted from differential
bird predation giving an advantage to the melanistic phenotype in polluted regions, but not in unpolluted
regions where the light coloured typica moths had the advantage.[12] Various experiments have been
performed on predation of the peppered moth and each has supported this hypothesis.
The most famous experiments on the peppered moth were carried out by Bernard Kettlewell under
the supervision of E. B. Ford, who helped him gain a grant from the Nuffield Foundation to perform the
experiments. In one of Kettlewell's experiments, moths were released into a large (18 m by 6 m) aviary,
where they were fed on by Great Tits (Parus major). In 1953, Kettlewell experimented at Cadbury Nature
Reserve in Birmingham, England, marking, releasing and recapturing marked moths. He found that in this
polluted woodland typica morphs were preferentially preyed. He thus showed that the melanistic phenotype
was important to the survival of peppered moths in such a habitat. Kettlewell repeated the experiment in
1955 at unpolluted woodland in Dorset and again in the polluted woods in Birmingham. He was accompanied
by Nico Tinbergen, and they made a film together. Further studies by others found similar results, culminating
in 1996 when reporting work on both sides of the Atlantic found a correlation between changes in melanic
frequencies and pollution levels.[12][13]
An experiment in field biology will always suffer from some level of artificiality, but that has to be
balanced against practicality, costs and in this case the history of field biology; the most important aspect is
that an experiment generates useful statistics. The only previous experiments of this type were R.A. Fisher
and E.B. Ford's (1947) with the scarlet tiger moth.
Michael Majerus in his 1998 book Melanism: Evolution in Action discussed criticisms concerning
Kettlewell's experimental methods.[12] Criticism and controversy arose when the book was misrepresented
in reviews, and the story was picked up by creationist campaigners. The journalist Judith Hooper suggested
in her book Of Moths and Men (2002) that Kettlewell committed scientific fraud. Careful studies of Kettlewell's
surviving papers by Rudge (2005) and Young (2004) have revealed that Hooper's allegation of fraud is
unjustified, and "that Hooper does not provide one shred of evidence to support this serious allegation”.[13]
[14]
In 2000 Majerus developed plans for experiments to establish where peppered moths rest through
the day, and to examine if the various valid criticisms of Kettlewell’s experimental protocols could have
altered the qualitative validity of his conclusions. In the following year he piloted a new field predation
experiment designed to overcome criticisms that Kettlewell had used too few release sites, resulting in the
density of moths being too high; moths had been released onto tree trunks rather than branches; moths
released during the day might not have found the best places to hide; mixtures of wild-caught and lab-bred
moths might have behaved differently; and the behaviour of translocated moths might have changed
because of local adaptation. During the main experiment in Cambridge over the seven years 2001-2007
Majerus noted the natural resting positions of the moths, and of the 135 moths examined over half were on
tree branches, mostly on the lower half of the branch, 37% were on tree trunks, mostly on the north side, and
only 12.6% were resting on or under twigs. Following correspondence with Hooper he added an experiment
to find if bat predation might have skewed the results – this found that bats preyed equally on both forms of
the moth. He observed a number of species of bird preying on the moths, and the overall data led him to
conclude that differential bird predation was a major factor responsible for the decline in carbonaria
frequency compared to typica in Cambridge during the study period.[12] He described his results as a
complete vindication of the peppered moth story, and said "If the rise and fall of the peppered moth is one of
the most visually impacting and easily understood examples of Darwinian evolution in action, it should be
taught. It provides after all the proof of evolution."[15]
[edit] Alternative hypotheses

Several alternative hypotheses to explain industrial melanism, particularly noted in the peppered
moth, were proposed during the 1920s and 1930s. Some dissenters within the scientific community have
criticized the peppered moth story, notably Sargent et al. (1998), but peppered moth researchers remain
unconvinced.[16]
Several alternative selection mechanisms have been proposed. Note that a change in allele
frequency, be it caused by natural selection, mutation, migration or genetic drift by definition, is differential.[3]
However, the magnitude of the changes observed can only be accounted for by natural selection. It can be
seen from population genetics that a non-differential change will not cause evolution. If the allele frequencies
are denoted by the algebraic terms p and q, and (say) p = 0.6 and q = 0.4, then a non-differential reduction in
population size from say 2000 to 100 individuals, will still produce the same values of (approximately) p = 0.6
and q = 0.4.
[edit] Phenotypic induction

John William Heslop-Harrison (1920) rejected Tutt's differential bird predation hypothesis, on the
basis that he did not believe that birds ate moths. Instead he advocated the idea that pollutants could cause
changes to the soma and germ plasm of the organism. The origin of this hypothesis probably has its roots in
the 1890s, when it was proposed as a form of Lamarckism. It is important to note its historical context.
Hasebroek (1925) was the first who tried to prove this hypothesis, he contended that air pollution
altered lepidopteran physiology, thus producing an excess of black pigment. He exposed pupae of
Lepidoptera to various doses of pollutant gases, namely hydrogen sulfide (H2S), ammonia (NH3) and
"pyredin" (presumably his spelling of pyridine). He used eight species in his studies, four of which were
species of butterfly that did not exhibit melanism. Ford (1964) contends that Hasebroek's illustrations showed
that the abnormal forms that appeared were not melanics, and Hasebroek failed to study their genetics.
Heslop Harrison (Harrison and Garrett 1926; Harrison 1928) suggested that the increase of melanic
moths in industrialised regions was due to "mutation pressure", not to selection by predators which he
regarded as negligible. Salts of lead and manganese were present in the airborne pollutant particles, and he
suggested that these caused the mutation of genes for melanin production but of no others. He used Selenia
bilunaria and Tephrosia bistortata as material. The larvae were fed with leaves that had incorporated these
salts and melanics subsequently appeared.
Similar experiments by Hughes McKenney (1932) and Thomasen and Lemche (1933) failed to
replicate these results. However, the statistician and geneticist Ronald Fisher, showed that Heslop Harrison's
controls were inadequate.[17] This hypothesis, however, appeared to be falsified by breeding experiments.
Further evidence, if it were needed, is likely to come from research into the biochemistry of melanism.
[edit] Criticism and controversy
Creationists have disputed the occurrence or significance of the melanic carbonaria morph
increasing in frequency.
In recent years, the use of the peppered moth as an example of evolution has come under attack by
advocates of intelligent design and other creationists, who allege that it is not reliable as evidence of
evolution.
Creationists have argued that the "peppered moth story" showed only microevolution, rather than
speciation or other changes at the larger macroevolutionary scale.[18] Biologists[who?] agree that this
example shows natural selection causing evolution within a species, demonstrating rapid and obvious
adaptiveness with such change,[19] and accept that it is not proof of the theory of evolution as a whole.
However, though creationists accept "microevolution" of varieties within a "kind", they claim that
"macroevolution" does not happen. To biologists there is no dividing line between the two, and in the modern
evolutionary synthesis the same mechanisms are seen operating at various scales to cause both evolution
within species and speciation at a macroevolution level or wider changes, the only difference being of time
and scale.[20][21]
Another common, but unfounded, criticism involves well-known pictures of moths resting on trunks,
used in many textbooks. These photos were prepared (dead moths pinned to branches), which has been
conflated into the idea that all the studies were staged, ignoring the point that professional photography to
illustrate textbooks uses dead insects because of the considerable difficulty in getting good images of small,
relatively fast moving, animals, and that the studies actually consisted of observational data rather than using
such photographs. The photographs in Michael Majerus's 1998 book Melanism: Evolution in Action are
unstaged pictures of live moths in the wild, and the photographs of moths on tree-trunks, apart from some
slight blurring, look no different than the "staged" photographs.[22]
Furthermore, while an experiment did involve the gluing of dead moths to trees, this practice was just
one of many different ways used to study different individual elements of the overall hypothesis. This
particular experiment was not meant to exactly reproduce natural conditions, but instead was used to assess
how the numbers of moths available (their density) affected the foraging practices of birds.[23]
The methodology of Bernard Kettlewell's classic study was questioned in a review by the biologist
Jerry Coyne in Nature of Michael Majerus's 1998 book Melanism: Evolution in Action which includes a
critique of Kettlewell's experiment, matching a similar 1998 analysis by Sargent et al.[16] Coyne stated that
the most serious problem found by Majerus was that only two peppered moths had been found on tree
trunks. He also noted that the white moths had increased in numbers before the lichen had returned, and that
Kettlewell's findings of moths choosing matching backgrounds had not been replicated in later experiments.
Coyne compared his reaction to "the dismay attending my discovery, at the age of 6, that it was my father
and not Santa who brought the presents on Christmas Eve". He concluded that "for the time being we must
discard Biston as a well-understood example of natural selection in action, although it is clearly a case of
evolution. There are many studies more appropriate for use in the classroom", and that further studies of the
animal's habits were needed.[24] At the beginning of his second paragraph on the peppered moths, Majerus
emphasises that the wealth of additional data obtained since Kettlewell's initial predation papers does not
undermine the basic qualitative deductions from that work, and that differential bird predation of the dark and
light moths in habitats affected by industrial pollution to different degrees (directional selection) "is the
primary influence of the evolution of melanism in the peppered moth".[22][25] Coyne had erred in his
statement that only two peppered moths had been found on tree trunks, as the book gives the resting
positions of 47 peppered moths Majerus had found in the wild between 1964 and 1996; twelve were on tree
trunks (six exposed, six unexposed), twenty were at the trunk/branch joint, and fifteen resting on branches.
[22] Majerus found that the review did not reflect the factual content of the book or his own views,[26] and
cites an assessment by the entomologist Donald Frack that there was essentially no resemblance between
the book and Coyne's review,[27] which appeared to be a summary of the Sargent et al. paper rather than
Majerus's book.[28]
The review was subsequently picked up by journalist Robert Matthews, who wrote an article for The
Sunday Telegraph, March 14, 1999, claiming that "Evolution experts are quietly admitting that one of their
most cherished examples of Darwin's theory, the rise and fall of the peppered moth, is based on a series of
scientific blunders. Experiments using the moth in the Fifties and long believed to prove the truth of natural
selection are now thought to be worthless, having been designed to come up with the 'right' answer". Majerus
regarded this view as surprising, and not one that would be shared by those involved in the field. He noted
numerous scientific inaccuracies, misquotations and misrepresentations in the article, but thought this was
common in press reports.[27] He stated that he had spoken to Matthews for over half an hour and had to
explain many details as Matthews hadn't read the book, but "Even then, he got nearly everything wrong."[26]
The story was taken up by creationists, and at a seminar presenting his wedge strategy on March 13,
1999, the leading intelligent design proponent Phillip E. Johnson asserted that the moths "do not sit on tree
trunks", "moths had to be glued to the trunks" for pictures and that the experiments were "fraudulent" and a
"scam."[29] This led Frack to exchanges with intelligent design proponent Jonathan Wells, who conceded
that Majerus listed six moths on exposed tree trunks (out of 47), but argued that this was "an insignificant
proportion".[30] Wells wrote an essay on the subject, a shortened version of which appeared in The Scientist
of May 24, 1999, claiming that "In 25 years of fieldwork, C.A. Clarke and his colleagues found only one
peppered moth on a tree trunk", and concluding that "The fact that peppered moths do not normally rest on
tree trunks invalidates Kettlewell's experiments".[31] In 2000 he wrote Icons of Evolution: Why much of what
we Teach About Evolution is Wrong, which claims "What the textbooks don't explain, however, is that
biologists have known since the 1980s that the classical story has some serious flaws. The most serious is
that peppered moths in the wild don't even rest on tree trunks. The textbook photographs, it turns out, have
been staged."[32] The arguments put by Wells have been dismissed by Majerus, Cook and peppered moth
researcher Bruce Grant who describes Wells as distorting the picture by selectively omitting or scrambling
references in a way that is basically dishonest.[22]
On November 27, 2000, the school board of Pratt County, Kansas continued efforts to favor
intelligent design teaching by requiring the use of specific resources.[33] These included the article by Jerry
Coyne, who wrote to object strongly to this creationist misrepresentation of his critical re-evaluation,
emphasising that the moth story is a sound example of evolution produced by natural selection and stating
that his call for additional research was only to resolve uncertainty regarding bird predation as the cause of
the natural selection and evolutionary change. Bruce Grant also wrote to challenge allegations of fraud in the
moth experiments based on misrepresentations by Wells.[34]
In 2002, Judith Hooper's Of Moths and Men added to the chorus of accusations of scientific fraud.
She accused Kettlewell of manipulating his data to prove his hypothesis.[35] The book received strong
criticism from the scientific press (e.g., Coyne, B.C. Clarke, Grant).[36][37] Majerus described it as "littered
with errors, misrepresentations, misinterpretations and falsehoods".[27]
[edit] References
1. ^ a b c Miller, Ken (1999). The Peppered Moth: An Update
2. ^ a b A modelling exercise for students using the peppered moth as its example
3. ^ a b Dobzhansky, T.G. (1937). Genetics and the Evolutionary Process. Columbia University
Press. ISBN 0-231-08306-8.
4. ^ Haldane, J.B.S. (1924). A Mathematical Theory of Natural and Artificial Selection .
5. ^ Grant BS. (2004). "Allelic melanism in American and British peppered moths..journal = J.
Hered". Journal of Heredity 95 (2): 97–102. doi:10.1093/jhered/esh022. PMID 15073224.
6. ^ Edleston, R.S. (1864). Amphydaris betularia. Entomologist 2, 150
7. ^ Hart et al., Hart A.G., Stafford R., Smith A.L. and Goodenough A.E. 2010. Evidence for
contemporary evolution during Darwin’s lifetime. Current Biology. 20 (3): R95
8. ^ Farn, A.B. (1878). Farn, A.B. to Darwin C.R. 18 Nov 1878, Darwin Correspondence Project
Letter 11747, held as DAR 164:26 as part of The Darwin Papers, Manuscripts Room, Cambridge
University Library, West Road, Cambridge, England. http://www.darwinproject.ac.uk/entry-11747
9. ^ Steward, R.C. (1977). "Industrial and non-industrial melanism in the peppered moth Biston
betularia (L.)", Ecological Entomology 2 (pp. 231–243).
10.^ http://www.talkorigins.org/faqs/wells/images/grantfile.jpg
11.^ Cook LM. (2003). "The rise and fall of the Carbonaria form of the peppered moth.journal =
Q Rev Biol. = 78". The Quarterly Review of Biology 78 (4): 399–417. doi:10.1086/378925.
PMID 14737825.
12.^ a b c d Michael E. N. Majerus (August 2007). "The Peppered Moth: The Proof of Darwinian
Evolution" (PDF). Archived from the original on 2008-02-21.
http://web.archive.org/web/20080221224640/http://www.gen.cam.ac.uk/Research/Majerus/Swedenta
lk220807.pdf. Retrieved 2007-09-09.
13.^ a b Young, M. (2003). Moonshine: Why the Peppered Moth Remains an Icon of Evolution.
14.^ Rudge, D.W. (2005). "Did Kettlewell Commit Fraud? Re-examining the Evidence.", Public
Understanding of Science 14 (3) (pp. 249–268).
15.^ Steve Connor, Science Editor (25 August 2007). "Moth study backs classic 'test case' for
Darwin's theory - Independent Online Edition > Sci_Tech". The Independent.
http://news.independent.co.uk/sci_tech/article2893896.ece. Retrieved 2007-09-09.
16.^ a b Sargent, T.D., Millar, C.D., and Lambert, D.M. (1998). "The 'classical' explanation of
industrial melanism: Assessing the evidence.", Hecht and Wallace (Eds.), Evolutionary Biology
volume 23, chapter 9.
17.^ Fisher, R.A. (1933). "On the Evidence Against the Chemical Induction of Melanism in
Lepidoptera.", Proceedings of the Royal Society of London, B 112 (pp. 407–416).
18.^ Dr. Tommy Mitchell (2005-05-02). "Much Ado About Moths". Answers in Genesis.
http://www.answersingenesis.org/articles/am/v3/n2/much-ado-about-moths. (also Watchtower Bible
and Tract Society, 1985)
19.^ "Icon of Obfuscation". http://www.talkorigins.org/faqs/wells/iconob.html#moths. Retrieved
2008-05-22.
20.^ The Straight Dope: Do creationists accept microevolution but not macroevolution?
21.^ "Macroevolution: Its definition, Philosophy and History".
http://www.talkorigins.org/faqs/macroevolution.html#barriers. Retrieved 2008-05-22.
22.^ a b c d Nick Matzke (2002-2004). "Icon of Obfuscation". Jonathan Wells's book Icons of
Evolution and why most of what it teaches about evolution is wrong . TalkOrigins Archive.
http://www.talkorigins.org/faqs/wells/iconob.html. Retrieved 2007-08-25.
23.^ Bruce Grant (December 13, 2000). "Charges of Fraud Misleading". Pratt Tribune (Kansas).
http://www.millerandlevine.com/km/evol/Moths/grant-pratt-tribune.html. Retrieved 2008-02-18.
24.^ Coyne, Jerry A. (1998-11-05). "Not Black and White. Review of Melanism: Evolution in
Action by Michael E.N. Majerus" (PDF). Nature 396: 35–36. doi:10.1038/23856.
http://pondside.uchicago.edu/ceb/Majerus_review.pdf. Retrieved 2006-06-30. [dead link]
25.^ Majerus, M.E.N. (1998) Melanism: Evolution in Action. Oxford University Press, New York.
26.^ a b Donald Frack (30 March 1999). "Evolution - March 1999: Peppered Moths - in black and
white (part 2 of 2)". http://www.asa3.org/archive/evolution/199903/0312.html. Retrieved 2007-08-26.
27.^ a b c Michael Majerus (2004). "The Peppered moth: decline of a Darwinian disciple" (.doc).
Archived from the original on 2007-09-26.
http://web.archive.org/web/20070926131158/http://www.gen.cam.ac.uk/Research/Majerus/Darwinian
disciple.doc. Retrieved 2007-09-10.
28.^ Donald Frack (30 March 1999). "Evolution - March 1999: RE: Peppered Moths - in black
and white (part 1 of 2)". http://www.asa3.org/archive/evolution/199903/0314.html. Retrieved 2007-08-
26.
29.^ Donald Frack (16 April 1999). "Evolution - April 1999: Peppered Moths and Creationists".
http://www.asa3.org/archive/evolution/199904/0201.html. Retrieved 2007-08-26.
30.^ Donald Frack (16 April 1999). "Evolution - April 1999: RE: My last word".
http://www.asa3.org/archive/evolution/199904/0207.html. Retrieved 2007-08-26.
31.^ Wells, J. (1999). "Second Thoughts about Peppered Moths; This classical story of evolution
by natural selection needs revising." The Scientist 13, 11 (p. 13, May 24, 1999)
32.^ Wells J. (2000). Icons of Evolution: Science or Myth? Why Much of What We Teach About
Evolution is Wrong. Regnery Press, Washington, D.C., p. 138 (book available from
Iconsofevolution.com)
33.^ Molleen Matsumura. "Intelligent Design in Pratt County, Kansas". National Center Science
Education. http://ncse.com/rncse/20/4/intelligent-design-pratt-county-kansas. Retrieved 2007-08-28.
34.^ "Icons of Evolution". Evolution and the Nature of Science Institutes for High School Biology
Teachers: Resources. Department of Biology, Indiana University.
http://www.indiana.edu/~ensiweb/lessons/icon.cr.html. Retrieved 2007-08-28.
35.^ Reclaiming the peppered moth for science New Scientist, 08 December 2007, page 46-49
36.^ Coyne, J.A. (2002). (Review of Of Moths and Men)
37.^ Matt Young. "Talk Reason: arguments against creationism, intelligent design, and religious
apologetics". Moonshine: Why the Peppered Moth remains an Icon of Evolution. Department of
Physics, Colorado School of Mines. http://www.talkreason.org/articles/moonshine.cfm. Retrieved
2007-08-28.
[edit] See also

• Polymorphism

Wikimedia Commons has media related to: Biston betularia
• Bruce Grant has written several papers on melanism in the peppered moth which are listed
on his home page.
• Online lecture: "The rise and fall of the melanic Peppered Moth" presented by Laurence
Cook.
• Matt Young. "Moonshine: Why the Peppered Moth remains an Icon of Evolution".
Department of Physics, Colorado School of Mines. http://www.talkreason.org/articles/moonshine.cfm.
• The Peppered Moth: Decline of a Darwinian Disciple . This is the transcript of Michael
Majerus' lecture delivered to the British Humanist Association on Darwin Day 2004.
• The Peppered Moth: The Proof of Darwinian Evolution . This is the transcript of Majerus'
lecture given at the European Society for Evolutionary Biology meeting on 23 August 2007. The
accompanying powerpoint presentation is also available.
• Michael E. N. Majerus (6 December 2008). "Industrial Melanism in the Peppered Moth,
Biston betularia: An Excellent Teaching Example of Darwinian Evolution in Action" . 10.1007/s12052-
008-0107-y. Springer Science+Business Media, LLC 2008.
http://www.springerlink.com/content/h7n4r6h026q1u6hk/fulltext.html. Retrieved 2009-01-13.
"Accusations of data fudging and scientific fraud in the case are found to be vacuous."
• On 19 June 2009, Telegraph.co.uk published an article on this evolutionary phenomenon
and implored UK readers to visit the Moths Count website and record their observations of local
moths, in an effort to help increase the available data for researchers.

Retrieved from "http://en.wikipedia.org/wiki/Peppered_moth_evolution"
Categories: Peppered moth | Biology experiments | Evolution by taxon | Selection
W000
Origin of birds

The famous Berlin specimen of Archaeopteryx lithographica
The origin of birds is a contentious and central topic within evolutionary biology. A close relationship
between birds and dinosaurs was first proposed in the nineteenth century after the discovery of the primitive
bird Archaeopteryx in Germany. To date, most researchers support the view that birds are a group of
theropod dinosaurs that evolved during the Mesozoic Era.
Birds share a myriad of unique skeletal features with dinosaurs.[1] Moreover, fossils of more than
twenty species of dinosaur have been collected which preserve feathers. There are even very small
dinosaurs, such as Microraptor and Anchiornis, which have long, vaned, arm and leg feathers forming wings.
The Jurassic basal avialan Pedopenna also shows these long foot feathers. Witmer (2009) has concluded
that this evidence is sufficient to demonstrate that avian evolution went through a four-winged stage.[2]
Fossil evidence also demonstrates that birds and dinosaurs shared features such as hollow,
pneumatized bones, gastroliths in the digestive system, nest-building and brooding behaviors. The ground-
breaking discovery of fossilized Tyrannosaurus rex soft tissue allowed a molecular comparison of cellular
anatomy and protein sequencing of collagen tissue, both of which demonstrated that T. rex and birds are
more closely related than either is to Alligator.[3] A second molecular study robustly supported the
relationship of birds to dinosaurs, though it did not place birds within Theropoda, as expected. This study
utilized eight additional collagen sequences extracted from a femur of Brachylophosaurus canadensis, a
hadrosaur.[4]
Only a few scientists still debate the dinosaurian origin of birds, suggesting descent from other types
of archosaurian reptiles. Among the consensus that supports dinosaurian ancestry, the exact sequence of
evolutionary events that gave rise to the early birds within maniraptoran theropods is a hot topic. The origin of
bird flight is a separate but related question for which there are also several proposed answers.
Contents
[hide]
• 1 Research history
• 1.1 Huxley, Archaeopteryx and early research
• 1.2 Heilmann and the thecodont hypothesis
• 1.3 Ostrom, Deinonychus and the Dinosaur
Renaissance
• 1.4 Modern research and feathered dinosaurs in
China
• 2 Phylogeny
• 3 Features linking birds and dinosaurs
• 3.1 Feathers
• 3.2 Skeleton
• 3.3 Lungs
• 3.4 Heart and sleeping posture
• 3.5 Reproductive biology
• 3.6 Brooding and care of young
• 3.7 Gizzard stones
• 3.8 Molecular evidence and soft tissue
• 4 Debates
• 4.1 Origin of bird flight
• 4.1.1 Cursorial ("from the ground up") theory
[edit] Research history
[edit] Huxley, Archaeopteryx and early research
Thomas Henry Huxley (1825-1895)

Scientific investigation into the origin of birds began shortly after the 1859 publication of Charles
Darwin's On the Origin of Species, the ground-breaking book which described his theory of evolution by
natural selection.[5] In 1860, a fossilized feather was discovered in Germany's Late Jurassic solnhofen
limestone. Christian Erich Hermann von Meyer described this feather as Archaeopteryx lithographica the
next year,[6] and Richard Owen described a nearly complete skeleton in 1863, recognizing it as a bird
despite many features reminiscent of reptiles, including clawed forelimbs and a long, bony tail.[7]
Biologist Thomas Henry Huxley, known as "Darwin's Bulldog" for his ferocious support of the new
theory of evolution, almost immediately seized upon Archaeopteryx as a transitional fossil between birds and
reptiles. Starting in 1868, Huxley made detailed comparisons of Archaeopteryx with various prehistoric
reptiles and found that it was most similar to dinosaurs like Hypsilophodon and Compsognathus.[8][9] The
discovery in the late 1870s of the iconic "Berlin specimen" of Archaeopteryx, complete with a set of reptilian
teeth, provided further evidence. Huxley was the first to propose an evolutionary relationship between birds
and dinosaurs, although he was opposed by the very influential Owen, who remained a staunch creationist.
Huxley's conclusions were accepted by many biologists, including Baron Franz Nopcsa,[10] while others,
notably Harry Seeley,[11] argued that the similarities were due to convergent evolution.
[edit] Heilmann and the thecodont hypothesis
Heilmann's hypothetical illustration of a pair of fighting 'Proaves' from 1916

A turning point came in the early twentieth century with the writings of Gerhard Heilmann of
Denmark. An artist by trade, Heilmann had a scholarly interest in birds and from 1913 to 1916 published the
results of his research in several parts, dealing with the anatomy, embryology, behavior, paleontology, and
evolution of birds.[12] His work, originally written in Danish as Vor Nuvaerende Viden om Fuglenes
Afstamning, was compiled, translated into English, and published in 1926 as The Origin of Birds.
Like Huxley, Heilmann compared Archaeopteryx and other birds to an exhaustive list of prehistoric
reptiles, and also came to the conclusion that theropod dinosaurs like Compsognathus were the most similar.
However, Heilmann noted that birds possessed clavicles (collar bones) fused to form a bone called the
furcula ("wishbone"), and while clavicles were known in more primitive reptiles, they had not yet been
recognized in dinosaurs. Since he was a firm believer in Dollo's law, which states that evolution is not
reversible, Heilmann could not accept that clavicles were lost in dinosaurs and re-evolved in birds. He was
therefore forced to rule out dinosaurs as bird ancestors and ascribe all of their similarities to convergent
evolution. Heilmann stated that bird ancestors would instead be found among the more primitive "thecodont"
grade of reptiles.[13] Heilmann's extremely thorough approach ensured that his book became a classic in the
field, and its conclusions on bird origins, as with most other topics, were accepted by nearly all evolutionary
biologists for the next four decades.[14]
Bronze cast of the furcula of "Sue" the Tyrannosaurus, Field Museum
Clavicles are relatively delicate bones and therefore in danger of being destroyed or at least
damaged beyond recognition. Nevertheless clavicles had been found in theropod dinosaurs before Heilman
wrote his book, but had gone unrecognized.[15] The absence of clavicles in dinosaurs became the orthodox
view despite the discovery of clavicles in the primitive theropod Segisaurus in 1936.[16] The next report of
clavicles in a dinosaur was in 1983, and that was in a Russian article published before the end of the Cold
War.[17]
Contrary to what Heilman believed, paleontologists now accept that clavicles and in most cases
furculae are a standard feature not just of theropods but of saurischian dinosaurs. Up to late 2007 ossified
furculae (i.e. made of bone rather than cartilage) have been found in nearly all types of theropods except the
most basal ones, Eoraptor and Herrerasaurus.[18] The original report of a furcula in the primitive theropod
Segisaurus (1936) has been confirmed by a re-examination in 2005.[19] Joined, furcula-like clavicles have
also been found in Massospondylus, an Early Jurassic sauropodomorph.[20]
[edit] Ostrom, Deinonychus and the Dinosaur Renaissance
The similarity of the forelimbs of Deinonychus (left) and Archaeopteryx (right) led John Ostrom to
revive the link between dinosaurs and birds.
The tide began to turn against the 'thecodont' hypothesis after the 1964 discovery of a new theropod
dinosaur in Montana. In 1969, this dinosaur was described and named Deinonychus by John Ostrom of Yale
University.[21] The next year, Ostrom redescribed a specimen of Pterodactylus in the Dutch Teyler Museum
as another skeleton of Archaeopteryx.[22] The specimen consisted mainly of a single wing and its description
made Ostrom aware of the similarities between the wrists of Archaeopteryx and Deinonychus.[23]
In 1972, British paleontologist Alick Walker hypothesized that birds arose not from 'thecodonts' but
from crocodile ancestors like Sphenosuchus.[24] Ostrom's work with both theropods and early birds led him
to respond with a series of publications in the mid-1970s in which he laid out the many similarities between
birds and theropod dinosaurs, resurrecting the ideas first put forth by Huxley over a century before.[25][26]
[27] Ostrom's recognition of the dinosaurian ancestry of birds, along with other new ideas about dinosaur
metabolism,[28] activity levels, and parental care,[29] began what is known as the Dinosaur renaissance,
which began in the 1970s and continues to this day.
Ostrom's revelations also coincided with the increasing adoption of phylogenetic systematics
(cladistics), which began in the 1960s with the work of Willi Hennig.[30] Cladistics is a method of arranging
species based strictly on their evolutionary relationships, using a statistical analysis of their anatomical
characteristics. In the 1980s, cladistic methodology was applied to dinosaur phylogeny for the first time by
Jacques Gauthier and others, showing unequivocally that birds were a derived group of theropod dinosaurs.
[31] Early analyses suggested that dromaeosaurid theropods like Deinonychus were particularly closely
related to birds, a result which has been corroborated many times since.[32][33]
[edit] Modern research and feathered dinosaurs in China
Fossil of Sinosauropteryx prima.

The early 1990s saw the discovery of spectacularly preserved bird fossils in several Early
Cretaceous geological formations in the northeastern Chinese province of Liaoning.[34][35] In 1996, Chinese
paleontologists described Sinosauropteryx as a new genus of bird from the Yixian Formation,[36] but this
animal was quickly recognized as a theropod dinosaur closely related to Compsognathus. Surprisingly, its
body was covered by long filamentous structures. These were dubbed 'protofeathers' and considered to be
homologous with the more advanced feathers of birds,[37] although some scientists disagree with this
assessment.[38] Chinese and North American scientists described Caudipteryx and Protarchaeopteryx soon
after. Based on skeletal features, these animals were non-avian dinosaurs, but their remains bore fully-
formed feathers closely resembling those of birds.[39] "Archaeoraptor," described without peer review in a
1999 issue of National Geographic,[40] turned out to be a smuggled forgery,[41] but legitimate remains
continue to pour out of the Yixian, both legally and illegally. Feathers or "protofeathers" have been found on a
wide variety of theropods in the Yixian,[42][43] and the discoveries of extremely bird-like dinosaurs,[44] as
well as dinosaur-like primitive birds,[45] have almost entirely closed the morphological gap between
theropods and birds.
A small minority, including ornithologists Alan Feduccia and Larry Martin, continues to assert that
birds are instead the descendants of earlier archosaurs, such as Longisquama or Euparkeria.[46][47]
Embryological studies of bird developmental biology have raised questions about digit homology in bird and
dinosaur forelimbs.[48] However, due to the cogent evidence provided by comparative anatomy and
phylogenetics, as well as the dramatic feathered dinosaur fossils from China, the idea that birds are derived
dinosaurs, first championed by Huxley and later by Nopcsa and Ostrom, enjoys near-unanimous support
among today's paleontologists.[14]
[edit] Phylogeny
Archaeopteryx has historically been considered the first bird, or Urvogel. Although newer fossil
discoveries eliminated the gap between theropods and Archaeopteryx, as well as the gap between
Archaeopteryx and modern birds, phylogenetic taxonomists, in keeping with tradition, almost always use
Archaeopteryx as a specifier to help define Aves.[49][50] Aves has more rarely been defined as a crown
group consisting only of modern birds.[31] Nearly all palaeontologists regard birds as coelurosaurian
theropod dinosaurs.[14] Within Coelurosauria, multiple cladistic analyses have found support for a clade
named Maniraptora, consisting of therizinosauroids, oviraptorosaurs, troodontids, dromaeosaurids, and birds.
[32][33][51] Of these, dromaeosaurids and troodontids are usually united in the clade Deinonychosauria,
which is a sister group to birds (together forming the node-clade Eumaniraptora) within the stem-clade
Paraves.[32][52]
Other studies have proposed alternative phylogenies in which certain groups of dinosaurs that are
usually considered non-avian are suggested to have evolved from avian ancestors. For example, a 2002
analysis found oviraptorosaurs to be basal avians.[53] Alvarezsaurids, known from Asia and the Americas,
have been variously classified as basal maniraptorans,[32][33][54][55] paravians,[51] the sister taxon of
ornithomimosaurs,[56] as well as specialized early birds.[57][58] The genus Rahonavis, originally described
as an early bird,[59] has been identified as a non-avian dromaeosaurid in several studies.[52][60]
Dromaeosaurids and troodontids themselves have also been suggested to lie within Aves rather than just
outside it.[61][62]
[edit] Features linking birds and dinosaurs

Many distinct anatomical[63] features are shared by birds and
theropod dinosaurs. Some of the more interesting similarities are discussed
here:
[edit] Feathers
Main article: Feathered dinosaurs
Archaeopteryx, the first good example of a "feathered dinosaur", was
discovered in 1861. The initial specimen was found in the solnhofen
limestone in southern Germany, which is a lagerstätte, a rare and remarkable
geological formation known for its superbly detailed fossils. Archaeopteryx is
a transitional fossil, with features clearly intermediate between those of
modern reptiles and birds. Discovered just two years after Darwin's seminal
Origin of Species, its discovery spurred the nascent debate between
proponents of evolutionary biology and creationism. This early bird is so
Parts of a feather
dinosaur-like that, without a clear impression of feathers in the surrounding rock, at least one specimen was
mistaken for Compsognathus.[64]
Since the 1990s, a number of additional feathered dinosaurs have been found, providing even
stronger evidence of the close relationship between dinosaurs and modern birds. Most of these specimens
were unearthed in Liaoning province, northeastern China, which was part of an island continent during the
Cretaceous period. Though feathers have been found only in the lagerstätte of the Yixian Formation and a
few other places, it is possible that non-avian dinosaurs elsewhere in the world were also feathered. The lack
of widespread fossil evidence for feathered non-avian dinosaurs may be because delicate features like skin
and feathers are not often preserved by fossilization and thus are absent from the fossil record.
A recent development in the debate centers around the discovery of impressions of "protofeathers"
surrounding many dinosaur fossils. These protofeathers suggest that the tyrannosauroids may have been
feathered.[65] However, others claim that these protofeathers are simply the result of the decomposition of
collagenous fiber that underlaid the dinosaurs' integument.[47]
Fossil cast of NGMC 91, a probable specimen of Sinornithosaurus.
The feathered dinosaurs discovered so far include Beipiaosaurus, Caudipteryx, Dilong, Microraptor,
Protarchaeopteryx, Shuvuuia, Sinornithosaurus, Sinosauropteryx, and Jinfengopteryx, along with dinosaur-
like birds, such as Confuciusornis, which are anatomically closer to modern avians. All of them have been
found in the same area and formation, in northern China. The Dromaeosauridae family, in particular, seems
to have been heavily feathered and at least one dromaeosaurid, Cryptovolans, may have been capable of
flight.
[edit] Skeleton
Because feathers are often associated with birds, feathered dinosaurs are often touted as the
missing link between birds and dinosaurs. However, the multiple skeletal features also shared by the two
groups represent the more important link for paleontologists. Furthermore, it is increasingly clear that the
relationship between birds and dinosaurs, and the evolution of flight, are more complex topics than previously
realized. For example, while it was once believed that birds evolved from dinosaurs in one linear progression,
some scientists, most notably Gregory S. Paul, conclude that dinosaurs such as the dromaeosaurs may have
evolved from birds, losing the power of flight while keeping their feathers in a manner similar to the modern
ostrich and other ratites.
Comparisons of bird and dinosaur skeletons, as well as cladistic analysis, strengthens the case for
the link, particularly for a branch of theropods called maniraptors. Skeletal similarities include the neck, pubis,
wrist (semi-lunate carpal), arm and pectoral girdle, shoulder blade, clavicle, and breast bone.
[edit] Lungs
Comparison between the air sacs of Majungasaurus and a bird

Large meat-eating dinosaurs had a complex system of air sacs similar to those found in modern
birds, according to an investigation which was led by Patrick M. O'Connor of Ohio University. The lungs of
theropod dinosaurs (carnivores that walked on two legs and had birdlike feet) likely pumped air into hollow
sacs in their skeletons, as is the case in birds. "What was once formally considered unique to birds was
present in some form in the ancestors of birds", O'Connor said. The study was funded in part by the National
Science Foundation.[66][67]
[edit] Heart and sleeping posture

Modern computed tomography (CT) scans of a dinosaur chest cavity (conducted in 2000) found the
apparent remnants of complex four-chambered hearts, much like those found in today's mammals and birds.
[68] The idea is controversial within the scientific community, coming under fire for bad anatomical
science[69] or simply wishful thinking.[70] A recently discovered troodont fossil demonstrates that the
dinosaurs slept like certain modern birds, with their heads tucked under their arms.[71] This behavior, which
may have helped to keep the head warm, is also characteristic of modern birds.
[edit] Reproductive biology

When laying eggs, female birds grow a special type of bone in their limbs. This medullary bone,
which is rich in calcium, forms a layer inside the hard outer bone that is used to make eggshells. The
presence of endosteally-derived bone tissues lining the interior marrow cavities of portions of a
Tyrannosaurus rex specimen's hind limb suggested that T. rex used similar reproductive strategies, and
revealed the specimen to be female.[72] Further research has found medullary bone in the theropod
Allosaurus and ornithopod Tenontosaurus. Because the line of dinosaurs that includes Allosaurus and
Tyrannosaurus diverged from the line that led to Tenontosaurus very early in the evolution of dinosaurs, this
suggests that dinosaurs in general produced medullary tissue.[73]
[edit] Brooding and care of young
A nesting Citipati osmolskae specimen, at the American Museum of Natural History in New York.
Several Citipati specimens have been found resting over the eggs in its nest in a position most
reminiscent of brooding.[74]
Numerous dinosaur species, for example Maiasaura, have been found in herds mixing both very
young and adult individuals, suggesting rich interactions between them.
A dinosaur embryo was found without teeth, which suggests some parental care was required to feed
the young dinosaur, possibly the adult dinosaur regurgitated food into the young dinosaur's mouth ( see
altricial). This behaviour is seen in numerous bird species; parent birds regurgitate food into the hatchling's
mouth.
[edit] Gizzard stones
Both birds and dinosaurs use gizzard stones. These stones are swallowed by animals to aid
digestion and break down food and hard fibres once they enter the stomach. When found in association with
fossils, gizzard stones are called gastroliths.[75] Gizzard stones are also found in some fish (mullets, mud
shad, and the gilaroo, a type of trout) and in crocodiles.
[edit] Molecular evidence and soft tissue
Fossil of a juvenile individual of Scipionyx samniticus. The fossil preserves clear traces of soft
tissues.
One of the best examples of soft tissue impressions in a fossil dinosaur was discovered in Petraroia,
Italy. The discovery was reported in 1998, and described the specimen of a small, very young coelurosaur,
Scipionyx samniticus. The fossil includes portions of the intestines, colon, liver, muscles, and windpipe of this
immature dinosaur.[76]
In the March 2005 issue of Science, Dr. Mary Higby Schweitzer and her team announced the
discovery of flexible material resembling actual soft tissue inside a 68-million-year-old Tyrannosaurus rex leg
bone from the Hell Creek Formation in Montana. After recovery, the tissue was rehydrated by the science
team. The seven collagen types obtained from the bone fragments, compared to collagen data from living
birds (specifically, a chicken), suggest that older theropods and birds are closely related.
When the fossilized bone was treated over several weeks to remove mineral content from the
fossilized bone marrow cavity (a process called demineralization), Schweitzer found evidence of intact
structures such as blood vessels, bone matrix, and connective tissue (bone fibers). Scrutiny under the
microscope further revealed that the putative dinosaur soft tissue had retained fine structures
(microstructures) even at the cellular level. The exact nature and composition of this material, and the
implications of Dr. Schweitzer's discovery, are not yet clear; study and interpretation of the specimens is
ongoing.[77]
The successful extraction of ancient DNA from dinosaur fossils has been reported on two separate
occasions, but upon further inspection and peer review, neither of these reports could be confirmed.[78]
However, a functional visual peptide of a theoretical dinosaur has been inferred using analytical phylogenetic
reconstruction methods on gene sequences of related modern species such as reptiles and birds.[79] In
addition, several proteins have putatively been detected in dinosaur fossils,[80] including hemoglobin.[81]
[edit] Debates
[edit] Origin of bird flight
Debates about the origin of bird flight are almost as old as the idea that birds evolved from dinosaurs,
which arose soon after the discovery of Archaeopteryx in 1862. Two theories have dominated most of the
discussion since then: the cursorial ("from the ground up") theory proposes that birds evolved from small, fast
predators that ran on the ground; the arboreal ("from the trees down") theory proposes that powered flight
evolved from unpowered gliding by arboreal (tree-climbing) animals. A more recent theory, "wing-assisted
incline running" (WAIR), is a variant of the cursorial theory and proposes that wings developed their
aerodynamic functions as a result of the need to run quickly up very steep slopes, for example to escape
from predators.
[edit] Cursorial ("from the ground up") theory

Reconstruction of Rahonavis, a ground-dwelling feathered dinosaur that some researchers think was
well-equipped for flight.
The cursorial theory of the origin of flight was first proposed by Samuel Wendell Williston, and
elaborated upon by Baron Nopcsa. This hypothesis proposes that some fast-running animals with long tails
used their arms to keep their balance while running. Modern versions of this theory differ in many details from
the Williston-Nopcsa version, mainly as a result of discoveries since Nopcsa's time.
Nopcsa theorized that increasing the surface area of the outstretched arms could have helped small
cursorial predators to keep their balance, and that the scales of the forearms became elongated, evolving
into feathers. The feathers could also have been used as a trap to catch insects or other prey. Progressively,
the animals would have leapt for longer distances, helped by their evolving wings. Nopcsa also proposed that
there were three main stages in the evolution of flight. First, passive flight was realized, in which the
developed wing structures served as a sort of parachute. Second, active flight was possible, in which the
animal achieved flight by flapping its wings. He used Archaeopteryx as an example of this second stage.
Finally, birds gained the ability to soar.[82]
It is now thought that feathers did not evolve from scales, as feathers are made of different proteins.
[83] More seriously, Nopcsa's theory assumes that feathers evolved as part of the evolution of flight, and
recent discoveries prove that assumption is false.
Feathers are very common in coelurosaurian dinosaurs (including the early tyrannosauroid Dilong).
[84] Modern birds are classified as coelurosaurs by nearly all palaeontologists,[85] though not by a few
ornithologists.[86][87] The modern version of the "from the ground up" hypothesis argues that birds'
ancestors were small, feathered, ground-running predatory dinosaurs (rather like roadrunners in their hunting
style[88]) that used their forelimbs for balance while pursuing prey, and that the forelimbs and feathers later
evolved in ways that provided gliding and then powered flight. The most widely-suggested original functions
of feathers include thermal insulation and competitive displays, as in modern birds.[89][90]
All of the Archaeopteryx fossils come from marine sediments and it has been suggested that wings
may have helped the birds run over water in the manner of the Jesus Christ Lizard (Common basilisk).[91]
Most recent refutations of the "from the ground up" hypothesis attempt to refute the modern version's
assumption that birds are modified coelurosaurian dinosaurs. The strongest attacks are based on
embryological analyses which conclude that birds' wings are formed from digits 2, 3, and 4 (corresponding to
the index, middle, and ring fingers in humans; the first of a bird's three digits forms the alula, which they use
to avoid stalling in low-speed flight, for example when landing); but the hands of coelurosaurs are formed by
digits 1, 2, and 3 (thumb and first two fingers in humans).[92] However these embryological analyses were
immediately challenged on the embryological grounds that the "hand" often develops differently in clades that
have lost some digits in the course of their evolution, and that birds' "hands" do develop from digits 1, 2, and
3.[93][94][94] This debate is complex and not yet resolved - see "Digit homology" below.
[edit] Wing-assisted incline running

The WAIR hypothesis was prompted by observation of young chukar chicks, and proposes that
wings developed their aerodynamic functions as a result of the need to run quickly up very steep slopes such
as tree trunks, for example to escape from predators.[95] This makes it a specialized type of cursorial ("from
the ground up") theory. Note that in this scenario birds need downforce to give their feet increased grip.[96]
[97] But early birds, including Archaeopteryx, lacked the shoulder mechanism by which modern birds' wings
produce swift, powerful upstrokes; since the downforce on which WAIR depends is generated by upstrokes, it
seems that early birds were incapable of WAIR.[98]
[edit] Arboreal ("from the trees down") theory
The remarkable four-winged Microraptor, a "cousin" of the birds.

Most versions of the arboreal hypothesis state that the ancestors of birds were very small dinosaurs
that lived in trees, springing from branch to branch. This small dinosaur already had feathers, which were co-
opted by evolution to produce longer, stiffer forms that were useful in aerodynamics, eventually producing
wings. Wings would have then evolved and become increasingly refined as devices to give the leaper more
control, to parachute, to glide, and to fly in stepwise fashion. The arboreal hypothesis also notes that, for
arboreal animals, aerodynamics are far more energy efficient, since such animals simply fall in order to
achieve minimum gliding speeds.[99][100]
Several small dinosaurs from the Jurassic or Early Cretaceous, all with feathers, have been
interpreted as possibly having arboreal and/or aerodynamic adaptations. These include Epidendrosaurus,
Epidexipteryx, Microraptor, Pedopenna, and Anchiornis. Anchiornis is particularly important to this subject, as
it is the smallest known non - avian dinosaur, and it lived at the beginning of the Late Jurassic, long before
Archaeopteryx.[101]
Analysis of the proportions of the toe bones of the most primitive birds Archaeopteryx and
Confuciusornis, compared to those of living species, suggest that the early species may have lived both on
the ground and in trees.[102]
One study suggested that the earliest birds and their immediate ancestors did not climb trees. This
study determined that the amount of toe claw curvature of early birds was more like that seen in modern
ground-foraging birds than in perching birds.[103]
[edit] Diminished significance of Archaeopteryx
The supracoracoideus works using a pulley-like system to lift the wing while the pectorals provide the
powerful downstroke
Archaeopteryx was the first and for a long time the only known feathered Mesozoic animal (or
dinosaur, if one accepts the majority view that birds are modified dinosaurs). As a result, discussion of the
evolution of birds and of bird flight centered on Archaeopteryx at least until the mid-1990s.
There has been debate about whether Archaeopteryx could really fly. It appears that Archaeopteryx
had the brain structures and inner-ear balance sensors that birds use to control their flight.[104]
Archaeopteryx also had a wing feather arrangement like that of modern birds and similarly asymmetrical
flight feathers on its wings and tail. But Archaeopteryx lacked the shoulder mechanism by which modern
birds' wings produce swift, powerful upstrokes (see diagram above of supracoracoideus pulley); this may
mean that it and other early birds were incapable of flapping flight and could only glide.[98]
Proposed development of flight in a book from 1922: Tetrapteryx, Archaeopteryx, Hypothetical Stage,
Modern Bird
But the discovery since the early 1990s of many feathered dinosaurs means that Archaeopteryx is no
longer the key figure in the evolution of bird flight. Other small, feathered coelurosaurs from the Cretaceous
and Late Jurassic show features that may be precursors of avian flight, for example: Rahonavis, a ground-
runner which had a Velociraptor-like raised sickle claw on the second toe and which some paleontologists
think was better adapted for flight than Archaeopteryx;[105] Epidendrosaurus, an arboreal dinosaur that may
provide some support for the "from the trees down" theory;[106] Microraptor, an arboreal dinosaur that may
have been capable of powered flight but, if so, more like a biplane, as it had well-developed feathers on its
legs.[107] As early as 1915, some scientists had argued that the evolution of bird flight may have gone
through a four-winged (or tetrapteryx) stage.[108][109]
[edit] Secondary flightlessness in dinosaurs

Coelurosaurs
Alvarezs
Therizinosauroids
Oviraptosaurs
Archaeopteryx
and Rahonavis
(birds)
Troodontids
Deinonychosaurs
Confuciusornis
(bird)
Microraptor
(dromaeosaur)
Dromaeosaurs
Simplified cladogram from Mayr et al. (2005)
Groups usually regarded as birds are in bold type.[62]
A hypothesis, credited to Gregory Paul and propounded in his books Predatory Dinosaurs of the
World (1988) and Dinosaurs of the Air (2002), suggests that some groups of non-flying carnivorous
dinosaurs, especially deinonychosaurs but perhaps others such as oviraptorosaurs, therizinosaurs,
alvarezsaurids and ornithomimosaurs, are actually descended from birds. Paul also proposed that the bird
ancestor of these groups was more advanced in its flight adaptations than Archaeopteryx. This would mean
that Archaeopteryx is thus less closely related to extant birds than these dinosaurs are.[110]
Paul's hypothesis received additional support when Mayr et al. (2005) analyzed a new, tenth
specimen of Archaeopteryx, and concluded that Archaeopteryx was the sister clade to the Deinonychosauria,
but that the more advanced bird Confuciusornis was within the Dromaeosauridae. This result supports Paul's
hypothesis, suggesting that the Deinonychosauria and the Troodontidae are part of Aves, the bird lineage
proper, and secondarily flightless.[111] This paper, however, excluded all other birds and thus did not sample
their character distributions. The paper was criticized by Corfe and Butler (2006) who found the authors could
not support their conclusions statistically. Mayr et al. agreed that the statistical support was weak, but added
that it is also weak for the alternative scenarios.[112]
Paul's hypothesis about the position of Archaeopteryx is not supported by current cladistic analyses
which generally find that Archaeopteryx is closer to birds, within the clade Avialae, than it is to
deinonychosaurs or oviraptorosaurs. However, the version of this theory stating that some non-flying
carnivorous dinosaurs may have had flying ancestors is supported by some fossils. Especially, Microraptor,
Pedopenna, and Anchiornis all have winged feet, share many features, and lie close to the base of the clade
Paraves. This suggests that the ancestral paravian was a four-winged glider, and that larger
Deinonychosaurs secondarily lost the ability to glide, while the bird lineage increased in aerodynamic ability
as it progressed.[2]
[edit] Digit homology

There is a debate between embryologists and paleontologists whether the hands of theropod
dinosaurs and birds are essentially different, based on phalangeal counts, a count of the number of
phalanges (fingers) in the hand. This is an important and fiercely debated area of research because its
results may challenge the consensus that birds are descendants of dinosaurs.
Embryologists and some paleontologists who oppose the bird-dinosaur link, have long numbered the
digits of birds II-III-IV on the basis of multiple studies of the development in the egg.[113][114][115] [116][117]
This is based on the fact that in most amniotes, the first digit to form in a 5-fingered hand is digit IV, which
develops a primary axis. Therefore, embryologists have identified the primary axis in birds as digit IV, and the
surviving digits as II-III-IV. The fossils of advanced theropod (Tetanurae) hands appear to have the digits I-II-
III (some genera within Avetheropoda also have a reduced digit IV[118]). If this is true, then the II-III-IV
development of digits in birds is an indication against theropod (dinosaur) ancestry. However, with no
ontogenical (developmental) basis to definitively state which digits are which on a theropod hand (because
no non-avian theropods can be observed growing and developing today), the labelling of the theropod hand
is not absolutely conclusive.
Paleontologists have traditionally identified avian digits as I-II-III. They argue that the digits of birds
number I-II-III, just as those of theropod dinosaurs do, by the conserved phalangeal formula. The phalangeal
count for archosaurs is 2-3-4-5-3; many archosaur lineages have a reduced number of digits, but have the
same phalangeal formula in the digits that remain. In other words, paleontologists assert that archosaurs of
different lineages tend to lose the same digits when digit loss occurs, from the outside to the inside. The three
digits of dromaeosaurs, and Archaeopteryx have the same phalangeal formula of I-II-III as digits I-II-III of
basal archosaurs. Therefore, the lost digits would be V and IV. If this is true, then modern birds would also
possess digits I-II-III.[117] Also, one research team has proposed a frame-shift in the digits of the theropod
line leading to birds (thus making digit I into digit II, II to III, and so forth).[119][120] However, such frame
shifts are rare in amniotes and would have had to occur solely in the forelimbs and not the hindlimbs (a
condition presently unknown in any animal) in the bird-theropod lineage in order to be consistent with the
theropod origin of birds.[121] This is called Lateral Digit Reduction (LDR) versus Bilateral Digit Reduction
(BDR) (see also Limusaurus[122])
[edit] See also

Dinosaurs portal
• Bird ichnology
• List of extinct birds
• Feathered dinosaurs
• Flightless birds
• Origin of avian flight
• Temporal paradox (paleontology)
[edit] Footnotes
1. ^ Chiappe, Luis M. (2009). "Downsized Dinosaurs: The Evolutionary Transition to Modern
Birds". Evolution: Education and Outreach: 248–256.
http://www.springerlink.com/content/66w3755838876571/. Retrieved 2009-11-14.
2. ^ a b Witmer, Lawrence M. (2009) "Feathered dinosaurs in a tangle"NATURE|Vol 461|1
October 2009 pg 601-602
3. ^ Asara, JM; Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007). "Protein
Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry". Science 316
(5822): 280–285. doi:10.1126/science.1137614. PMID 17431180.
4. ^ Schweitzer, M. H.; Zheng W., Organ C. L., Avci R., Suo Z., Freimark L. M., Lebleu V. S.,
Duncan M. B., Vander Heiden M. G., Neveu J. M., Lane W. S., Cottrell J. S., Horner J. R., Cantley L.
C., Kalluri R. & Asara J. M. (2009). "Biomolecular Characterization and Protein Sequences of the
Campanian Hadrosaur B. canadensis". Science 324 (5927): 626–631. doi:10.1126/science.1165069.
PMID 19407199.
5. ^ Darwin, Charles R. (1859). On the Origin of Species by Means of Natural Selection, or the
Preservation of Favoured Races in the Struggle for Life. London: John Murray. p. 502pp.
itemID=F373&viewtype=side&pageseq=16.
6. ^ von Meyer, C.E. Hermann. (1861). "Archaeopteryx lithographica (Vogel-Feder) und
Pterodactylus von Solnhofen" (in German). Neues Jahrbuch für Mineralogie, Geologie und
Paläontologie 1861: 678–679.
7. ^ Owen, Richard. (1863). "On the Archeopteryx [sp] of von Meyer, with a description of the
fossil remains of a long-tailed species, from the lithographic stone of Solenhofen [sp]". Philosophical
Transactions of the Royal Society of London 153: 33–47. doi:10.1098/rstl.1863.0003.
8. ^ Huxley, T.H. (1868). "On the animals which are most nearly intermediate between birds
and reptiles". Annals and Magazine of Natural History.. 4th 2: 66–75.
http://biodiversitylibrary.org/page/22247928.
9. ^ Huxley, Thomas H. (1870). "Further evidence of the affinity between the dinosaurian
reptiles and birds". Quarterly Journal of the Geological Society of London 26: 12–31.
doi:10.1144/GSL.JGS.1870.026.01-02.08.
10.^ Nopcsa, Franz. (1907). "Ideas on the origin of flight". Proceedings of the Zoological Society
of London: 223–238.
11.^ Seeley, Harry G. (1901). Dragons of the Air: An Account of Extinct Flying Reptiles. London:
Methuen & Co.. p. 239pp.
12.^ Nieuwland, Ilja J.J. (2004). "Gerhard Heilmann and the artist’s eye in science, 1912-1927".
PalArch's Journal of Vertebrate Palaeontology 3 (2). http://www.palarch.nl/wp-
content/ver_2004_3_2.pdf.
13.^ Heilmann, Gerhard (1926). The Origin of Birds. London: Witherby. p. 208pp.
ISBN 0486227847.
14.^ a b c Padian, Kevin. (2004). "Basal Avialae". In Weishampel, David B.; Dodson, Peter; &
Osmólska, Halszka (eds.). The Dinosauria (Second ed.). Berkeley: University of California Press.
pp. 210–231. ISBN 0-520-24209-2.
15.^ For example in 1923, 3 years before Heilmans's book, Roy Chapman Andrews found a
good Oviraptor fossil in Mongolia, but Henry Fairfield Osborn, who analyzed the fossil in 1924, mis-
identified the furcula as an interclavicle; described in Paul, G.S. (2002). Dinosaurs of the Air: The
Evolution and Loss of Flight in Dinosaurs and Birds. JHU Press. ISBN 0801867630.
http://books.google.com/?id=OUwXzD3iihAC&pg=PA9&lpg=PA9&dq=oviraptor+furcula.
16.^ Camp, Charles L. (1936). "A new type of small theropod dinosaur from the Navajo
Sandstone of Arizona". Bulletin of the University of California Department of Geological Sciences 24:
39–65.
17.^ In an Oviraptor: Barsbold, R. (1983). "[Carnivorous dinosaurs from the Cretaceous of
Mongolia". Trudy Soumestnaya Sovetsko-Mongol'skaya Paleontogicheskaya Ekspeditsiya 19: 1–
117. (in Russian!) See the summary an pictures at "A wish for Coelophysis".
http://www.hmnh.org/archives/2007/10/11/a-wish-for-coelophysis/.
18.^ Lipkin, C., Sereno, P.C., and Horner, J.R. (November 2007). "THE FURCULA IN
SUCHOMIMUS TENERENSIS AND TYRANNOSAURUS REX (DINOSAURIA: THEROPODA:
TETANURAE)". Journal of Paleontology 81 (6): 1523–1527. doi:10.1666/06-024.1.
http://jpaleontol.geoscienceworld.org/cgi/content/extract/81/6/1523. - full text currently online at "The
Furcula in Suchomimus Tenerensis and Tyrannosaurus rex".
http://www.redorbit.com/news/health/1139122/the_furcula_in_suchomimus_tenerensis_and_tyranno
saurus_rex_dinosauria_theropoda/index.html. This lists a large number of theropods in which
furculae have been found, as well as describing those of Suchomimus Tenerensis and
Tyrannosaurus rex.
19.^ Carrano, M,R., Hutchinson, J.R., and Sampson, S.D. (December 2005). "New information
on Segisaurus halli, a small theropod dinosaur from the Early Jurassic of Arizona" . Journal of
Vertebrate Paleontology 25 (4): 835–849. doi:10.1671/0272-4634(2005)025[0835:NIOSHA]2.0.CO;2.
http://www.rvc.ac.uk/AboutUs/Staff/jhutchinson/documents/JH18.pdf.
20.^ Yates, Adam M.; and Vasconcelos, Cecilio C. (2005). "Furcula-like clavicles in the
prosauropod dinosaur Massospondylus". Journal of Vertebrate Paleontology 25 (2): 466–468.
doi:10.1671/0272-4634(2005)025[0466:FCITPD]2.0.CO;2.
21.^ Ostrom, John H. (1969). "Osteology of Deinonychus antirrhopus, an unusual theropod from
the Lower Cretaceous of Montana". Bulletin of the Peabody Museum of Natural History 30: 1–165.
22.^ Ostrom, John H. (1970). "Archaeopteryx: Notice of a "new" specimen". Science 170 (3957):
537–538. doi:10.1126/science.170.3957.537. PMID 17799709.
23.^ Chambers, Paul (2002). Bones of Contention: The Archaeopteryx Scandals. London: John
Murray Ltd. pp. 183–184. ISBN 0719560543.
24.^ Walker, Alick D. (1972). "New light on the origin of birds and crocodiles". Nature 237
(5353): 257–263. doi:10.1038/237257a0.
25.^ Ostrom, John H. (1973). "The ancestry of birds". Nature 242 (5393): 136.
doi:10.1038/242136a0.
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• DinoBuzz A popular-level discussion of the dinosaur-bird hypothesis
• Archaeopteryx - FAQs - from the Usenet newsgroup talk.origins.
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Anatomy Bird anatomy • Flight • Eggs • Feathers • Plumage • Beak • Vision • Dactyly •
Preen gland
Behaviour Singing • Intelligence • Migration • Incubation • Brood parasites • Nesting •

Hybrids
Evolution Evolution of birds • Origin of birds • Darwin's finches • Seabirds

Superorder: Palaeognathae
Struthioniformes (ratites) • Tinamiformes (tinamous)
Superorder: Neognathae
Accipitriformes • Anseriformes (waterfowl) • Apodiformes (swifts and

Subclass: hummingbirds) • Caprimulgiformes (nightjars and relatives) • Cariamae (seriemas and
Neornithes relatives) • Charadriiformes (gulls and relatives) • Ciconiiformes (storks) • Coliiformes
(29 orders of (mousebirds) • Columbiformes (doves and pigeons) • Coraciiformes (kingfishers and
modern birds) relatives) • Cuculiformes (cuckoos and relatives) • Falconiformes (falcons and
relatives) • Galliformes (gamebirds) • Gaviiformes (loons or divers) • Gruiformes
(cranes and relatives) • Passeriformes (perching birds) • Pelecaniformes (pelicans
and relatives) • Phaethontiformes (tropicbirds) • Phoenicopteriformes (flamingos) •
Piciformes (woodpeckers and relatives) • Podicipediformes (grebes) •
Procellariiformes (albatrosses and petrels) • Psittaciformes (parrots) • Pteroclidiformes
(sandgrouses) • Sphenisciformes (penguins) • Strigiformes (owls) • Trogoniformes
(trogons and quetzals)
Fossil birds Archaeopteryx • Enantiornithes • Hesperornithes

Birds and Ringing • Ornithology • Bird collections • Birdwatching • Bird feeding •
humans Conservation • Aviculture • Waterfowl hunting • Pigeon racing
Lists Families and orders • Genera • Lists by region • Extinct birds • Late Quaternary
prehistoric birds • Sibley-Ahlquist taxonomy
Category • Portal
Retrieved from "http://en.wikipedia.org/wiki/Origin_of_birds"
Categories: Bird evolution | Dinosaurs

W000
Strengths and weaknesses of evolution


Scientists are always probing the strengths and weakness of their hypotheses.
That is the very nature of the enterprise. But evolution is no longer a hypothesis. It is a
theory rigorously supported by abundant evidence. The weaknesses that creationists
“ ”
hope to teach as a way of refuting evolution are themselves antiquated, long since filed
away as solved. The religious faith underlying creationism has a place, in church and
social studies courses. Science belongs in science classrooms.
—The Cons of Creationism, editorial from The New York Times[1]

"Strengths and weaknesses of evolution" is a controversial phrase that has been proposed for (and
in Texas introduced into) public school science curricula. Those proposing the phrase, such as Texas State
Board of Education (SBOE) chairman Don McLeroy, purport that there are weaknesses in the theory of
evolution and in the evidence that life has evolved that should be taught for a balanced treatment of the
subject of evolution. The scientific community rejects that any substantive weaknesses exist in this scientific
theory, or in the data that it explains, and views the examples that have been given in support of the phrasing
as being without merit and long refuted.[2][3] This has led scientists and journalists to conclude that this
phrase is creationist code-language, and represents an attempt to introduce religion into science courses.[4]
The phrase was introduced by the SBOE in the late 1980s. Since then it has been promoted in
California and Missouri. In late 2008, it became a highly publicized issue as the Texas SBOE held public
hearings on whether this language should be removed from the curriculum.
According to the National Center for Science Education, the phrase, like 'Teach the controversy' and
'Critical Analysis of Evolution', is another attempt in a series of legal and political tactics adopted by intelligent
design advocates to encourage educators to teach fallacious information — that a controversy exists among
scientists over whether evolution has occurred.[5]
Contents
[hide]
• 1 History
• 1.1 Texas SBOE
• 1.2 California
• 1.3 Discovery Institute
• 1.4 Missouri
• 2 Educational and scientific value
• 3 Specific weaknesses and their scientific rebuttals
• 4 See also
• 5 References
[edit] History
[edit] Texas SBOE
The "strengths and weaknesses" language was included in the curriculum standards in Texas to
appease creationists when the SBOE first mandated the teaching of evolution in the late 1980s.[2]
In 2003, the "strengths and weaknesses" language in the standards was employed by members of
the board in an unsuccessful attempt to dilute the treatment of evolution in the biology textbooks they were
considering.[6]
In September 2008 the 21st Century Science Coalition released a petition to remove the phrase
"strengths and weaknesses" from the public school guidelines for science classrooms in Texas. As of
November 2008, 588 scientists at Texas universities and 777 other scientists across the state have signed
the petition.[7]
In the summer of 2008/2009 the Texas SBOE is determining the curriculum for the next decade,
including deciding whether the "strengths and weaknesses" of evolution should be taught. While this
language was described by the New York Times as a "benign-sounding phrase", they mention that critics
state that it is a new strategy to undermine the teaching of evolution, and for students to hear religious
objections under the heading of scientific discourse. The SBOE Chairman, Don McLeroy, a Young Earth
creationist dentist from Central Texas, denied that the language "is subterfuge for bringing in creationism."
McLeroy views the debate as being between "two systems of science" — "a creationist system and a
naturalist system". These views have alarmed Texas educators, including former chairman of the department
of medicine at the University of Texas Southwestern Medical Center at Dallas Dan Foster, who stated that
"[s]erious students will not come to study in our universities if Texas is labeled scientifically backward".[2]
In December 2008, the San Antonio Express-News stated in an editorial that the Texas SBOE has a
"long history of trying to water down the science curriculum with criticisms of evolution that lack scientific
credibility."[8]
“ The lesson we draw from these shenanigans is that scientifically illiterate ”
boards of education should leave the curriculum to educators and scientists who know
what constitutes a sound education.
—Texas Two-Step, editorial from The New York Times condemning the amendments[9]
In January 2009, the Texas SBOE voted to remove the 'Strengths and Weaknesses" language, but
its conservative faction, led by Don McLeroy, managed to pass several amendments to the science
curriculum that opponents describe as opening the door to teaching objections to evolution that might lead
students to reject it. These included one amendent that compels science teachers to teach about aspects of
the fossil record that do not neatly fit with gradualism, but rather show the relatively sudden appearance of
some species while others seem to remain unchanged for millions of years. Prominent University of Texas
biology professor David Hillis described the amendments as "mak[ing] no sense to me ... It's a clear
indication that the chairman of the state school board doesn’t understand the science."[10] Board member
Ken Mercer, who voted to keep "strengths and weaknesses" described his support for the language in
explicitly religious terms: "It's an issue of freedom of religion."[11] This view was contradicted by fellow social
conservative board member Barbara Cargill, who stated "[t]his isn’t about religion."[12]
On March 13, 2009 a bill (HB 4224) was introduced in the Texas House of Representatives that
would require the Texas SBOE to restore the "strengths and weaknesses" language in the state science
standards.[13]
[edit] California
In 2003 and 2004, creationist lawyer Larry Caldwell sought to persuade the Roseville Joint Union
High School District Board of Trustees to adopt a policy which included teaching "the scientific strengths and
weaknesses" of evolution. When this was rejected, he filed a complaint in federal court against the district,
alleging that his civil rights were violated during the controversy, resulting in a summary judgment against
him in September 2007.[14][15]
[edit] Discovery Institute

In February 2008 the Discovery Institute created an Academic Freedom petition that stated
"Teachers should be protected from being fired, harassed, intimidated, or discriminated against for
objectively presenting the scientific strengths and weaknesses of Darwinian theory."
[edit] Missouri
In February 2009, House Bill 656, introduced in the Missouri House of Representatives, proposed
that "teachers shall be permitted to help students understand, analyze, critique, and review in an objective
manner the scientific strengths and scientific weaknesses of theories of biological and chemical
evolution."[16] This bill died when the Missouri legislative session ended on May 15, 2009.[17]
[edit] Educational and scientific value

See also: Creation and evolution in public education
While anti-evolution members of the Texas SBOE have claimed their "weaknesses" campaign has
nothing to do with faith, that "We're not putting religion in books", scientists have rebutted that these
weaknesses are simply falsehoods. Scientists testified at the state board hearing in November 2008 that
evolution is a scientific theory, not a hypothesis and thus does not have weaknesses.[18]
Some scientists, including University of Texas biochemistry professor Andrew Ellington and Houston
Independent School District's AP science lead teacher Robert Dennison, are concerned that the mention of
"weaknesses" in the curriculum standards has had a chilling effect on science teachers.[18]
In a survey commissioned by the Texas Freedom Network, "94% of Texas scientists indicated that
claimed "weaknesses" are not valid scientific objections to evolution (with 87% saying that they “strongly
disagree” that such weaknesses should be considered valid)."[19]
[edit] Specific weaknesses and their scientific rebuttals

Main article: Objections to evolution
Supporters of the 'strengths and weaknesses of evolution' language have proposed the following as
weaknesses of evolution, and the scientific community has responded with the following rebuttals:
Argument Scientific rebuttal
Sunlight is the ultimate source of energy for life on Earth and

Evolution violates the first law provides the energy needed for organisms to live and reproduce. As
of thermodynamics[20] the existence and evolution of life neither creates nor destroys this
energy, it does not violate the first law of thermodynamics.[21]
Evolution violates the second The second law only applies to closed systems that do not
law of thermodynamics[20] exchange matter or energy with their surroundings. Both the Earth
and all living organisms are open systems. For further details see
Evolution and the second law of thermodynamics and Entropy and
life.
Pasteur's law only disproved the (then current) idea that life
Evolution violates the Law of forms such as mice, maggots, and bacteria can appear fully formed.
Biogenesis[20] It does not say that very primitive life cannot form from increasingly
complex molecules.[22]
Evolution is unable to explain • How real was the explosion?

the Cambrian Explosion[2] • Possible causes of the “explosion”
Alleged frauds and forgeries Rebuttal of allegations that past evidence for evolution has
such as Piltdown Man and Haeckel's been overturned
embryo drawings[23] Further information: Icons of Evolution
Evolution is not
Observability of evolution
observable[24][25]
Evolution is only a theory and

Evolution is both a theory and a fact.
not a fact[24][25]
[edit] See also

• Academic Freedom bills
• Christine Comer
• Critical Analysis of Evolution
• Free Speech on Evolution
• Neo-creationism
• Stand up for science
• Teach the controversy
[edit] References
1. ^ The Cons of Creationism, Editorial, The New York Times, June 7, 2008
2. ^ a b c d Opponents of Evolution Adopting a New Strategy, Laura Beil, New York Times, June
4, 2008
3. ^ See also, for example, List of scientific societies rejecting intelligent design and Objections
to evolution
4. ^ Those so concluding have included:
• Americans United for Separation of Church and State : Dinosaurs Spotted In Texas!,
Sandhya Bathija, November 20, 2008;
• The National Center for Science Education: "Strengths and weaknesses" nixed in
Texas, December 24th, 2008;
• The Houston Chronicle: It's time for education to evolve, Lisa Falkenberg, Nov. 24,
2008;
• "588 scientists at Texas universities and 777 other scientists across the state":
Scientist statement, 21st Century Science Coalition, cited in Professors debate creationism's
place in public schools, Lauren Rausch and Rylee Nye, Texas Christian University Daily
Skiff, 25 November 2008; Texas university scientists criticize attempts to water down
evolution instruction, Associated Press, October 1, 2008
• Historian of the Intelligent Design Movement Barbara Forrest: The Discovery Institute
Targets Texas, Louisiana Coalition for Science
• The New York Times: The Cons of Creationism, Editorial, June 7, 2008, Texas Two-
Step, Editorial, The New York Times, January 25, 2009.
5. ^ What is "Intelligent Design" Creationism?, National Center for Science Education, October
17th, 2008
6. ^ Concern mounting about Texas state science standards, National Center for Science
Education, June 5th, 2008
7. ^ Professors debate creationism's place in public schools, Lauren Rausch and Rylee Nye,
Texas Christian University Daily Skiff, 25 November 2008
8. ^ Don't water down science curriculum, San Antonio Express-News, 1 December 2008
9. ^ Texas Two-Step, Editorial, The New York Times, January 25, 2009
10.^ Split Outcome in Texas Battle on Teaching of Evolution, James C. McKinley Jr., The New
York Times, January 23, 2009
11.^ Evolution teaching provision fails first test, Gary Scharrer, San Antonio Express-News, 23
January 2009
12.^ [http://www.chron.com/disp/story.mpl/front/6227807.html Scientists: Board proposals
undermine evolution teaching, Gary Charrer, Houston Chronicle, January 23, 2009
13.^ "Weaknesses" by the back door in Texas, National Center for Science Education, March
14th, 2009
14.^ Over in Roseville, National Center for Science Education, September 11th, 2007
15.^ What Happens When You Challenge A School's Science Curriculum, Larry Caldwell, Salvo
magazine, Winter 2008
16.^ http://www.house.mo.gov/billtracking/bills091/biltxt/intro/HB0656I.htm
17.^ Antievolution bill dead in Missouri, May 15, 2009
18.^ a b It's time for education to evolve, Lisa Falkenberg, Houston Chronicle, Nov. 24, 2008
19.^ EVOLUTION, CREATIONISM & PUBLIC SCHOOLS: Surveying What Texas Scientists
Think about Educating Our Kids in the 21st Century, Texas Freedom Network
20.^ a b c Study evolution facts and judge for yourself, Scott Lane, president of the San Antonio
Bible Based Sciences Association, San Antonio Express-News, 12 December 2008
21.^ Steven L. Morris (2005) Creationism and the Laws of Thermodynamics Reports of the
National Center for Science Education Volume 25, issue 5-6 pp 31–32
22.^ CB000: Law of Biogenesis, TalkOrigins Archive
23.^ It’s right to ask questions about evolution, Ken Mercer, San Antonio Express-News, 14
December 2008
24.^ a b Texas: Your “Weaknesses” Are Weak — And Old, Too, Wesley R. Elsberry, 20 Nov 2008
25.^ a b Look who’s determining science standards in Texas, Nick Matzke, Panda's Thumb
(blog), November 21, 2008

• Index to Creationist Claims at TalkOrigins Archive
• Spontaneous Generation and the Origin of Life by John S. Wilkins
• Archived Audio Files of Texas SBOE meetings
• Transcript (and link to audio file) of a lecture given by Texas SBOE Chairman Don McLeroy
on Evolution and Creationism
Retrieved from "http://en.wikipedia.org/wiki/Strengths_and_weaknesses_of_evolution"
Categories: Intelligent design movement | Religion and politics | Intelligent design controversies |
Discovery Institute campaigns | Denialism
W000
List of participants in the creation–evolution
controversy

This is a list of people and organisations involved in the creation-evolution controversy.
Contents
[hide]
• 1 Evolutionary Scientific Community
• 2 Creationist community
• 2.1 Intelligent Design
• 2.2 Old-Earth Creationists
• 2.3 Young-Earth Creationists
• 3 See also
• 4 References
[edit] Evolutionary Scientific Community

• The United States National Academy of Sciences has made a number of statements
opposing creationism. They state, "Creationism, intelligent design, and other claims of supernatural
intervention in the origin of life or of species are not science because they are not testable by the
methods of science."[1]
• The American Association for the Advancement of Science (the world's largest general
scientific society) contrasts the "scientific robustness of the contemporary theory of biological
evolution"[2] with the proposed teaching of intelligent design that will "confuse students about the
nature of science."[3]
• The Royal Society is opposed to creationism being taught as science. The society is
committed to the teaching of evolution as the best explanation for the history of life on earth.[4]
• The National Science Teachers Association (NSTA) supports the teaching of evolutionary
biology in schools, and opposes the teaching of creationism. They hold that science classes should
teach evolution; that teachers should be "nonjudgmental" of students' religious views; and that
"creation science" and "intelligent design" should not be taught.[5]
• The National Center for Science Education was founded in 1981 to oppose creationism and
is led by Eugenie Scott. It has 4,000 members and operates a website. It also runs Project Steve, a
list of 772+ certified Doctorate holding pro-evolution signatories named Steve (or Stephen or some
variant thereof), as a parody of creationist attempts to collect signature lists of experts who doubt
evolution.
• The American Association of Physics Teachers states that "we do not endorse teaching the
'evidence against evolution,' because currently no such scientific evidence exists. Nor can we
condone teaching "scientific creationism," "intelligent design," or other non-scientific viewpoints as
valid scientific theories."[6]
• The American Astronomical Society supports teaching evolution, noting that many
astronomical observations show changes in the universe over a long period of time consistent with
evolution. They state that "'Intelligent Design' fails to meet the basic definition of a scientific idea" and
"does not belong in the science curriculum."[7]
• The American Geophysical Union states that "Earth History and the Evolution of Life Must Be
Taught: Creationism Is Not Science," thus the AGU "opposes all efforts to require or promote
teaching creationism or any other religious tenets as science."[8] In addition, the American
Geological Institute, the Association for Women Geoscientists, the Geological Society of America,
the Paleontological Society, the Society of Vertebrate Paleontology and the Society for Organic
Petrology all have position statements supporting the teaching of evolution and opposing the
teaching of non-scientific ideas.
• The Board of Directors of the American Chemical Society supports "evolution as the only
scientifically accepted explanation for the origin and diversity of species." [9]
• The American Physical Society's governing Council has long expressed its opposition to the
inclusion of religious concepts such as intelligent design and related forms of creationism in science
classes.[10] APS is the world's largest professional body of physicists, representing over 43,000
physicists in academia and industry in the US and internationally.
• Kansas Citizens for Science is a group that is trying to fight the revision of science standards
in Kansas.
• CSICOP and The Skeptics Society are anti-pseudoscience organizations with creationism
among their targets.
• The Talk.Origins Archive is a large website of articles critiquing creationary ideas, plus a
discussion forum; there is an extensive set of links to sites of interest on both sides of the debate -
including True. Origins.
• Talk Reason is a take-off of the talk.origins archive that deals exclusively with debunking
intelligent design.
People
• Richard Dawkins is a noted atheist and outspoken critic of religion and creationism.
• Kenneth R. Miller, a biology professor from Brown University and author and
commentator opposed to the intelligent design movement. Miller as an expert witness for the
plaintiff in Kitzmiller v. Dover Area School District.
• Robert T. Pennock is a philosopher now working on the Avida digital organism project
at Michigan State University where he is an associate professor. The author of many books
and articles critical of intelligent design. He testified as an expert witness for the plaintiff in
Kitzmiller v. Dover Area School District.
• Barbara Forrest is a professor in philosophy in the Department of History and Political
Science at Southeastern Louisiana University. Her testimony as an expert witness for the
plaintiff in Kitzmiller v. Dover Area School District was central to the judge's ruling for the
plaintiff. She and scientist Paul R. Gross co-authored the book Creationism's Trojan Horse:
The Wedge of Intelligent Design (Oxford University Press 2004).
• Brian Alters is an Associate Professor of Education and Sir William Dawson Scholar at
McGill University, where he also holds the Tomlinson Chair in Science Education and is both
founder and Director of the Evolution Education Research Centre. He has taught science
education at both Harvard and McGill Universities, and is regarded as a specialist in evolution
education. Alters testified as an expert witness for the plaintiff in Kitzmiller v. Dover Area
School District.
• Kevin Padian is a Professor of Integrative Biology at the University of California,
Berkeley, Curator of Paleontology, University of California Museum of Paleontology and
President of the National Center for Science Education. Padian's area of interest is in
vertebrate evolution. He served as an expert witness for the plaintiffs in Kitzmiller v. Dover
Area School District where his testimony was repeatedly cited in the court's decision.
• Michael Ruse is a philosopher of science, working on the philosophy of biology, and is
well known for his work on the argument between creationism and evolutionary biology. Ruse
was a witness for the plaintiff in McLean v. Arkansas.
• The late Carl Sagan and Stephen Jay Gould figure among the well-known scientists
who have been outspoken against creationism.
• Wesley R. Elsberry hosts The Panda's Thumb blog which sponsors articles and posts
by some of the most active debaters of creationists and Intelligent Design advocates.
• PZ Myers, a biologist at the University of Minnesota Morris, and an outspoken critic of
creationism on his blog Pharyngula.
[edit] Creationist community

[edit] Intelligent Design
• The Discovery Institute is a Seattle-based think tank which has been the primary driver
behind intelligent design. Its members include Phillip E. Johnson - father of the intelligent design
movement, Stephen C. Meyer, Michael Behe and William Dembski. Its goal as stated in its Wedge
strategy document is to "defeat [scientific] materialism" represented by evolution, "reverse the stifling
materialist world view and replace it with a science consonant with Christian and theistic
convictions" ... "We are building on this momentum, broadening the wedge with a positive scientific
alternative to materialistic scientific theories, which has come to be called the theory of intelligent
design (ID). Design theory promises to reverse the stifling dominance of the materialist worldview,
and to replace it with a science consonant with Christian and theistic convictions."[11] The institute's
ultimate goal is to "renew" American culture by shaping public policy to reflect conservative Christian,
namely evangelical Protestant, values.[12]
Persons
• Phillip E. Johnson is considered many to be the father of the intelligent design
movement but has advocated for big tent inclusion of creationists in his proposed attack on
philosophical naturalism.
• Raymond Bohlin, Ph.D., is the president of Probe Ministries and a fellow of the
Discovery Institute. Bohlin received his Ph.D. in molecular and cell biology from the University
of Texas at Dallas and has published in the Journal of Thermal Biology, Journal of the
American Scientific Affiliation and the Journal of Mammalogy. He also authored the book The
Natural Limits to Biological Change in 1984.
• Cornelius G. Hunter, Ph.D., is an adjunct professor of biophysics at Biola University.
His research has mainly been in nonlinear systems and molecular biophysics. He is known as
an author and as a proponent of intelligent design. Hunter is a Fellow of the Discovery
Institute, hub of the intelligent design movement.[13]
• Jonathan Wells, author of Icons of Evolution and other intelligent design books and
popular articles.
• Thomas E. Woodward is professor of missions, evangelism and science at Trinity
College of Florida/Dallas Theological Seminary (Tampa Bay Extension) and a prominent
Christian apologist. Woodward has published widely defending intelligent design and attacking
Darwin's theory of evolution.
[edit] Old-Earth Creationists

• The American Scientific Affiliation is an organization of professional scientists who also have
a commitment to the Christian faith and has been in existence since 1948. There has been long-
standing dialog in this organization between members who believe that there is no conflict between
evolutionary science and religious ideas and other members who believe that there is a conflict.
• Reasons to Believe is a progressive creationist organisation founded in 1986 by Hugh Ross.
It publishes a number of books and operates a website. Ross opposes biological evolution but
accepts mainstream theories of geological and astronomical history.
• Answers In Creation is an old-earth creationist website that supports both progressive
creationists and theistic evolutionists. This is accomplished by examining young-earth creationist
arguments and showing the flaws they contain.
[edit] Young-Earth Creationists

• The Creation Research Society, an organization that limits voting members to those with a
postgraduate degree, supports the study of origins with regard to creation science.
• The Institute for Creation Research is based in San Diego and was founded in 1970 by
Henry Morris. It is now led by his son, John Morris. ICR publishes a number of books and
newsletters, as well as producing radio spots and operating a website and a small museum.
• Answers in Genesis (AiG) is a Christian apologetics organization devoted to the beliefs of
Young Earth creationism, specifically a plain reading of the first chapters of the Book of Genesis. Ken
Ham is a notable creationist from AiG.
• The Center for Scientific Creation, founded by creationist Dr. Walter Brown, is dedicated to
studying origins from two different perspectives. It studies the earth as it exists today and formulates
theories about what past events could have occurred to generate what we see today. It also looks at
the Genesis account of origins and history, and formulates theories and predictions (of which there
are 38) that science has not yet discovered, but based on Dr. Brown's theories, will be discovered
when technology and research is applied in those areas. Creationists claim that some of his
predictions of scientific discovery have already been found to be true, including his prediction about
comet composition, discovered by the Deep Impact Mission on 4 July 2005.[14]
• The True.Origins Archive is a website that responds to claims made on the Talk.Origins
Archive.
• The Center for Origins Research, at Bryan College.
• Probe Ministries is an evangelical Christian organization founded in 1973 by James F.
Williams Jr. and Jon Buell, based in Richardson, Texas. It is a Christian worldview and apologetics
ministry headed by Ray Bohlin, a fellow of the Discovery Institute.[15]
• Christian Answers provides online access to "over 45-thousand files" of Christian apologetics
(including creationist) materials in 42 languages. Team members behind Christian Answers include:
AIIA Institute; Answers in Genesis; Associates for Biblical Research; Creation Research Society;
Eden Communications/Films for Christ; Ray Comfort/Living Waters Summit Ministries. Christian
Answers maintains a list of scientists that subscribe to creationism.[16]
• The Creation Science Association of Mid America (CSAMA) is Young Earth creationist
organization[17] based in St Louis, Missouri.[18] In 1999 the Kansas State Board of Education relied
heavily on CSAMA material in constructing science standards that minimized the tuition of evolution.
[19]
Persons
• Ken Ham is the president of Answers in Genesis USA. A vocal advocate for a literal
interpretation of the Book of Genesis, his cross-country speaking tours and many books make
him one of the better known young-Earth creationists.
• Henry Morris and John Whitcomb in the early 1960s co-authored The Genesis Flood,
the book credited with reviving interest in creation as an alternative to evolution. Dr. Morris is
considered the "father" of modern creationism.
• Duane Gish is a creationist who has become well-known for debating evolutionists
across America and in other countries. He is also Senior Vice President of ICR. His Creation
Scientists Answer Their Critics was a creationist response to Strahler's book (see below) and
many other anti-creationist books.
• Robert V. Gentry concluded that a phenomenon,, "polonium haloes", was an indication
of a young earth. Additionally, Gentry has devised his own creationist cosmology.
• Kent Hovind, aka Dr. Dino, is a creationist enthusiast who started a creationist theme
park and tours churches arguing against evolution. He has been the proponent of a number of
ideas, including advocating that dinosaurs lived at the same time as human beings. Hovind
has been at the center of a number of controversies including a questionable doctoral degree
granted by a university without official accredation and is currently serving a federal prison
term for various crimes related to failure to pay federal income and employment taxes.
• Walt Brown is a famous proponent of creation science including flood geology and
creationist cosmologies. He runs his own ministry called the Center for Scientific Creation and
is famous for claiming that "evolutionists" refuse to debate him.
[edit] See also

• A Scientific Dissent from Darwinism
• A Scientific Support for Darwinism
• Clergy Letter Project, a signed statement by 10,000 Christian clergy members rejecting
Creationism.
• Project Steve
• Level of support for evolution
• Conflict thesis
[edit] References
1. ^ Conclusion, Science and Creationism, National Academy of Sciences
2. ^ Dialogue on Science, Ethics and Religion at the Wayback Machine (archived February 26,
2006).
3. ^ AAAS Statement on Changes to Kansas Science Education Standards
4. ^ Royal Society press release
5. ^ NSTA Position Statement: The Teaching of Evolution
6. ^ AAPT Statement on the Teaching of Evolution and Cosmology
7. ^ AAS press release
8. ^ Earth History and the Evolution of Life Must Be Taught: Creationism Is Not Science
9. ^ Evolution Under Fire
10.^ APS statement on creationism
11.^ Wedge Strategy Discovery Institute, 1999.
12.^ "Five Year Objectives. Spiritual & cultural renewal: Mainline renewal movements begin to
appropriate insights from design theory, and to repudiate theologies influenced by materialism; Major
Christian denomination(s) defend(s) traditional doctrine of creation & repudiate(s); Darwinism
Seminaries increasingly recognize & repudiate naturalistic presuppositions; Positive uptake in public
opinion polls on issues such as sexuality, abortion and belief in God" Wedge Strategy Discovery
Institute, 1999.
13.^ Hunter's biography, Discovery Institute
14.^ In the Beginning: Compelling Evidence for Creation and the Flood - Comet Composition
15.^ "Ray Bohlin". Probe Ministries. 2008.
http://www.probe.org/site/c.fdKEIMNsEoG/b.4415415/k.936C/Dr_Ray_Bohlin.htm. Retrieved 2008-
12-17.
16.^ Creationists holding DOCTORATES IN SCIENCE, Who's who in Creation/Evolution
17.^ Creationism's Trojan Horse, p222
18.^ Evolution Vs. Creationism, Eugenie Scott, Niles Eldredge, p103
19.^ The Christian Right in American Politics, John Clifford Green, Mark J. Rozell, Clyde Wilcox,
p 157
Retrieved from "http://en.wikipedia.org/wiki/List_of_participants_in_the_creation
%E2%80%93evolution_controversy"
Categories: Creationism | Evolution and religion

W000
Adaptive radiation

Four of the 14 finch species found on the Galápagos Archipelago, are thought to have evolved by an
adaptive radiation that diversified their beak shapes to adapt them to different food sources.
In evolutionary biology, an adaptive radiation is the evolution of ecological and phenotypic diversity
within a rapidly multiplying lineage.[1] Starting with a recent single ancestor, this process results in the
speciation and phenotypic adaptation of an array of species exhibiting different morphological and
physiological traits with which they can exploit a range of divergent environments. [1]
Adaptive radiation, a characteristic example of cladogenesis, can be graphically illustrated as a
"bush", or clade, of coexisting species (on the tree of life). [2]
Contents
[hide]
• 1 Identification
• 2 Causes
• 2.1 Innovation
• 2.2 Opportunity
• 3 See also
• 4 References
[edit] Identification
Four features can be used to identify an adaptive radiation:[1]
1. A common ancestry of component species: specifically a recent ancestry. Note that this is
not the same as a monophyly in which all descendants of a common ancestor are included.
2. A phenotype-environment correlation: a significant association between environments and
the morphological and physiological traits used to exploit those environments.
3. Trait utility: the performance or fitness advantages of trait values in their corresponding
environments.
4. Rapid speciation: presence of one or more bursts in the emergence of new species around
the time that ecological and phenotypic divergence is underway.
[edit] Causes
[edit] Innovation
The evolution of a novel feature may permit a clade to diversify by making new areas of
morphospace accessible. A classic example is the evolution of a fourth cusp is the mammalian tooth. This
trait permits a vast increase in the range of foodstuffs which can be fed on. Evolution of this character has
thus increased the number of ecological niches available to mammals. The trait arose a number of times in
different groups during the Cenozoic, and in each instance was immediately followed by an adaptive
radiation.[3] Birds find other ways to provide for each other, i.e. the evolution of flight opened new avenues
for evolution to explore, initiating an adaptive radiation.[4] Other examples include placental gestation (for
eutherian mammals), or bipedal locomotion (in hominins).[2]
[edit] Opportunity
Adaptive radiations often occur as a result of an organism arising in an environment with unoccupied
niches, such as a newly formed lake or isolated island chain. The colonizing population may diversify rapidly
to take advantage of all possible niches.
In Lake Victoria, an isolated lake which formed recently in the African rift valley, over 300 species of
cichlid fish adaptively radiated from one parent species in just 15,000 years.
Adaptive radiations commonly follow mass extinctions: following an extinction, many niches are left
vacant. A classic example of this is the replacement of the non-avian dinosaurs with mammals at the end of
the Cretaceous, and of brachiopods by bivalves at the Permo-Triassic boundary.
[edit] See also
• Evolutionary radiation—a more general term to describe any radiation
• Cambrian explosion—the most famous evolutionary radiation
• List of adaptive radiated Hawaiian honeycreepers by form
• List of adaptive radiated marsupials by form
[edit] References
1. ^ a b c Schluter, Dolph (2000). The Ecology of Adaptive Radiation. Oxford University Press.
pp. 10–11. ISBN 019850523X. http://www.google.com/books?id=Q1wxNmLAL10C&pg=PA10.
2. ^ a b Lewin, Roger (2005). Human evolution : an illustrated introduction (5th ed.). p. 21.
ISBN 1-4051-0378-7. http://books.google.com/books?doi=SopsLRo1QyUC&pg=PA21.
3. ^
4. ^ Feduccia, Alan (1999). The Origin and Evolution of Birds.

• Wilson, E. et al. Life on Earth, by Wilson, E.; Eisner, T.; Briggs, W.; Dickerson, R.;
Metzenberg, R.; O'brien,R.; Susman, M.; Boggs, W.; (Sinauer Associates, Inc., Publishers, Stamford,
Connecticut), c 1974. Chapters: The Multiplication of Species; Biogeography, pp 824–877. 40
Graphs, w species pictures, also Tables, Photos, etc. Includes Galápagos Islands, Hawaii, and
Australia subcontinent, (plus St. Helena Island, etc.).
• Leakey, Richard. The Origin of Humankind—on adaptive radiation in biology and human
evolution, pp. 28–32, 1994, Orion Publishing.
• Grant, P.R. 1999. The ecology and evolution of Darwin's Finches. Princeton University
Press, Princeton, NJ.
• Mayer, Ernst. 2001. What evolution is. Basic Books, New York, NY.
• Kemp, A.C. 1978. A review of the hornbills: biology and radiation. The Living Bird 17: 105–
136.
Retrieved from "http://en.wikipedia.org/wiki/Adaptive_radiation"
Categories: Speciation | Evolutionary biology terminology

W000
Aquatic ape hypothesis


The aquatic ape hypothesis (AAH) is an alternative explanation of human evolution which theorizes
that the common ancestors of modern humans spent a period of time adapting to life in a partially-aquatic
environment. The theory is based on differences between humans and great apes, and apparent similarities
between humans and some aquatic mammals. First proposed in 1942 and expanded in 1960, its greatest
proponent has been the writer Elaine Morgan, who has spent more than forty years discussing the AAH.
While it is uncontroversial that both H. neanderthalensis and early H. sapiens were better suited to
aquatic environments than other great apes,[1][2] and there have been theories suggesting protohumans
underwent some adaptations due to interaction with water[3] the sort of radical specialization posited by the
AAH has not been accepted within the scientific community as a valid explanation for human divergence from
related primates. It has been criticized for possessing a variety of theoretical problems, for lacking evidentiary
support, and for there being alternative explanations for many of the observations suggested to support the
theory. Morgan has also suggested that her status as an academic outsider has hindered acceptance of the
theory.
Contents
[hide]
• 1 History
• 2 The hypothesis
• 3 Criticisms
• 3.1 Theoretical considerations
• 3.2 Habitat
• 3.3 Anatomical and physiological claims
• 4 Reception
• 5 See also
• 6 Footnotes
[edit] History
In a 1942 book, the German pathologist Max Westenhöfer published the idea of humans evolving in
proximity to water with the statement "The postulation of an aquatic mode of life during an early stage of
human evolution is a tenable hypothesis, for which further inquiry may produce additional supporting
evidence."[4]
In 1930 marine biologist Alister Hardy theorised that humans may have had ancestors more aquatic
than previously imagined. Because it was outside his field and he was aware of the controversy it would
cause, Hardy delayed reporting his theory. After he had become a respected academic, Hardy finally voiced
his thoughts in a speech to the British Sub-Aqua Club in Brighton on 5 March 1960, not expecting any
attention, but it was reported in a national newspaper. This generated immediate controversy in the field of
paleoanthropology. Consequently Hardy published the theory in an article in New Scientist on 17 March
1960. He defined his idea:
My thesis is that a branch of this primitive ape-stock was forced by competition from life in the
trees to feed on the sea-shores and to hunt for food, shell fish, sea-urchins etc., in the shallow
waters off the coast. I suppose that they were forced into the water just as we have seen happen
in so many other groups of terrestrial animals. I am imagining this happening in the warmer
parts of the world, in the tropical seas where Man could stand being in the water for relatively
long periods, that is, several hours at a stretch.[5]
The idea received some interest after the article was published,[6] but was generally ignored by the
scientific community thereafter. In 1967, the hypothesis was briefly mentioned (and dismissed) in The Naked
Ape, a book by Desmond Morris in which can be found the first use of the term "aquatic ape".[7] Writer Elaine
Morgan read about the idea in Morris' book and was struck by its potential explanatory power, becoming its
main promoter and publishing six books over the next 40 years.[8] The context of initial presentations of the
idea (a popular work and a political text) prevented the AAH from garnering serious interest or an exploration
of its scientific merit.[9]
Despite maintaining some popular and scientific interest over several decades, the aquatic ape
theory has not been accepted by a large majority of researchers within the field of paleoanthropology.[10] A
small but active number of promoters working outside of mainstream paleoanthropology, non-anthropologists
and the occasional professional still cite and bring attention to the AAH but it has never been completely
discredited to its adherents nor fully explored by researchers.[9]
[edit] The hypothesis

The AAH suggests that many of the features that distinguish humans from their nearest evolutionary
relatives can be explained through a period of aquatic adaptation in which protohumans spent time wading,
swimming and feeding on the shores of fresh, saline or brackish waters (though there has been
disagreement and modification of the theory regarding the salinity of the purported watery environment[11]
[12][13]) and suggests comparisons with other aquatic or semiaquatic species with similar characteristics.
Some observations include:
• Bipedalism out of water causes considerable problems for the back, knees and organs, while
water would support the joints and torso and permit breathing[14][15]
• Humans are relatively hairless compared to great apes, similar to the hairlessness of land-
dwelling rhinoceros and elephant which both have aquatic ancestors;[16] what body hair humans do
have also follows water flow-lines[17]
• Increased subcutaneous fat for insulation, especially in human infants[5]
• A descended larynx[17][18]
• A hooded nose, muscular nostril aperture control and the philtrum preventing water from
entering the nostrils[17]
• Extensive coverage of the skin by sebaceous glands[19]
• The requirement of the human brain for certain nutrients including iodine[20] and some
essential fatty acids[21] which are most easily found and absorbed in seafood[22]
• Voluntary breath control which allows diving and swimming,[14][23] and a more streamlined
shape compared to other apes[17]
• The mammalian diving reflex which occurs when the head is immersed in cold water[24]
• Vestigial webbing between the fingers[25]
• The waxy coating found on newborns[17]
• Certain morphological adaptations within the kidney[26]
The timelines hypothesized for a period of adjusting to aquatic living vary from the Miocene about 6
million years ago,[5] to nearly 2 million years ago in the late Pliocene or early Pleistocene.[27][28] It is also
theorized that the semi-aquatic phase occurred when protohumans migrated along the southern Asian
coastline during a previous ice age when sea levels were considerably lower; this is also proffered as a
reason why human fossils are not found in aquatic habitats, as those regions were inundated when the polar
ice caps melted.[29]
Review of the individual claims used as evidence for the AAH generally does not support the
hypothesis overall, and most of these traits have an explanation within conventional theories of human
evolution.[9] Other authors have suggested that wading and other interactions with watery environments may
have provided a less extreme but still present role in human evolution.[3]
[edit] Criticisms
Several theoretical problems have been found with the AAH, and some claims made by the AAH
have been challenged as having explanations aside from a period of aquatic adaptation.[9]
[edit] Theoretical considerations
The AAH has been criticized for containing multiple inconsistencies and lacking evidence from the
fossil record to support its claims.[9][30] It is also described as lacking parsimony, despite purporting to be a
simple theory uniting many of the unique anatomical features of humans.[9]
Though describing the theory as plausible, Henry Gee went on to criticize it for being untestable, as
most of the evolutionary adaptations described by Morgan would not have fossilized. Gee also stated that,
while purely aquatic mammals such as whales show strong skeletal evidence of adaptation to water, humans
and human fossils lack such adaptations; that there are many hypothetical and equally plausible scenarios
explaining the unique characteristics of human adaptation without involving an aquatic phase of evolution;
and that proponents are basing arguments about past adaptations on present physiology, when humans are
not significantly aquatic.[31] There is ultimately only circumstantial evidence to suggest, and no solid
evidence to support the AAH.[32][33] ScienceBlogs author Greg Laden has described the AAH as a "human
evolution theory of everything" that attempts to explain all anatomical and physiological features of humans
and is correct in some areas only by chance. Laden also states that the AAH was proposed when knowledge
of human evolutionary history was unclear, while more recent research has found that many human traits
have emerged at different times over millions of years, rather than simultaneously due to a single
evolutionary pressure.[10]
[edit] Habitat
Morgan presented the AAH as an alternative to the "savanna model", which uses very vague
descriptive statements portraying protohumans as moving out from forested environments and into a hot dry
savanna. However, this idea has been called a caricature of the actual environments in which protohumans
are thought to have evolved, and presents a false dichotomy as more recent theories propose a tree or
forest-based habitat providing the driving forces for adaptation,[32] and a straw man of the actual theories
and arguments used in the study of paleoanthropology. Morgan further criticized scientists for admitting they
were uncertain regarding the reasons for the development of hairlessness, bipedalism, brain size and
speech. This ignores the fact that science legitimately admits ignorance when it is unclear and that a lack of
"final answers" does not legitimize a competing theory by default.[9]
The belief that wading into shallow water would help proto-humans avoid dry-land predation
discounts the risks presented by aquatic animals such as crocodiles and hippopotamuses that present a
current risk to Africans living near bodies of water,[34] and that protohumans lacked the fangs, claws or size
to defend themselves from these threats.[35]
The susceptibility of humans to waterborne parasites have been suggested as evidence against the
AAH,[35] though the presence of certain parasites that appear to co-exist with humans has also been
presented as evidence for the AAH.[3][36]
[edit] Anatomical and physiological claims

• Hairlessness – Most aquatic mammals that are comparably sized to humans are not hairless,
but have dense, insulating fur and swim very well, with fatty layers beneath the skin.[34] Aquatic
mammals do not vary greatly in their body hair, while humans do.[10] Hairless skin is also only an
advantage for fully-aquatic mammals that dive, swim quickly or migrate long distances such as
whales and dolphins,[35] and only appears and is an advantage for extremely large aquatic
mammals who would overheat with large amounts of body hair, who are fully-aquatic and have
evolved as an aquatic species for millions of years. The loss of body hair is also explainable through
a lower parasite load, and maintenance through sexual selection.[37] Furthermore, while shaving
human swimmers to eliminate the little body hair that remains results in a minor decrease in drag,[38]
[39] this cannot be extrapolated to a beneficial effect of loss of a full coat of fur, which has been
shown to have superior drag reduction ability.[40] While relative hairlessness and hair direction is
cited as an adaptation to swimming and diving, there is no evidence of similar skeletal or soft tissue
adaptations that are expected to accompany such adaptations.[9]
• Breath control – The position, evolutionary timing of changes, and size of the nerve openings
in the vertebrae suggest that breath control in humans improved because of the increased
complexity and use of speech rather than an aquatic phase of evolution.[41] In addition, breath
control is thought to be preceded by bipedalism, which frees the muscles around the upper torso
from locomotion and allows breathing rates to occur independent of locomotion. Voluntary speech is
thought to be a sufficient evolutionary pressure to explain breath control, independent of other
explanations. The vocalizations of dolphins and other aquatic species are not thought to be
comparable to humans. In addition, certain birds have speech and breath control comparable to
humans, without a phase of aquatic adaptation.[9]
• Diet – a broad terrestrial diet would ensure sufficient access to required essential fatty acids
without a high consumption of seafood[42] and the "best" fats found in fish are from cold water fish
that did not occupy the same coastal environments as humans. In addition, the requirements of these
fats are very minimal, with no evidence that extra fats would result in an evolutionary pressure
towards a larger brain. Humans without access to shoreline foods also develop normal brains.[9][43]
• Diving reflex – the mammalian diving reflex is exhibited by terrestrial mammals as well as
aquatic ones and humans have not been compared to other living hominoids; there is not enough
information on for this reflex for it to be used to support the AAH.[9]
• Body fat – the subcutaneous fat distribution in humans is more similar to a domesticated
animal than an aquatic one, and is nearly identical to that of other primates. The subcutaneous fat of
aquatic mammals and humans also seems to serve different uses – it forms the streamlined shape of
seals, while in humans it is used for sexual selection.[44] In addition, the distribution of fat and blood
vessels allows for improved thermoregulation, as hot blood from the body can bypass the fat to
radiate heat through the skin.[9]
• Bipedalism – the disadvantages cited for bipedalism within the AAH are often the result of
comparing humans to medium, terrestrial quadrupeds, but human evolution never included a period
of quadrupedal locomotion. Instead, human evolution features mainly brachiation, suspension and
climbing as the primary method of transportation, with a gradual increase in bipedal locomotion over
time. In addition, the elongated lower limbs of humans, which is explained as improving swimming
speeds, appears only after the evolution of the Homo genus.[9]
• Descended larynx – the human larynx is not shaped like the larynxes of aquatic animals; it
forms and descends as an infant begins to speak, making it easier to aspirate water and drown.
Additionally, a descended larynx is not unique to aquatic animals, and permanently or temporarily
descended larynxes are seen in dogs, pigs, goats, monkeys,[45] big cats,[46] deer,[47] and young
chimps.[48] Mainstream anthropology explain the descended larynx as an adaptation to improve
vocalizations by increasing the number of pronounceable vowels and improving the ability of humans
to control their speech.[9]
• Nose shape – the shape of the human nose is extremely variable within the species, and
believed to be related to climatic adaptations and the warming and moistening of air before it enters
the respiratory tract, not to prevent water entry while swimming. In addition, the muscles surrounding
the nose show no evidence of having been previously more developed, but are part of a complex of
muscles that are specially developed in humans to show emotion and aid in communication.[9]
• Interdigital webbing – Morgan's claims for syndactylism, the presence of webbing between
the fingers, were based on the purported "rareness" of birth defects "adding" features normally
thought absent from an evolutionary order. Interdigital webbing is not the "addition" of new tissue, it
results from the failure to eliminate skin cells connecting the fingers, a process common to all
tetrapods.[9]
• Sebaceous gland – many aquatic animals have rudimentary or no sebaceous glands. In
humans, sebaceous glands become active during puberty with men having far more than women
while women have much better scent receptors. This suggests the glands are sexually dimorphic for
sexual selection rather than waterproofing. In seals that use sebaceous glands for waterproofing, the
glands are active from birth and are secreted by hard, keratinized skin that is very different from
human skin.[citation needed]
• Swimming – humans are inefficient swimmers, with shapes that are not well suited to rapid
travel through water.[49] Swimming is also a learned trait, and though newborns are able to propel
themselves inefficiently through water, they are unable to lift their faces to breathe.[50]
Generally the evidence provided for the AAH is equally well accounted for by land-based adaptations
without needing to posit an aquatic phase of human development. In addition, the AAH is contradictory in
several places; the AAH theorizes humans developed some unique skin features due to adaptation to water,
but other features emerged after leaving the habitat, and the specialization that is hypothesized for an
aquatic life are uneven, with humans lacking many truly specialized features of aquatic species (such as
head shape, repositioned nostrils and streamlining of the body). Parallels made by proponents of the AAH
between humans and the proboscis monkey, which shows mainly behavioral adaptations to a water-based
habitat, contradicts any claims of anatomical evidence for the theory.[9] Many species of modern primates
demonstrate some sort of aquatic behaviors (such as swimming, wading or diving) and use of aquatic
environments (for thermoregulation, display behavior, range, diet and predation) but many do not display the
traits posited by AAH, suggesting the traits listed above facilitate aquatic behavior rather than evolving as a
result of it.[51]
[edit] Reception
The AAH has received little serious scrutiny from mainstream paleoanthropologists[52] and has been
met with significant skepticism.[53] The AAH is thought by some anthropologists to be accepted readily by
popular audiences, students and non-specialist scholars because of its simplicity.[9] In 1987 a symposium
was held in Valkenburg, the Netherlands, titled "Aquatic Ape: Fact or fiction?", which published its
proceedings in 1991.[54] The chief editor summarized the results of the symposium as failing to support the
idea that human ancestors were aquatic, but there is also some evidence that they may have swum and fed
in inland lakes and rivers with the result that modern humans can enjoy brief periods of time spent in the
water.[55] The results of the conference were reported in the anthropological press as having rejected the
hypothesis.[9] A review of Morgan's book The Scars of Evolution stated that it did not address the central
questions of anthropology – how the human and chimpanzee gene lines diverged – which was why it was
ignored by the scholarly community. The review also stated that Morgan ignored the fossil record and skirted
the absence of evidence that australopithecine underwent any adaptations to water, making the hypothesis
impossible to validate from fossils.[30]
Morgan has claimed the AAH was rejected for a variety of reasons unrelated to its explanatory
power: old academics were protecting their careers, sexism on the part of male researchers, and her status
as a non-academic intruding on academic debates. Despite modifications to the theory and occasional forays
into scientific conferences, the AAH has neither been accepted as a mainstream theory nor managed to
venture a genuine challenge to orthodox theories of human evolution.[56] However, anthropologist Colin
Groves has stated that Morgan's theories are sophisticated enough that they should be taken seriously as a
possible explanation for bipedalism.[57]
The appeal of the theory has been explained in several ways:[9]
1. The theory appears to offer absolute answers while orthodox science is qualified and
reserved, a situation which has great appeal to students and the public
2. Unusual ideas challenge the authority of science and scientists, which appeals to antiscience
sentiments
3. The AAH as developed by Morgan has a strong feminist component, which particularly
appeals to a specific, feminist audience
4. The AAH can be explained simply and easily, lacking the myriad details and complicated
theorizing involved in dealing with primary sources and materials
5. The AAH uses negative arguments, pointing to the flaws and gaps in conventional theories;
though the criticisms of mainstream science and theories can be legitimate, in this case, as with
Creationism and AIDS denialism the flaws in one theory do not automatically prove a proposed
alternative is true
6. The consensus views of conventional anthropology are complicated, require specialized
knowledge and qualified answers, and the investment of considerable time to understand.
[edit] See also

• Endurance running hypothesis
[edit] Footnotes
1. ^ Walter, R.; Buffler, R.; Bruggemann, J.; Guillaume, M.; Berhe, S.; Negassi, B.; Libsekal, Y.;
Cheng, H. et al. (May 2000). "Early human occupation of the Red Sea coast of Eritrea during the last
interglacial". Nature 405 (6782): 65–69. doi:10.1038/35011048. ISSN 0028-0836. PMID 10811218.
edit
2. ^ Stringer, C.; Finlayson, J.; Barton, R.; Fernández-Jalvo, Y.; Cáceres, I.; Sabin, R.; Rhodes,
E.; Currant, A. et al. (Sep 2008). "Neanderthal exploitation of marine mammals in Gibraltar" (Free full
text). Proceedings of the National Academy of Sciences of the United States of America 105 (38):
14319–14324. doi:10.1073/pnas.0805474105. ISSN 0027-8424. PMID 18809913. PMC 2567146.
http://www.pnas.org/cgi/pmidlookup?view=long&pmid=18809913. edit
3. ^ a b c Niemitz, C. (2010). "The evolution of the upright posture and gait--a review and a new
synthesis.". Die Naturwissenschaften 97 (3): 241–263. doi:10.1007/s00114-009-0637-3.
PMID 20127307. edit
4. ^ Westenhöfer, M. (1942). Der Eigenweg des Menschen. Mannstaedt & Co.
5. ^ a b c Hardy, A. (1960). "Was man more aquatic in the past" (pdf). New Scientist 7: 642–645.
http://www.riverapes.com/AAH/Hardy/Hardy1960.pdf.
6. ^ Sauer, C O. (1960). "Seashore – Primitive home of man?". Proceedings of the American
Philosopical Society 106 (1): 41–47.
7. ^ Morris, Desmond (1967). The Naked Ape. McGraw-Hill. pp. 29. ISBN 0 09 948201 0.
8. ^ Morgan's books on the topic include:
• Morgan, Elaine (1972). The Descent of Woman. Souvenir Press. ISBN 0 285 62700
7.
• Morgan, Elaine (1982). The Aquatic Ape. Stein & Day Pub. ISBN 0-285-62509-8.
• Morgan, Elaine (1990). The Scars of Evolution. Souvenir Press. ISBN 0-285-62996-
4.
• Morgan, Elaine (1994). The Descent of the child. Souvenir Press. ISBN 0-285-
63377-5.
• Morgan, Elaine (1997). The Aquatic Ape Hypothesis. Penguin. ISBN 0-285-63518-2.
• Morgan, Elaine (2008). The Naked Darwinist. Eildon Press. ISBN 0-9525620-30.
9. ^ a b c d e f g h i j k l m n o p q r s t Langdon JH (1997). "Umbrella hypotheses and parsimony in
human evolution: a critique of the Aquatic Ape Hypothesis". J. Hum. Evol. 33 (4): 479–94.
doi:10.1006/jhev.1997.0146. PMID 9361254.
10.^ a b c Laden, G (2009-08-04). "Musings on the Aquatic Ape Theory". ScienceBlogs.
http://scienceblogs.com/gregladen/2009/08/musings_on_the_aquatic_ape_the.php. Retrieved 2009-
09-02.
11.^ Ellis DV (1993). "Wetlands or aquatic ape? Availability of food resources". Nutrition and
health 9 (3): 205–17. PMID 8183488.
12.^ Cunnane SC, Plourde M, Stewart K, Crawford MA (2007). "Docosahexaenoic acid and
shore-based diets in hominin encephalization: a rebuttal". Am. J. Hum. Biol. 19 (4): 578–81.
doi:10.1002/ajhb.20673. PMID 17546620.
13.^ Cunnane, S; Stewart K (2010). Environmental Influences on Human Brain Evolution . John
Wiley & Sons. ISBN 978-0-470-45268-4.
14.^ a b Niemitz C (2002). "A Theory on the Evolution of the Habitual Orthograde Human
Bipedalism – The "Amphibisce Generalistheorie"". Anthropologischer Anzeiger 60: 3–66.
15.^ Verhaegen M (1987). "Origin of hominid bipedalism". Nature 325: 305–6.
doi:10.1038/325305d0.
16.^ Morgan, E (1982). The Aquatic Ape. Stein & Day Pub. ISBN 0-285-62509-8.
17.^ a b c d e Morgan, Elaine (1997). The Aquatic Ape Hypothesis. Souvenir Press. ISBN 0-285-
63518-2.
18.^ Crelin, Edmund S (1987). The Human Vocal Tract: Anatomy, Function, Development, and
Evolution. New York: Vantage Press. ISBN 0 533 06967 X.
19.^ Kingdon J (2003). Lowly origin: where, when, and why our ancestors first stood up.
Princeton, N.J: Princeton University Press. pp. 242. ISBN 0-691-05086-4.
20.^ Venturi, S; Bégin ME (2010). "Thyroid Hormone, Iodine and Human Brain Evolution". In
Cunnane S; Stewart K. Environmental Influences on Human Brain Evolution. John Wiley & Sons.
pp. 105–124. ISBN 978-0-470-45268-4.
21.^ Crawford MA (2010). "Long-Chain Polyunsaturated Fatty Acids in Human Brain Evolution".
In Cunnane S; Stewart K. Environmental Influences on Human Brain Evolution. John Wiley & Sons.
pp. 13–32. ISBN 978-0-470-45268-4.
22.^ Ellis DV (1993). "Wetlands or aquatic ape? Availability of food resources". Nutrition and
health (Berkhamsted, Hertfordshire) 9 (3): 205–17. PMID 8183488. ; Cunnane, S., Plourde, M.,
Stewart, K., Crawford, M (2007). "Docosahexaenoic Acid and Shore-Based Diets in Hominin
Encephalization: A Rebuttal". American Journal of Human Biology 19 (4): 578–591.
doi:10.1002/ajhb.20673. PMID 17546620. ; Crawford, M; et al. (2000). "Evidence for the unique
function of docosahexanoic acid (DHA) during the evolution of the modern hominid brain". Lipids 34:
S39–S47. doi:10.1007/BF02562227. PMID 10419087.
23.^ Patrick, John (1991). Human Respiratory Adaptations for Swimming and Diving . Souvenir
Press. ISBN 0-285-63033 4.
24.^ Odent M (1996). We are All Water Babies. Celestial Arts. ISBN 0890877580.
25.^ Roede M (1991). The aquatic ape: fact or fiction?: the first scientific evaluation of a
controversial theory of human evolution. London: Souvenir Press. pp. 99. ISBN 0-285-63033-4.
26.^ Williams M F (2006). "Morphological evidence of marine adaptations in human kidneys".
Medical Hypotheses 66 (2): 247–257. doi:10.1016/j.mehy.2005.09.024. PMID 16263222.
27.^ Verhaegen, M.; Puech, P.F.; Munro, S. (2002). "Aquarboreal ancestors?" (pdf). Trends in
Ecology & Evolution 17 (5): 212–217. doi:10.1016/S0169-5347(02)02490-4.
http://allserv.rug.ac.be/~mvaneech/OP%20Verhaegen%20final%20styled.doc.pdf. Retrieved 2007-
10-29.
28.^ Verhaegen M; Munro S; Vaneechoutte M; Bender R; Oser N (2007). "The original econiche
of the genus Homo: Open Plain or Waterside?" (pdf). SI Muñoz ed. Ecology Research Progress: 155–
186. http://users.ugent.be/%7Emvaneech/Verhaegen%20et%20al.%202007.%20Econiche%20of
%20Homo.pdf.
29.^ Verhaegen M & Munro S (2002). "The continental shelf hypothesis". Nutrition & Health 16:
25–28.
30.^ a b Zihlman, A (1991-01-19). "Review: Evolution, a suitable case for treatment". New
Scientist. Archived from the original on 2008-12-30.
http://web.archive.org/web/20080123085610/http://www.newscientist.com/article/mg12917525.300.h
tml. Retrieved 2009-05-03.
31.^ Gee, H (2001). In search of deep time: beyond the fossil record to a new history of life .
Cornell University Press. pp. 100–101. ISBN 0801487137.
32.^ a b Meier, R (2003). The complete idiot's guide to human prehistory . Alpha Books. pp. 57–
59. ISBN 0028644212.
33.^ Bridgeman, B (2003). Psychology & evolution: the origins of mind. SAGE Publications.
pp. 64. ISBN 0761924795.
34.^ a b Vanstrum GS (2003). The saltwater wilderness. Oxford [Oxfordshire]: Oxford University
Press. pp. 95. ISBN 0-19-515937-3.
35.^ a b c Jablonski, Nina G. (2008). Skin a natural history. Berkeley: University of California
Press. pp. 40–2. ISBN 0-520-25624-7.
36.^ Aspöck H, Walochnik J. (2007). "Die parasiten des menschen aus der sicht der
koevolution". Zugleich Kataloge der oberösterreichischen Landesmuseen Neue Serie 66: 179–254.
37.^ Pagel M; Bodmer W (August 2003). "A naked ape would have fewer parasites" (pdf). Proc.
Biol. Sci. 270 Suppl 1: S117–9. doi:10.1098/rsbl.2003.0041. PMID 12952654.
38.^ Sharp, RL; Costill DI (1989). "Influence of body hair removal on physiological responses
during breaststroke swimming". Medicine and Science in Sports and Exercise 21 (5): 576–580.
PMID 2691818.
39.^ Krüger, J; Mikoleit J; Heck H (2000). "The influence of total body shaving on performance
and lactic acid behaviour in swimming". Deutsche Zeitschrift Fur Sportmedizin 51 (2): 55–8.
40.^ Sokolov, VE (1982). Mammal Skin. Berkeley: University of California Press.
ISBN 0520031989.
41.^ MacLarnon, A.M.; Hewitt, G.P. (1999). "The evolution of human speech: The role of
enhanced breathing control". American Journal of Physical Anthropology 109 (3): 341–363.
doi:10.1002/(SICI)1096-8644(199907)109:3<341::AID-AJPA5>3.3.CO;2-U. PMID 10407464.
42.^ Carlson BA, Kingston JD (2007). "Docosahexaenoic acid biosynthesis and dietary
contingency: Encephalization without aquatic constraint". Am. J. Hum. Biol. 19 (4): 585–588.
doi:10.1002/ajhb.20683. PMID 17546613.
43.^ Milton, K (2000). "Reply to S.C. Cunnane". American Journal of Clinical Nutrition 72 (6):
1586–1588.
44.^ Pond, C (1998). The Fats of Life. Cambridge University Press. pp. 236–8.
ISBN 0521635772.
45.^ Fitch, WT (2002). "Comparative Vocal Production and the Evolution of Speech:
Reinterpreting the Descent of the Larynx"". In Wray A. The Transition to Language. Oxford: Oxford
46.^ Hauser, MD; Fitch WT (2003). "What Are the Uniquely Human Components of the
Language Faculty?". In Christiansen MH Kirby S. Language Evolution: The States of the Art. Oxford
47.^ McElligott, AG; Birrer M; Vannoni E (2006). "Retraction of the mobile descended larynx
during groaning enables fallow bucks (Dama dama) to lower their formant frequencies". Journal of
Zoology 270 (2): 340–345. doi:10.1111/j.1469-7998.2006.00144.x.
48.^ Nishimura T, Mikami A, Suzuki J, Matsuzawa T (June 2003). "Descent of the larynx in
chimpanzee infants". Proc. Natl. Acad. Sci. U.S.A. 100 (12): 6930–3. doi:10.1073/pnas.1231107100.
PMID 12775758.
49.^ Vogel SK (1994). Life in moving fluids: the physical biology of flow . Princeton, N.J:
Princeton University Press. ISBN 0-691-02616-5.
50.^ McGraw, MB (1939). "Swimming behavior of the human infant". Journal of Pediatrics 15:
485–490. doi:10.1016/S0022-3476(39)80003-8. http://psycnet.apa.org/psycinfo/1940-01122-001.
51.^ Kempf, E. (2009). "Patterns of water use in primates". Folia primatologica; international
journal of primatology 80 (4): 275–294. doi:10.1159/000252586. PMID 19864919. edit
52.^ McNeill, D (2000). The Face: A Natural History. Back Bay. pp. 36–37. ISBN 0316588121.
53.^ Graham, JM; Scadding GK; Bull PD (2008). Pediatric ENT. Springer. pp. 27.
ISBN 3540699309.
54.^ Roede, Machteld (1991). Aquatic Ape: Fact of Fiction: Proceedings from the Valkenburg
Conference. Souvenir Press. ISBN 0 285 63033 4.
55.^ Reynolds, Vernon (1991). Cold and Watery? Hot and Dusty? Our Ancestral Environment
and Our Ancestors Themselves: an Overview (in Roede et al. 1991). Souvenir Press. pp. 340.
ISBN 0 285 63033 4.
56.^ Regal, B (2004). Human evolution: a guide to the debates. ABC-CLIO. pp. 208–212.
ISBN 1851094180.
57.^ Groves, Colin (with David W.Cameron) (2004). Bones, Stones and Molecules. Elsevier
Academic Press. pp. 68. ISBN 0 121 56933 0.
• Aquatic ape hypothesis at the Open Directory Project

• Presentation by Elaine Morgan at TED July, 2009; Comment on ScienceBlogs by
paleoanthropologist Greg Laden
• Scuttling the Aquatic Ape Hypothesis by Brian Switek
• Aquatic ape theory: Sink or Swim? – website critical of the AAH
Retrieved from "http://en.wikipedia.org/wiki/Aquatic_ape_hypothesis"
Categories: Human evolution | Hypotheses

W000
Kin selection

Kin selection refers to apparent strategies in evolution that favor the reproductive success of an
organism's relatives, even at a cost to their own survival and/or reproduction. The classic example is a
eusocial insect colony, in which sterile females act as workers to assist their mother in the production of
additional offspring.
The earliest expressions of the basic concepts were by R.A. Fisher in 1930,[1] J. B. S. Haldane in
1955,[2] but it was W. D. Hamilton who truly formalized the concept, in works published in 1963[3] and—most
importantly—in 1964.[4] The term "kin selection" may first have been coined by John Maynard Smith in 1964
when he wrote:
These processes I will call kin selection and group selection respectively. Kin selection has been
discussed by Haldane and by Hamilton. … By kin selection I mean the evolution of
characteristics which favour the survival of close relatives of the affected individual, by
processes which do not require any discontinuities in the population breeding structure.[5]
Kin selection refers to changes in gene frequency across generations that are driven at least in part
by interactions between related individuals, and this forms much of the conceptual basis of the theory of
social evolution. Indeed, some cases of evolution by natural selection can only be understood by considering
how biological relatives influence one another's fitness. Under natural selection, a gene encoding a trait that
enhances the fitness of each individual carrying it should increase in frequency within the population; and
conversely, a gene that lowers the individual fitness of its carriers should be eliminated. However, a
hypothetical gene that prompts behaviour which enhances the fitness of relatives but lowers that of the
individual displaying the behavior, may nonetheless increase in frequency, because relatives often carry the
same gene; this is the fundamental principle behind the theory of kin selection. According to the theory, the
enhanced fitness of relatives can at times more than compensate for the fitness loss incurred by the
individuals displaying the behaviour. As such, this is a special case of a more general model, called inclusive
fitness (in that inclusive fitness refers simply to gene copies in other individuals, without requiring that they be
kin). However the validity of this analysis has recently been challenged [6]
Contents
[hide]
• 1 Hamilton's rule
• 2 Mechanisms
• 3 Kin Selection in evolutionary psychology
• 4 Examples
• 5 Criticism
• 6 See also
• 7 References
[edit] Hamilton's rule

Formally, such genes should increase in frequency when
where
r = the genetic relatedness of the recipient to the actor, often defined as the probability that a
gene picked randomly from each at the same locus is identical by descent.
B = the additional reproductive benefit gained by the recipient of the altruistic act,
C = the reproductive cost to the individual of performing the act.
This inequality is known as Hamilton's rule after W. D. Hamilton who published, in 1964, the first
formal quantitative treatment of kin selection to deal with the evolution of apparently altruistic acts. Altruistic
acts are those that benefit the recipient but harm the actor. The phrase Kin selection, however, was coined
by John Maynard Smith.
Originally, the definition for relatedness (r) in Hamilton's rule was explicitly given as Sewall Wright's
coefficient of relationship: the probability that at a random locus, the alleles there will be identical by descent
(Hamilton 1963, American Naturalist, p. 355). Subsequent authors, including Hamilton, sometimes
reformulate this with a regression, which, unlike probabilities, can be negative, and so it is possible for
individuals to be negatively related, which simply means that two individuals can be less genetically alike
than two random ones on average (Hamilton 1970, Nature & Grafen 1985 Oxford Surveys in Evolutionary
Biology). This has been invoked to explain the evolution of spiteful behaviours. Spiteful behavior defines an
act (or acts) that results in harm, or loss of fitness, to both the actor and the recipient.
In the 1930s J.B.S. Haldane had full grasp of the basic quantities and considerations that play a role
in kin selection. He famously said that, "I would lay down my life for two brothers or eight cousins".[7] Kin
altruism is the term for altruistic behaviour whose evolution is supposed to have been driven by kin selection.
Haldane's remark alluded to the fact that if an individual loses its life to save two siblings, four
nephews, or eight cousins, it is a "fair deal" in evolutionary terms, as siblings are on average 50% identical by
descent, nephews 25%, and cousins 12.5% (in a diploid population that is randomly mating and previously
outbred). But Haldane also joked that he would truly die only to save more than a single identical twin of his
or more than two full siblings.
[edit] Mechanisms
An altruistic case is one where the instigating individual suffers a fitness loss while the receiving
individual benefits by a fitness gain. The sacrifice of one individual to help another is an example of altruism.
Hamilton (1964) outlined two ways in which kin selection altruism could be favoured.
Kin Recognition: Firstly, if individuals have the capacity to recognize kin (kin recognition) and to
adjust their behaviour on the basis of kinship (kin discrimination), then the average relatedness of the
recipients of altruism could be high enough for this to be favoured. Because of the facultative nature of this
mechanism, it is generally regarded that kin recognition and discrimination are unimportant except among
'higher' forms of life (although there is some evidence for this mechanism among protozoa). A special case of
the kin recognition/discrimination mechanism is the hypothetical 'green beard', where a gene for social
behaviour also causes a distinctive phenotype that can be recognised by other carriers of the gene.
Hamilton's discussion of greenbeard altruism serves as an illustration that relatedness is a matter of genetic
similarity and that this similarity is not necessarily caused by genealogical closeness (kinship).
Viscous Populations: Secondly, even indiscriminate altruism may be favoured in so-called viscous
populations, i.e. those characterized by low rates or short ranges of dispersal. Here, social partners are
typically genealogically-close kin, and so altruism may be able to flourish even in the absence of kin
recognition and kin discrimination faculties—spatial proximity serves as a rudimentary form of discrimination.
This suggests a rather general explanation for altruism. Directional selection will always favor those with
higher rates of fecundity within a certain population. Social individuals can often ensure the survival of their
own kin by participating in, and following the rules of a group (assuming the implied faculties for group
discrimination).
These mechanisms explain a relatively high r between interacting individuals. Absolute genetic
similarity is not a measure of r; rather, r shows the “excess” relatedness between an actor and a recipient
compared with the relatedness between an actor and a random member of the population. Thus, in a clonal
population with 100% genetic similarity, r = 0 (as strange as that may sound). This is because there can be
no correlation between genetic similarity and interaction strengths if genetic similarity is constant.
It has often been observed that altruism cannot be maintained in a population of randomly interacting
individuals (see Michod [1982][8] and references therein). In such a population, the correlation between
genetic similarity and interaction strength is necessarily absent, thus r = 0 and rB < C for any C > 0. This is
why mechanisms such as spatial structure and kin recognition are so important for the long-term stability of
altruistic traits, and why measures such as "population-wide average r" are meaningless in the absence of
such mechanisms.
[edit] Kin Selection in evolutionary psychology

See also: Evolution of morality
Evolutionary psychologists have attempted to explain prosocial behavior through kin selection by
stating that “behaviors that help a genetic relative are favored by natural selection.” Human beings have
developed a tendency over time to frame and interpret their actions as an avenue to the survival of their
genetic material, making kin selection not a completely altruistic form of prosocial behavior and is perhaps
better described as a component of social exchange theory. This theory does not necessarily imply that
people “compute” genetic benefit when helping others, but there is an indication that those who behave in
such a way are more likely to pass on their genes to future generations.[9]
[edit] Examples
Experiment about Kin Selection

Eusociality (true sociality) is used to describe social systems with three characteristics: one is an
overlap in generations between parents and their offspring, two is cooperative brood care, and the third
characteristic is specialized castes of nonreproductive individuals.[10] Social insects are an excellent
example of organisms that display presumed kin selected traits. The workers of some species are sterile, a
trait that would not occur if individual selection was the only process at work. The relatedness coefficient r is
abnormally high between the worker sisters in a colony of Hymenoptera due to haplodiploidy, and Hamilton's
rule is presumed to be satisfied because the benefits in fitness for the workers are believed to exceed the
costs in terms of lost reproductive opportunity, though this has never been demonstrated empirically. There
are competing hypotheses, as well, which may also explain the evolution of social behavior in such
organisms (see Eusociality).[6]
Alarm calls in ground squirrels are another example. While they may alert others of the same species
to danger, they draw attention to the caller and expose it to increased risk of predation. Paul Sherman, of
Cornell University, studied the alarm calls of ground squirrels. He observed that they occurred most
frequently when the caller had relatives nearby.[11] In a similar study, John Hoogland was able to follow
individual males through different stages of life. He found that the male prairie dogs modified their rate of
calling when closer to kin. These behaviors show that self-sacrifice is directed towards close relatives and
that there is an indirect fitness gain.[10]
Alan Krakauer of University of California, Berkeley has studied kin selection in the courtship behavior
of wild turkeys. Like a teenager helping her older sister prepare for prom night, a subordinate turkey may help
his dominant brother put on an impressive team display that is only of direct benefit to the dominant member.
[12]
Recent studies provide evidence that even certain plants can recognize and respond to kinship ties.
Using sea rocket for her experiments, Susan Dudley at McMaster University in Canada compared the growth
patterns of unrelated plants sharing a pot to plants from the same clone. She found that unrelated plants
competed for soil nutrients by aggressive root growth. This did not occur with sibling plants.[13]
In human fertilization, some sperm cells consume their acrosome prematurely on the surface of the
egg cell, facilitating for surrounding sperms, having on average 50% genome similarity, to penetrate the egg
cell.[14]
In the wood mouse (Apodemus sylvaticus), aggregates of spermatozoa form mobile trains, some of
the spermatozoa undergo a premature acrosome reactions that correlate to improved mobility of the mobile
trains towards the female egg for fertilization. This association is thought to proceed as a result of a "green
beard effect" in which the spermatozoa perform a kin-selective altruistic act after identifying genetic similarity
with the surrounding spermatozoa.[15]
[edit] Criticism
The theory of Kin selection has had a profound impact on interpretations of genetic evolution of
eusociality but it has been recently criticized by Martin Nowak and EO Wilson. The authors argue that
"Inclusive fitness theory is not a simplification over the standard approach. It is an alternative accounting
method, but one that works only in a very limited domain. Whenever inclusive fitness does work, the results
are identical to those of the standard approach. Inclusive fitness theory is an unnecessary detour, which does
not provide additional insight or information."[6] These criticisms have been addressed on the inclusive
fitness page and its discussion (talk page).
[edit] See also

• Altruism
• Ethnic nepotism
• Group selection
• Inclusive fitness
• The Selfish Gene
• The kinship theory of genomic imprinting
[edit] References
1. ^ Fisher, R. A. (1930). The Genetical Theory of Natural Selection. Oxford: Clarendon Press.
2. ^ Haldane, J. B. S. (1955). "Population Genetics". New Biology 18: 34–51.
3. ^ Hamilton, W. D. (1963). "The evolution of altruistic behavior". American Naturalist 97: 354–
356. doi:10.1086/497114.
4. ^ Hamilton, W. D. (1964). "The Genetical Evolution of Social Behavior". Journal of
Theoretical Biology 7 (1): 1–52. doi:10.1016/0022-5193(64)90038-4. PMID 5875341.
5. ^ Smith, J. M. (1964). "Group Selection and Kin Selection". Nature 201 (4924): 1145–1147.
doi:10.1038/2011145a0.
6. ^ a b c Martin Nowak, Corina Tarnita & EO Wilson "The evolution of eusociality" Nature 466
1057–1062(26 August 2010) doi:10.1038/nature09205
7. ^ Kevin Connolly and Margaret Martlew, ed (1999). "Altruism". Psychologically Speaking: A
Book of Quotations. BPS Books. pp. 10. ISBN 1-85433-302-X. (see also: Haldane's Wikiquote entry)
8. ^ Michod, R. E. (1982). "The Theory of Kin Selection". Annual Review of Ecology and
Systematics 13: 23–55. doi:10.1146/annurev.es.13.110182.000323.
9. ^ Aronson, W. A.; et al. (2007). Social Psychology (6th ed.). Upper Saddle River, NJ:
Pearson Prentice-Hall. ISBN 0132382458.
10.^ a b Freeman, Scott; Herron, Jon C. (2007). Evolutionary Analysis (4th ed.). Upper Saddle
River, NJ: Pearson, Prentice Hall. p. 460. ISBN 0132275848.
11.^ Milius, Susan (1998). "The Science of Eeeeek!". Science News (Science News, Vol. 154,
No. 11) 154 (11): 174–175. doi:10.2307/4010761.
http://findarticles.com/p/articles/mi_m1200/is_n11_v154/ai_21156998. Retrieved 2008-07-02.
12.^ In the mating game, male wild turkeys benefit even when they do not get the girl, Robert
Sanders
13.^ Smith, Kerri (2007). "Plants can tell who's who". Nature News. doi:10.1038/news070611-4.
http://www.k8science.org/news/news.cfm?art=3379.
14.^ Angier, Natalie (2007-06-12). "Sleek, Fast and Focused: The Cells That Make Dad Dad".
New York Times. http://www.nytimes.com/2007/06/12/science/12angi.html.
15.^ Moore, Harry; et al. (2002). "Exceptional sperm cooperation in the wood mouse". Nature
418 (6894): 174–177. doi:10.1038/nature00832. PMID 12110888.

• Hamilton, W.D. (1964). "The Genetical Evolution of Social Behaviour. I". Journal of
• Hamilton, W.D. (1964). "The Genetical Evolution of Social Behaviour. II". Journal of
• Lucas, J.R.; Creel, S.R.; Waser, P.M. (1996). "How to Measure Inclusive Fitness, Revisited".
Animal Behaviour 51 (1): 225–228. doi:10.1006/anbe.1996.0019.
• Madsen, E.A.; Tunney, R.J.; Fieldman, G.; Plotkin, H.C.; Dunbar, R.I.M.; Richardson, J.M.;
McFarland, D. (2007). "Kinship and Altruism: a Cross-Cultural Experimental Study". British Journal of
Psychology 98 (2): 339–359. doi:10.1348/000712606X129213. PMID 17456276.
• Queller, D.C. & Strassman, J.E. (2002) Quick Guide: Kin Selection. Current Biology,12,R832.
• West, S.A., Gardner, A. & Griffin, A.S. (2006) Quick Guide: Altruism. Current
Biology,16,R482-R483.
[hide]v · d · eSociobiology
Related Altruism · Behavioral genetics · Dual inheritance theory · Ethology ·

topics Evolutionary psychology · Group selection · Kin selection · Eusociality · Morality ·
Presociality · Subsociality · Sexual selection · Biology of gender
Criticism Not in Our Genes · Evolutionary psychology controversy
Bibliography Sociobiology: The New Synthesis · Bibliography of evolution and human

behavior
[hide]v · d · eEvolutionary psychology

Processes Altruism · Group selection · Kin selection · Sexual selection · Sociobiology ·
Coevolution · Evolutionarily stable strategy
Areas Psychological development · Morality · Religion · Depression · Developmental

psychopathology · Educational psychology · Music
Pascal Boyer · David Buss · Leda Cosmides · Charles Darwin · Peter

Seminal Kropotkin · Richard Dawkins · Daniel Dennett · Jared Diamond · David Geary ·
writers Geoffrey Miller · Robin Dunbar · Steven Mithen · John Tooby · Robert Trivers · E. O.
Wilson · D. S. Wilson
Related Memetics · Sociobiology · Evolutionary neuroscience · Human evolution ·

subjects Sociocultural evolution · Evolutionary anthropology · Evolutionary medicine ·
Evolutionary linguistics
Lists Evolutionary psychologists · Evolutionary Psychology Research Groups and

Centers · Bibliography of evolution and human behavior
Retrieved from "http://en.wikipedia.org/wiki/Kin_selection"
Categories: Selection | Theories of history | Evolutionary biology

W000
Eye

For information specific to humans, see Human eye.
For other uses, see Eye (disambiguation).
Eye
Schematic diagram of the vertebrate eye.
Compound eye of Antarctic krill
Eyes are organs that detect light, and convert it to electro-chemical impulses in neurons. The
simplest photoreceptors in conscious vision connect light to movement. In higher organisms the eye is a
complex optical system which collects light from the surrounding environment; regulates its intensity through
a diaphragm; focuses it through an adjustable assembly of lenses to form an image; converts this image into
a set of electrical signals; and transmits these signals to the brain, through complex neural pathways that
connect the eye, via the optic nerve, to the visual cortex and other areas of the brain. Eyes with resolving
power have come in ten fundamentally different forms, and 96% of animal species possess a complex optical
system.[1] Image-resolving eyes are present in molluscs, chordates and arthropods.[2]
The simplest "eyes", such as those in microorganisms, do nothing but detect whether the
surroundings are light or dark, which is sufficient for the entrainment of circadian rhythms. From more
complex eyes, retinal photosensitive ganglion cells send signals along the retinohypothalamic tract to the
suprachiasmatic nuclei to effect circadian adjustment.
Contents
[hide]
• 1 Overview
• 2 Evolution
• 3 Types of eye
• 3.1 Non-compound eyes
• 3.1.1 Pit eyes
• 3.1.2 Spherical lensed eye
• 3.1.3 Multiple lenses
• 3.1.4 Refractive cornea
• 3.1.5 Reflector eyes
• 3.2 Compound eyes
• 3.2.1 Apposition eyes
• 3.2.2 Superposition eyes
• 3.2.3 Parabolic superposition
• 3.2.4 Other
• 3.2.5 Nutrients of the eye
• 4 Relationship to life requirements
• 5 Visual acuity
• 6 Perception of colours
• 7 Rods and cones
• 8 Pigmentation
[edit] Overview
Eye of the wisent,

the European bison
Complex eyes can distinguish shapes and colours. The visual fields of many organisms, especially
predators, involve large areas of binocular vision to improve depth perception; in other organisms, eyes are
located so as to maximize the field of view, such as in rabbits and horses, which have monocular vision.
The first proto-eyes evolved among animals 600 million years ago, about the time of the Cambrian
explosion.[3] The last common ancestor of animals possessed the biochemical toolkit necessary for vision,
and more advanced eyes have evolved in 96% of animal species in six of the thirty-plus[4] main phyla.[1] In
most vertebrates and some molluscs, the eye works by allowing light to enter and project onto a light-
sensitive panel of cells, known as the retina, at the rear of the eye. The cone cells (for colour) and the rod
cells (for low-light contrasts) in the retina detect and convert light into neural signals for vision. The visual
signals are then transmitted to the brain via the optic nerve. Such eyes are typically roughly spherical, filled
with a transparent gel-like substance called the vitreous humour, with a focusing lens and often an iris; the
relaxing or tightening of the muscles around the iris change the size of the pupil, thereby regulating the
amount of light that enters the eye,[5] and reducing aberrations when there is enough light.[6]
The eyes of most cephalopods, fish, amphibians and snakes have fixed lens shapes, and focusing
vision is achieved by telescoping the lens—similar to how a camera focuses.[7]
Compound eyes are found among the arthropods and are composed of many simple facets which,
depending on the details of anatomy, may give either a single pixelated image or multiple images, per eye.
Each sensor has its own lens and photosensitive cell(s). Some eyes have up to 28,000 such sensors, which
are arranged hexagonally, and which can give a full 360-degree field of vision. Compound eyes are very
sensitive to motion. Some arthropods, including many Strepsiptera, have compound eyes of only a few
facets, each with a retina capable of creating an image, creating vision. With each eye viewing a different
thing, a fused image from all the eyes is produced in the brain, providing very different, high-resolution
images.
Possessing detailed hyperspectral colour vision, the Mantis shrimp has been reported to have the
world's most complex colour vision system.[8] Trilobites, which are now extinct, had unique compound eyes.
They used clear calcite crystals to form the lenses of their eyes. In this, they differ from most other
arthropods, which have soft eyes. The number of lenses in such an eye varied, however: some trilobites had
only one, and some had thousands of lenses in one eye.
In contrast to compound eyes, simple eyes are those that have a single lens. For example, jumping
spiders have a large pair of simple eyes with a narrow field of view, supported by an array of other, smaller
eyes for peripheral vision. Some insect larvae, like caterpillars, have a different type of simple eye
(stemmata) which gives a rough image. Some of the simplest eyes, called ocelli, can be found in animals like
some of the snails, which cannot actually "see" in the normal sense. They do have photosensitive cells, but
no lens and no other means of projecting an image onto these cells. They can distinguish between light and
dark, but no more. This enables snails to keep out of direct sunlight. In organisms dwelling near deep-sea
vents, compound eyes have been secondarily simplified and adapted to spot the infra-red light produced by
the hot vents–in this way the bearers can spot hot springs and avoid being boiled alive.[9]
[edit] Evolution
Main article: Evolution of the eye
Evolution of the eye
Photoreception is phylogenetically very old, with various theories of phylogenesis.[10] The common
origin (monophyly) of all animal eyes is now widely accepted as fact. This is based upon the shared
anatomical and genetic features of all eyes; that is, all modern eyes, varied as they are, have their origins in a
proto-eye believed to have evolved some 540 million years ago.[11][12][13] The majority of the
advancements in early eyes are believed to have taken only a few million years to develop, since the first
predator to gain true imaging would have touched off an "arms race".[14] Prey animals and competing
predators alike would be at a distinct disadvantage without such capabilities and would be less likely to
survive and reproduce. Hence multiple eye types and subtypes developed in parallel.
Eyes in various animals show adaption to their requirements. For example, birds of prey have much
greater visual acuity than humans, and some can see ultraviolet light. The different forms of eye in, for
example, vertebrates and mollusks are often cited as examples of parallel evolution, despite their distant
common ancestry.
The very earliest "eyes", called eyespots, were simple patches of photoreceptor protein in unicellular
animals. In multicellular beings, multicellular eyespots evolved, physically similar to the receptor patches for
taste and smell. These eyespots could only sense ambient brightness: they could distinguish light and dark,
but not the direction of the lightsource.[15]
Through gradual change, as the eyespot depressed into a shallow "cup" shape, the ability to slightly
discriminate directional brightness was achieved by using the angle at which the light hit certain cells to
identify the source. The pit deepened over time, the opening diminished in size, and the number of
photoreceptor cells increased, forming an effective pinhole camera that was capable of dimly distinguishing
shapes.[16]
The thin overgrowth of transparent cells over the eye's aperture, originally formed to prevent damage
to the eyespot, allowed the segregated contents of the eye chamber to specialize into a transparent humour
that optimized color filtering, blocked harmful radiation, improved the eye's refractive index, and allowed
functionality outside of water. The transparent protective cells eventually split into two layers, with circulatory
fluid in between that allowed wider viewing angles and greater imaging resolution, and the thickness of the
transparent layer gradually increased, in most species with the transparent crystallin protein.[17]
The gap between tissue layers naturally formed a bioconvex shape, an optimally ideal structure for a
normal refractive index. Independently, a transparent layer and a nontransparent layer split forward from the
lens: the cornea and iris. Separation of the forward layer again formed a humour, the aqueous humour. This
increased refractive power and again eased circulatory problems. Formation of a nontransparent ring allowed
more blood vessels, more circulation, and larger eye sizes.[17]
[edit] Types of eye

There are ten different eye layouts—indeed every way of capturing an optical image commonly used
by man, with the exceptions of zoom and Fresnel lenses. Eye types can be categorized into "simple eyes",
with one concave photoreceptive surface, and "compound eyes", which comprise a number of individual
lenses laid out on a convex surface.[1] Note that "simple" does not imply a reduced level of complexity or
acuity. Indeed, any eye type can be adapted for almost any behaviour or environment. The only limitations
specific to eye types are that of resolution—the physics of compound eyes prevents them from achieving a
resolution better than 1°. Also, superposition eyes can achieve greater sensitivity than apposition eyes, so
are better suited to dark-dwelling creatures.[1] Eyes also fall into two groups on the basis of their
photoreceptor's cellular construction, with the photoreceptor cells either being cilliated (as in the vertebrates)
or rhabdomeric. These two groups are not monophyletic; the cnidaria also possess cilliated cells, [18] and
some annelids possess both.[19]
[edit] Non-compound eyes
Simple eyes are rather ubiquitous, and lens-bearing eyes have evolved at least seven times in
vertebrates, cephalopods, annelids, crustacea and cubozoa.[20]
[edit] Pit eyes

Pit eyes, also known as stemma, are eye-spots which may be set into a pit to reduce the angles of
light that enters and affects the eyespot, to allow the organism to deduce the angle of incoming light.[1]
Found in about 85% of phyla, these basic forms were probably the precursors to more advanced types of
"simple eye". They are small, comprising up to about 100 cells covering about 100 µm.[1] The directionality
can be improved by reducing the size of the aperture, by incorporating a reflective layer behind the receptor
cells, or by filling the pit with a refractile material.[1]
Pit vipers have developed pits that function as eyes by sensing thermal infra-red radiation, in addition
to their optical wavelength eyes like those of other vertebrates.
[edit] Spherical lensed eye

The resolution of pit eyes can be greatly improved by incorporating a material with a higher refractive
index to form a lens, which may greatly reduce the blur radius encountered—hence increasing the resolution
obtainable.[1] The most basic form, seen in some gastropods and annelids, consists of a lens of one
refractive index. A far sharper image can be obtained using materials with a high refractive index, decreasing
to the edges; this decreases the focal length and thus allows a sharp image to form on the retina.[1] This also
allows a larger aperture for a given sharpness of image, allowing more light to enter the lens; and a flatter
lens, reducing spherical aberration.[1] Such an inhomogeneous lens is necessary in order for the focal length
to drop from about 4 times the lens radius, to 2.5 radii.[1]
Heterogeneous eyes have evolved at least eight times: four or more times in gastropods, once in the
copepods, once in the annelids and once in the cephalopods.[1] No aquatic organisms possess
homogeneous lenses; presumably the evolutionary pressure for a heterogeneous lens is great enough for
this stage to be quickly "outgrown".[1]
This eye creates an image that is sharp enough that motion of the eye can cause significant blurring.
To minimize the effect of eye motion while the animal moves, most such eyes have stabilizing eye muscles.
[1]
The ocelli of insects bear a simple lens, but their focal point always lies behind the retina;
consequently they can never form a sharp image. This capitulates the function of the eye. Ocelli (pit-type
eyes of arthropods) blur the image across the whole retina, and are consequently excellent at responding to
rapid changes in light intensity across the whole visual field; this fast response is further accelerated by the
large nerve bundles which rush the information to the brain.[21] Focusing the image would also cause the
sun's image to be focused on a few receptors, with the possibility of damage under the intense light; shielding
the receptors would block out some light and thus reduce their sensitivity.[21] This fast response has led to
suggestions that the ocelli of insects are used mainly in flight, because they can be used to detect sudden
changes in which way is up (because light, especially UV light which is absorbed by vegetation, usually
comes from above).[21]
[edit] Multiple lenses

Some marine organisms bear more than one lens; for instance the copepod Pontella has three. The
outer has a parabolic surface, countering the effects of spherical aberration while allowing a sharp image to
be formed. Another copepod, Copilia's eyes have two lenses, arranged like those in a telescope.[1] Such
arrangements are rare and poorly understood, but represent an interesting alternative construction. An
interesting use of multiple lenses is seen in some hunters such as eagles and jumping spiders, which have a
refractive cornea (discussed next): these have a negative lens, enlarging the observed image by up to 50%
over the receptor cells, thus increasing their optical resolution.[1]
[edit] Refractive cornea

In the eyes of most mammals, birds, reptiles, and most other terrestrial vertebrates (along with
spiders and some insect larvae) the vitreous fluid has a higher refractive index than the air[1]. In general, the
lens is not spherical. Spherical lenses produce spherical aberration. In refractive corneas, the lens tissue is
corrected with inhomogeneous lens material (See Luneburg lens.), or with an aspheric shape[1]. Flattening
the lens has a disadvantage; the quality of vision is diminished away from the main line of focus. Thus,
animals that have evolved with a wide field-of-view often have eyes that make use of an inhomogeneous
lens.[1]
As mentioned above, a refractive cornea is only useful out of water; in water, there is little difference
in refractive index between the vitreous fluid and the surrounding water. Hence creatures that have returned
to the water—--penguins and seals, for example---lose their highly curved cornea and return to lens-based
vision. An alternative solution, borne by some divers, is to have a very strongly focusing cornea.[1]
[edit] Reflector eyes

An alternative to a lens is to line the inside of the eye with " mirrors", and reflect the image to focus at
a central point.[1] The nature of these eyes means that if one were to peer into the pupil of an eye, one would
see the same image that the organism would see, reflected back out.[1]
Many small organisms such as rotifers, copeopods and platyhelminths use such organs, but these
are too small to produce usable images.[1] Some larger organisms, such as scallops, also use reflector eyes.
The scallop Pecten has up to 100 millimeter-scale reflector eyes fringing the edge of its shell. It detects
moving objects as they pass successive lenses.[1]
There is at least one vertebrate, the spookfish, whose eyes include reflective optics for focusing of
light. Each of the two eyes of a spookfish collects light from both above and below; the light coming from
above is focused by a lens, while that coming from below, by a curved mirror composed of many layers of
small reflective plates made of guanine crystals.[22]
[edit] Compound eyes
An image of a house fly compound eye surface by using Scanning Electron Microscope
Anatomy of the compound eye of an insect
Arthropods such as this Calliphora vomitoria fly have compound eyes
A compound eye may consist of thousands of individual photoreceptor units or ommatidia
(ommatidium, singular). The image perceived is a combination of inputs from the numerous ommatidia
(individual "eye units"), which are located on a convex surface, thus pointing in slightly different directions.
Compared with simple eyes, compound eyes possess a very large view angle, and can detect fast movement
and, in some cases, the polarization of light.[23] Because the individual lenses are so small, the effects of
diffraction impose a limit on the possible resolution that can be obtained (assuming that they do not function
as phased arrays). This can only be countered by increasing lens size and number. To see with a resolution
comparable to our simple eyes, humans would require compound eyes which would each reach the size of
their head.
Compound eyes fall into two groups: apposition eyes, which form multiple inverted images, and
superposition eyes, which form a single erect image.[24] Compound eyes are common in arthropods, and
are also present in annelids and some bivalved molluscs.[25]
Compound eyes, in arthropods at least, grow at their margins by the addition of new ommatidia.[26]
Structure of the ommatidia of apposition compound eyes
[edit] Apposition eyes
Apposition eyes are the most common form of eye, and are presumably the ancestral form of
compound eye. They are found in all arthropod groups, although they may have evolved more than once
within this phylum.[1] Some annelids and bivalves also have apposition eyes. They are also possessed by
Limulus, the horseshoe crab, and there are suggestions that other chelicerates developed their simple eyes
by reduction from a compound starting point.[1] (Some caterpillars appear to have evolved compound eyes
from simple eyes in the opposite fashion.)
Apposition eyes work by gathering a number of images, one from each eye, and combining them in
the brain, with each eye typically contributing a single point of information.
The typical apposition eye has a lens focusing light from one direction on the rhabdom, while light
from other directions is absorbed by the dark wall of the ommatidium. In the other kind of apposition eye,
found in the Strepsiptera, lenses are not fused to one another, and each forms an entire image; these images
are combined in the brain. This is called the schizochroal compound eye or the neural superposition eye.
Because images are combined additively, this arrangement allows vision under lower light levels.[1]
[edit] Superposition eyes

The second type is named the superposition eye. The superposition eye is divided into three types;
the refracting, the reflecting and the parabolic superposition eye. The refracting superposition eye has a gap
between the lens and the rhabdom, and no side wall. Each lens takes light at an angle to its axis and reflects
it to the same angle on the other side. The result is an image at half the radius of the eye, which is where the
tips of the rhabdoms are. This kind is used mostly by nocturnal insects. In the parabolic superposition
compound eye type, seen in arthropods such as mayflies, the parabolic surfaces of the inside of each facet
focus light from a reflector to a sensor array. Long-bodied decapod crustaceans such as shrimp, prawns,
crayfish and lobsters are alone in having reflecting superposition eyes, which also have a transparent gap but
use corner mirrors instead of lenses.
[edit] Parabolic superposition

This eye type functions by refracting light, then using a parabolic mirror to focus the image; it
combines features of superposition and apposition eyes.[9]
[edit] Other
Good fliers like flies or honey bees, or prey-catching insects like praying mantis or dragonflies, have
specialized zones of ommatidia organized into a fovea area which gives acute vision. In the acute zone the
eyes are flattened and the facets larger. The flattening allows more ommatidia to receive light from a spot
and therefore higher resolution.
There are some exceptions from the types mentioned above. Some insects have a so-called single
lens compound eye, a transitional type which is something between a superposition type of the multi-lens
compound eye and the single lens eye found in animals with simple eyes. Then there is the mysid shrimp
Dioptromysis paucispinosa. The shrimp has an eye of the refracting superposition type, in the rear behind
this in each eye there is a single large facet that is three times in diameter the others in the eye and behind
this is an enlarged crystalline cone. This projects an upright image on a specialized retina. The resulting eye
is a mixture of a simple eye within a compound eye.
Another version is the pseudofaceted eye, as seen in Scutigera. This type of eye consists of a cluster
of numerous ocelli on each side of the head, organized in a way that resembles a true compound eye.
The body of Ophiocoma wendtii, a type of brittle star, is covered with ommatidia, turning its whole
skin into a compound eye. The same is true of many chitons.
[edit] Nutrients of the eye

The ciliary body is triangular in horizontal section and is coated by a double layer, the ciliary
epithelium. The inner layer is transparent and covers the vitreous body, and is continuous from the neural
tissue of the retina. The outer layer is highly pigmented, continuous with the retinal pigment epithelium, and
constitutes the cells of the dilator muscle.
The vitreous is the transparent, colorless, gelatinous mass that fills the space between the lens of the
eye and the retina lining the back of the eye.[27] It is produced by certain retinal cells. It is of rather similar
composition to the cornea, but contains very few cells (mostly phagocytes which remove unwanted cellular
debris in the visual field, as well as the hyalocytes of Balazs of the surface of the vitreous, which reprocess
the hyaluronic acid), no blood vessels, and 98-99% of its volume is water (as opposed to 75% in the cornea)
with salts, sugars, vitrosin (a type of collagen), a network of collagen type II fibers with the
mucopolysaccharide hyaluronic acid, and also a wide array of proteins in micro amounts. Amazingly, with so
little solid matter, it tautly holds the eye.
[edit] Relationship to life requirements

Eyes are generally adapted to the environment and life requirements of the organism which bears
them. For instance, the distribution of photoreceptors tends to match the area in which the highest acuity is
required, with horizon-scanning organisms, such as those that live on the African plains, having a horizontal
line of high-density ganglia, while tree-dwelling creatures which require good all-round vision tend to have a
symmetrical distribution of ganglia, with acuity decreasing outwards from the centre.
Of course, for most eye types, it is impossible to diverge from a spherical form, so only the density of
optical receptors can be altered. In organisms with compound eyes, it is the number of ommatidia rather than
ganglia that reflects the region of highest data acquisition.[1]:23-4 Optical superposition eyes are constrained
to a spherical shape, but other forms of compound eyes may deform to a shape where more ommatidia are
aligned to, say, the horizon, without altering the size or density of individual ommatidia.[28] Eyes of horizon-
scanning organisms have stalks so they can be easily aligned to the horizon when this is inclined, for
example if the animal is on a slope.[29] An extension of this concept is that the eyes of predators typically
have a zone of very acute vision at their centre, to assist in the identification of prey.[28] In deep water
organisms, it may not be the centre of the eye that is enlarged. The hyperiid amphipods are deep water
animals that feed on organisms above them. Their eyes are almost divided into two, with the upper region
thought to be involved in detecting the silhouettes of potential prey—or predators—against the faint light of the
sky above. Accordingly, deeper water hyperiids, where the light against which the silhouettes must be
compared is dimmer, have larger "upper-eyes", and may lose the lower portion of their eyes altogether.[28]
Depth perception can be enhanced by having eyes which are enlarged in one direction; distorting the eye
slightly allows the distance to the object to be estimated with a high degree of accuracy.[9]
Acuity is higher among male organisms that mate in mid-air, as they need to be able to spot and
assess potential mates against a very large backdrop.[28] On the other hand, the eyes of organisms which
operate in low light levels, such as around dawn and dusk or in deep water, tend to be larger to increase the
amount of light that can be captured.[28]
It is not only the shape of the eye that may be affected by lifestyle. Eyes can be the most visible parts
of organisms, and this can act as a pressure on organisms to have more transparent eyes at the cost of
function.[28]
Eyes may be mounted on stalks to provide better all-round vision, by lifting them above an
organism's carapace; this also allows them to track predators or prey without moving the head.[9]
[edit] Visual acuity
A hawk's eye
Visual acuity, or resolving power, is "the ability to distinguish fine detail" and is the property of cones.
[30] It is often measured in cycles per degree (CPD), which measures an angular resolution, or how much an
eye can differentiate one object from another in terms of visual angles. Resolution in CPD can be measured
by bar charts of different numbers of white/black stripe cycles. For example, if each pattern is 1.75 cm wide
and is placed at 1 m distance from the eye, it will subtend an angle of 1 degree, so the number of white/black
bar pairs on the pattern will be a measure of the cycles per degree of that pattern. The highest such number
that the eye can resolve as stripes, or distinguish from a gray block, is then the measurement of visual acuity
of the eye.
For a human eye with excellent acuity, the maximum theoretical resolution is 50 CPD[31] (1.2
arcminute per line pair, or a 0.35 mm line pair, at 1 m). A rat can resolve only about 1 to 2 CPD.[32] A horse
has higher acuity through most of the visual field of its eyes than a human has, but does not match the high
acuity of the human eye's central fovea region.
Spherical aberration limits the resolution of a 7 mm pupil to about 3 arcminutes per line pair. At a
pupil diameter of 3 mm, the spherical aberration is greatly reduced, resulting in an improved resolution of
approximately 1.7 arcminutes per line pair.[33] A resolution of 2 arcminutes per line pair, equivalent to a 1
arcminute gap in an optotype, corresponds to 20/20 (normal vision) in humans.
[edit] Perception of colours

"Colour vision is the faculty of the organism to distinguish lights of different spectral qualities."[34] All
organisms are restricted to a small range of electromagnetic spectrum; this varies from creature to creature,
but is mainly between 400 and 700 nm.[35] This is a rather small section of the electromagnetic spectrum,
probably reflecting the submarine evolution of the organ: water blocks out all but two small windows of the
EM spectrum, and there has been no evolutionary pressure among land animals to broaden this range.[36]
The most sensitive pigment, rhodopsin, has a peak response at 500 nm.[37] Small changes to the
genes coding for this protein can tweak the peak response by a few nm;[2] pigments in the lens can also filter
incoming light, changing the peak response.[2] Many organisms are unable to discriminate between colours,
seeing instead in shades of grey; colour vision necessitates a range of pigment cells which are primarily
sensitive to smaller ranges of the spectrum. In primates, geckos, and other organisms, these take the form of
cone cells, from which the more sensitive rod cells evolved.[37] Even if organisms are physically capable of
discriminating different colours, this does not necessarily mean that they can perceive the different colours;
only with behavioural tests can this be deduced.[2]
Most organisms with colour vision are able to detect ultraviolet light. This high energy light can be
damaging to receptor cells. With a few exceptions (snakes, placental mammals), most organisms avoid these
effects by having absorbent oil droplets around their cone cells. The alternative, developed by organisms that
had lost these oil droplets in the course of evolution, is to make the lens impervious to UV light — this
precludes the possibility of any UV light being detected, as it does not even reach the retina.[37]
[edit] Rods and cones

The retina contains two major types of light-sensitive photoreceptor cells used for vision: the rods
and the cones.
Rods cannot distinguish colours, but are responsible for low-light (scotopic) monochrome (black-and-
white) vision; they work well in dim light as they contain a pigment, rhodopsin (visual purple), which is
sensitive at low light intensity, but saturates at higher (photopic) intensities. Rods are distributed throughout
the retina but there are none at the fovea and none at the blind spot. Rod density is greater in the peripheral
retina than in the central retina.
Cones are responsible for colour vision. They require brighter light to function than rods require. In
humans, there are three types of cones, maximally sensitive to long-wavelength, medium-wavelength, and
short-wavelength light (often referred to as red, green, and blue, respectively, though the sensitivity peaks
are not actually at these colours). The colour seen is the combined effect of stimuli to, and responses from,
these three types of cone cells. Cones are mostly concentrated in and near the fovea. Only a few are present
at the sides of the retina. Objects are seen most sharply in focus when their images fall on the fovea, as
when one looks at an object directly. Cone cells and rods are connected through intermediate cells in the
retina to nerve fibres of the optic nerve. When rods and cones are stimulated by light, the nerves send off
impulses through these fibres to the brain.[37]
[edit] Pigmentation
The pigment molecules used in the eye are various, but can be used to define the evolutionary
distance between different groups, and can also be an aid in determining which are closely related – although
problems of convergence do exist.[37]
Opsins are the pigments involved in photoreception. Other pigments, such as melanin, are used to
shield the photoreceptor cells from light leaking in from the sides. The opsin protein group evolved long
before the last common ancestor of animals, and has continued to diversify since.[2]
There are two types of opsin involved in vision; c-opsins, which are associated with ciliary-type
photoreceptor cells, and r-opsins, associated with rhabdomeric photoreceptor cells.[38] The eyes of
vertebrates usually contain cilliary cells with c-opsins, and (bilaterian) invertebrates have rhabdomeric cells in
the eye with r-opsins. However, some ganglion cells of vertebrates express r-opsins, suggesting that their
ancestors used this pigment in vision, and that remnants survive in the eyes.[38] Likewise, c-opsins have
been found to be expressed in the brain of some invertebrates. They may have been expressed in ciliary
cells of larval eyes, which were subsequently resorbed into the brain on metamorphosis to the adult form.[38]
C-opsins are also found in some derived bilaterian-invertebrate eyes, such as the pallial eyes of the bivalve
molluscs; however, the lateral eyes (which were presumably the ancestral type for this group, if eyes evolved
once there) always use r-opsins.[38] Cnidaria, which are an outgroup to the taxa mentioned above, express
c-opsins - but r-opsins are yet to be found in this group.[38] Incidentally, the melanin produced in the cnidaria
is produced in the same fashion as that in vertebrates, suggesting the common descent of this pigment.[38]
[edit] See also

Book:Eye

• Arthropod eye
• Human eye
• Mammalian eye
• Cephalopod eye
[edit] References
[edit] Notes
1. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab Land, M F; Fernald, R D (1992). "The Evolution
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PMID 1575438.
2. ^ a b c d e Frentiu, Francesca D.; Adriana D. Briscoe (2008). "A butterfly eye's view of birds".
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3. ^ Breitmeyer, Bruno (2010). Blindspots: The Many Ways We Cannot See. New York: Oxford
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4. ^ The precise number depends on the author
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6. ^ Vicki Bruce, Patrick R. Green, and Mark A. Georgeson (1996). Visual Perception:
Physiology, Psychology and Ecology. Psychology Press. pp. 20. ISBN 0863774504.
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7. ^ BioMedia Associates Educational Biology Site: What animal has a more sophisticated eye,
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9. ^ a b c d Cronin, T. W.; Porter, M. L. (2008). "Exceptional Variation on a Common Theme: the
Evolution of Crustacean Compound Eyes". Evolution Education and Outreach 1: 463–475.
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10.^ Autrum, H. "Introduction". In H. Autrum (editor). Comparative Physiology and Evolution of
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11.^ Halder, G.; Callaerts, P.; Gehring, W.J. (1995). "New perspectives on eye evolution". Curr.
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14.^ Conway-Morris, S. (1998). The Crucible of Creation. Oxford: Oxford University Press.
15.^ Land, M.F.; Fernald, Russell D. (1992). "The evolution of eyes". Annu Rev Neurosci 15: 1–
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17.^ a b Fernald, Russell D. (2001). The Evolution of Eyes: Where Do Lenses Come From?
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20.^ "Vision Optics and Evolution". BioScience 39 (5): 298–307. 1 May 1989.
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22.^ Wagner, H.J., Douglas, R.H., Frank, T.M., Roberts, N.W., and Partridge, J.C. (Jan. 27,
2009). "A Novel Vertebrate Eye Using Both Refractive and Reflective Optics". Current Biology 19 (2):
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24.^ Gaten, Edward (1998). "Optics and phylogeny: is there an insight? The evolution of
superposition eyes in the Decapoda (Crustacea)". Contributions to Zoology 67 (4): 223–236.
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25.^ Ritchie, Alexander (1985). "Ainiktozoon loganense Scourfield, a protochordate? from the
Silurian of Scotland". Alcheringa 9: 137. doi:10.1080/03115518508618961.
26.^ Mayer, G. (2006). "Structure and development of onychophoran eyes: What is the ancestral
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27.^ Ali, Mohamed Ather; Klyne, M.A. (1985). Vision in Vertebrates. New York: Plenum Press.
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37.^ a b c d e Goldsmith, T. H. (1990). "Optimization, Constraint, and History in the Evolution of
Eyes" (PDF). The Quarterly Review of Biology 65 (10000): 281–322. doi:10.1086/416840.
PMID 2146698. http://www.jstor.org/stable/pdfplus/2832368.pdf.
38.^ a b c d e f Nilsson, E.; Arendt, D. (Dec 2008). "Eye Evolution: the Blurry Beginning". Current
Biology 18 (23): R1096. doi:10.1016/j.cub.2008.10.025. ISSN 0960-9822. PMID 19081043. edit
[edit] Bibliography

Wikimedia Commons has media related to: Eyes
• Evolution of the eye

• Diagram of the eye
• Webvision. The organisation of the retina and visual system. An in-depth treatment of retinal
function, open to all but geared most toward graduate students.
• Eye strips images of all but bare essentials before sending visual information to brain, UC
Berkeley research shows
• A collection of resources for eye anatomy.
• Anatomy of the eye - flash animated interactive.
• Eyes - Eyes are organs that detect light, and send signals along the optic nerve to the visual
and other areas of the brain.
• Detection of weak optical signals by the human visual system : Perspectives in Neuroscience
and in Quantum Physics
• Macro photo of Eye
• Are Your Eyes Right February 1944 Popular Science
[hide]v · d · eHuman systems and organs
Bone (Carpus · Collar bone (clavicle) · Thigh

bone (femur) · Fibula · Humerus · Mandible · Metacarpus ·
Skeletal system Metatarsus · Ossicles · Patella · Phalanges · Radius ·
Skull (cranium) · Tarsus · Tibia · Ulna · Rib · Vertebra ·
TA 2–4:
Pelvis · Sternum) · Cartilage
MS
Joints Fibrous joint · Cartilaginous joint · Synovial joint
Muscular system Muscle · Tendon · Diaphragm
TA 5–11: URT (Nose,

splanchnic/ mostly
Respiratory system Nasopharynx, Larynx) · LRT
viscus Thoracic
(Trachea, Bronchus, Lung)
mostly Digestive Mouth (Salivary gland,

Abdominopelvic system+ Tongue) · upper GI (Oropharynx,
adnexa Laryngopharynx, Esophagus,
Stomach) · lower GI (Small
intestine, Appendix, Colon,
Rectum, Anus) · accessory (Liver,
Biliary tract, Pancreas)
GU: Kidney · Ureter · Bladder ·

Urinary system Urethra
Female (Uterus, Vulva,

GU: Ovary, Placenta) · Male (Scrotum,
Reproductive system Penis, Prostate, Testicle, Seminal
vesicle)
Pituitary · Pineal · Thyroid · Parathyroid · Adrenal ·

Endocrine system
Islets of Langerhans
TA 12–16 peripheral
Cardiovascular system (Artery, Vein, Lymph
vessel) · Heart
Circulatory system
primary (Bone
marrow, Thymus) ·
Lymphatic system
secondary (Spleen,
Lymph node)
(Brain, Spinal cord, Nerve) · Sensory system
Nervous system
(Ear, Eye)
Skin · Subcutaneous tissue · Breast (Mammary

Integumentary system
gland)
Blood Myeloid Myeloid immune system

(Non-TA)
Lymphoid Lymphoid immune system
general anatomy: systems and organs, regional anatomy, planes and lines, superficial axial
anatomy, superficial anatomy of limbs
[hide]v · d · eSensory system – visual system – globe of eye (TA A15.2.1–6, GA 10.1005)
Episcleral
layer • Schlemm's
Sclera
canal • Trabecular
meshwork
Fibrous tunic (outer)
Limbus •
layers (Epithelium,
Cornea Bowman's, Stroma,
Descemet's,
Endothelium)
Uvea/vascular tunic (middle) Capillary

lamina of choroid •
Choroid
Bruch's membrane •
Sattler's layer
Ciliary
Ciliary
processes • Ciliary
body
muscle
Iris Stroma •
Pupil • Iris dilator
muscle • Iris
sphincter muscle
Inner limiting
membrane • Nerve
fiber layer • Ganglion
cell layer • Inner
plexiform layer • Inner
nuclear layer
Outer
Layers
plexiform layer • Outer
nuclear layer
Retina (inner)
External
limiting membrane •
Layer of rods and
cones • Retinal
pigment epithelium
Macula •
Foveola • Fovea •
Other
Optic disc • Optic cup
(anatomical)
Anterior chamber • Aqueous
Anterior segment humour • Posterior chamber • Lens
(Capsule of lens, Zonule of Zinn)
Posterior segment Vitreous humour
Other Ocular immune system •

Tapetum lucidum • Keratocytes
anat(
noco proc,
M: g, a,
/cong/tumr, drug(S1A/1E/
EYE p)/phys/devp/
epon 1F/1L)
cell/prot
Retrieved from "http://en.wikipedia.org/wiki/Eye"
Categories: Eye | Sensory organs | Visual system

W000
Unilineal evolution

Unilineal evolution (also referred to as classical social evolution) is a 19th century social theory about
the evolution of societies and cultures. It was composed of many competing theories by various sociologists
and anthropologists, who believed that Western culture is the contemporary pinnacle of social evolution.
Different social status is aligned in a single line that moves from most primitive to most civilized. This theory
is now generally considered obsolete in academic circles.
Contents
[hide]
• 1 Intellectual Thought
• 2 Scottish Thinkers
• 3 Rising Interests
• 4 Birth and Development of Unilineal Classical Social
Evolutionism
• 4.1 Progressivism
• 4.2 Comte
• 4.3 Spencer
• 4.4 Morgan
• 4.5 Durkheim
• 4.6 Tylor & Morgan
• 4.7 Ward
• 4.8 Tönnies
• 5 The Critique of Unilineal Classical Social Evolution and its
Impact
• 5.1 Boas
• 5.2 Global Change
• 5.3 Major Objections & Concerns
• 6 See also
• 7 References
[edit] Intellectual Thought
Theories of social and cultural evolution are common in modern European thought. Prior to the 18th
century, Europeans predominantly believed that societies on Earth were in a state of decline. European
society held up the world of antiquity as a standard to aspire to, and Ancient Greece and Ancient Rome
produced levels of technical accomplishment which Europeans of the Middle Ages sought to emulate. At the
same time, Christianity taught that people lived in a debased world fundamentally inferior to the Garden of
Eden and Heaven. During the Age of Enlightenment, however, European self-confidence grew and the notion
of progress became increasingly popular. It was during this period that what would later become known as
'sociological and cultural evolution' would have its roots.
The Enlightenment thinkers often speculated that societies progressed through stages of increasing
development and looked for the logic, order and the set of scientific truths that determined the course of
human history. Georg Wilhelm Friedrich Hegel, for example, argued that social development was an
inevitable and determined process, similar to an acorn which has no choice but to become an oak tree.
Likewise, it was assumed that societies start out primitive, perhaps in a Hobbesian state of nature, and
naturally progress toward something resembling industrial Europe.
[edit] Scottish Thinkers

While earlier authors such as Michel de Montaigne discussed how societies change through time, it
was truly the Scottish Enlightenment which proved key in the development of cultural evolution. After
Scotland's union with England in 1707, several Scottish thinkers pondered on the relationship between
progress and the 'decadence' brought about by increased trade with England and the affluence it produced.
The result was a series of 'conjectural histories.' Authors such as Adam Ferguson, John Millar, and Adam
Smith argued that all societies pass through a series of four stages: hunting and gathering, pastoralism and
nomadism, agricultural, and finally a stage of commerce. These thinkers thus understood the changes
Scotland was undergoing as a transition from an agricultural to a mercantile society.
Philosophical concepts of progress (such as those expounded by the German philosopher G.W.F.
Hegel) developed as well during this period. In France authors such as Claude Adrien Helvétius and other
philosophers were influenced by this Scottish tradition. Later thinkers such as Comte de Saint-Simon
developed these ideas. Auguste Comte in particular presented a coherent view of social progress and a new
discipline to study it -- sociology.
[edit] Rising Interests

These developments took place in a wider context. The first process was colonialism. Although
Imperial powers settled most differences of opinion with their colonial subjects with force, increased
awareness of non-Western peoples raised new questions for European scholars about the nature of society
and culture. Similarly, effective administration required some degree of understanding of other cultures.
Emerging theories of social evolution allowed Europeans to organize their new knowledge in a way that
reflected and justified their increasing political and economic domination of others: colonized people were
less-evolved, colonizing people were more evolved. The second process was the Industrial Revolution and
the rise of capitalism which allowed and promoted continual revolutions in the means of production.
Emerging theories of social evolution reflected a belief that the changes in Europe wrought by the Industrial
Revolution and capitalism were obvious improvements. Industrialization, combined with the intense political
change brought about by the French Revolution, US Constitution and Polish Constitution of the 3 May, which
were paving the way for the dominance of democracy, forced European thinkers to reconsider some of their
assumptions about how society was organized.
Eventually, in the 19th century three great, classical theories of social and historical change were
created: the social evolutionism theory, the social cycle theory and the Marxist historical materialism theory.
Those theories had one common factor: they all agreed that the history of humanity is pursuing a certain
fixed path, most likely that of the social progress. Thus, each past event is not only chronologically, but
causally tied to the present and future events. Those theories postulated that by recreating the sequence of
those events, sociology could discover the Laws of history.
[edit] Birth and Development of Unilineal Classical Social Evolutionism

While social evolutionists agree that the evolution-like process leads to the social progress, classical
social evolutionists have developed many different theories, known as theories of unilineal evolution. Social
evolutionism was the prevailing theory of early socio-cultural anthropology and social commentary, and is
associated with scholars like Auguste Comte, Edward Burnett Tylor, Lewis Henry Morgan, and Herbert
Spencer. Social evolutionism represented an attempt to formalize social thinking along scientific lines, later
influenced by the biological theory of evolution. If organisms could develop over time according to
discernible, deterministic laws, then it seemed reasonable that societies could as well. This really marks the
beginning of Anthropology as a scientific discipline and a departure from traditional religious views of
"primitive" cultures.
The term "Classical Social Evolutionism" is most closely associated with the 19th century writings of
Auguste Comte, Herbert Spencer (who coined the phrase "survival of the fittest") and William Graham
Sumner. In many ways Spencer's theory of 'cosmic evolution' has much more in common with the works of
Jean-Baptiste Lamarck and Auguste Comte than with contemporary works of Charles Darwin. Spencer also
developed and published his theories several years earlier than Darwin. In regard to social institutions,
however, there is a good case that Spencer's writings might be classified as 'Social Evolutionism'. Although
he wrote that societies over time progressed, and that progress was accomplished through competition, he
stressed that the individual (rather than the collectivity) is the unit of analysis that evolves, that evolution
takes place through natural selection and that it affects social as well as biological phenomenon.
[edit] Progressivism
Both Spencer and Comte view the society as a kind of organism subject to the process of growth -
from simplicity to complexity, from chaos to order, from generalisation to specialisation, from flexibility to
organisation. They agreed that the process of societies growth can be divided into certain stages, have their
beginning and eventual end, and that this growth is in fact social progress - each newer, more evolved
society is better. Thus progressivism became one of the basic ideas underlying the theory of social
evolutionism.
[edit] Comte
Auguste Comte, known as father of sociology, formulated the law of three stages: human
development progresses from the theological stage, in which nature was mythically conceived and man
sought the explanation of natural phenomena from supernatural beings, through metaphysical stage in which
nature was conceived of as a result of obscure forces and man sought the explanation of natural phenomena
from them until the final positive stage in which all abstract and obscure forces are discarded, and natural
phenomena are explained by their constant relationship. This progress is forced through the development of
human mind, and increasing application of thought, reasoning and logic to the understanding of world.[1]
[edit] Spencer
Herbert Spencer, who believed that society was evolving toward increasing freedom for individuals;
and so held that government intervention, ought to be minimal in social and political life, differentiated
between two phases of development, focusing is on the type of internal regulation within societies. Thus he
differentiated between military and industrial societies. The earlier, more primitive military society has a goal
of conquest and defence, is centralised, economically self-sufficient, collectivistic, puts the good of a group
over the good of an individual, uses compulsion, force and repression, rewards loyalty, obedience and
discipline. The industrial society has a goal of production and trade, is decentralised, interconnected with
other societies via economic relations, achieves its goals through voluntary cooperation and individual self-
restraint, treats the good of individual as the highest value, regulates the social life via voluntary relations,
and values initiative, independence and innovation.[2]
Regardless of how scholars of Spencer interpret his relation to Darwin, Spencer proved to be an
incredibly popular figure in the 1870s, particularly in the United States. Authors such as Edward L. Youmans,
William Graham Sumner, John Fiske, John W. Burgess, Lester Frank Ward, Lewis H. Morgan and other
thinkers of the gilded age all developed theories of social evolutionism as a result of their exposure to
Spencer as well as Darwin.
[edit] Morgan
Lewis H. Morgan, an anthropologist whose ideas have had much impact on sociology, in his 1877
classic "Ancient Societies" differentiated between three eras: savagery, barbarism and civilisation, which are
divided by technological inventions, like fire, bow, pottery in savage era, domestication of animals,
agriculture, metalworking in barbarian era and alphabet and writing in civilisation era. Thus Morgan
introduced a link between the social progress and technological progress. Morgan viewed the technological
progress as a force behind social progress, and any social change - in social institutions, organisations or
ideologies have their beginning in the change of technology.[3] Morgan's theories were popularised by
Friedrich Engels, who based his famous work "The Origin of the Family, Private Property and the State " on it.
For Engels and other marxists, this theory was important as it supported their conviction that materialistic
factors - economical and technological - are decisive in shaping the fate of humanity.
[edit] Durkheim
Émile Durkheim, another of the 'fathers' of sociology, has developed a similar, dichotomical view of
social progress. His key concept was social solidarity, as he defined the social evolution in terms of
progressing from mechanical solidarity to organic solidarity. In mechanical solidarity, people are self-
sufficient, there is little integration and thus there is the need for use of force and repression to keep society
together. In organic solidarity, people are much more integrated and interdependent and specialisation and
cooperation is extensive. Progress from mechanical to organic solidarity is based first on population growth
and increasing population density, second on increasing 'morality density' (development of more complex
social interactions) and thirdly, on the increasing specialisation in workplace. To Durkheim, the most
important factor in the social progress is the division of labor.
[edit] Tylor & Morgan

Anthropologists Sir E.B. Tylor in England and Lewis Henry Morgan in the United States worked with
data from indigenous people, whom they claimed represented earlier stages of cultural evolution that gave
insight into the process and progression of cultural evolution. Morgan would later have a significant influence
on Karl Marx and Friedrich Engels, who developed a theory of cultural evolution in which the internal
contradictions in society created a series of escalating stages that ended in a socialist society (see Marxism).
Tylor and Morgan elaborated upon, modified and expanded the theory of unilinear evolution, specifying
criteria for categorizing cultures according to their standing within a fixed system of growth of humanity as a
whole while examining the modes and mechanisms of this growth.
Their analysis of cross-cultural data was based on three assumptions:
1. contemporary societies may be classified and ranked as more "primitive" or more "civilized;"
2. There are a determinate number of stages between "primitive" and "civilized" (e.g. band,
tribe, chiefdom, and state),
3. All societies progress through these stages in the same sequence, but at different rates.
Theorists usually measured progression (that is, the difference between one stage and the next) in
terms of increasing social complexity (including class differentiation and a complex division of labor), or an
increase in intellectual, theological, and aesthetic sophistication. These 19th century ethnologists used these
principles primarily to explain differences in religious beliefs and kinship terminologies among various
societies.
[edit] Ward
There were however notable differences between the work of Lester Frank Ward's and Tylor's
approaches. Lester Frank Ward developed Spencer's theory but unlike Spencer, who considered the
evolution to be general process applicable to the entire world, physical and sociological, Ward differentiated
sociological evolution from biological evolution. He stressed that humans create goals for themselves and
strive to realise them, whereas there is no such intelligence and awareness guiding the non-human world,
which develops more or less at random. He created a hierarchy of evolution processes. First, there is
cosmogenesis, creation and evolution of the world. Then, after life develops, there is biogenesis.
Development of humanity leads to anthropogenesis, which is influenced by the human mind. Finally, when
society develops, so does sociogenesis, which is the science of shaping the society to fit with various
political, cultural and ideological goals.
Edward Burnett Tylor, pioneer of anthropology, focused on the evolution of culture worldwide, noting
that culture is an important part of every society and that it is also subject to the process of evolution. He
believed that societies were at different stages of cultural development and that the purpose of anthropology
was to reconstruct the evolution of culture, from primitive beginnings to the modern state.
[edit] Tönnies
Ferdinand Tönnies describes the evolution as the development from informal society, where people
have many liberties and there are few laws and obligations, to modern, formal rational society, dominated by
traditions and laws and are restricted from acting as they wish. He also notes that there is a tendency of
standardization and unification, when all smaller societies are absorbed into the single, large, modern
society. Thus Torbes can be said to describe part of the process known today as the globalisation. Torbes
was also one of the first sociologists to claim that the evolution of society is not necessarily going in the right
direction, that the social progress is not perfect, it can even be called a regress as the newer, more evolved
societies are obtained only after paying a high costs, resulting in decreasing satisfaction of individuals
making up that society. Tönnies' work became the foundation of neo-evolutionism.
[edit] The Critique of Unilineal Classical Social Evolution and its Impact
[edit] Boas
The early 20th century inaugurated a period of systematic critical examination, and rejection of
unilineal theories of cultural evolution. Cultural anthropologists such as Franz Boas, typically regarded as the
leader of anthropology's rejection of classical social evolutionism, used sophisticated ethnography and more
rigorous empirical methods to argue that Spencer, Tylor, and Morgan's theories were speculative and
systematically misrepresented ethnographic data. Additionally, they rejected the distinction between
"primitive" and "civilized" (or "modern"), pointing out that so-called primitive contemporary societies have just
as much history, and were just as evolved, as so-called civilized societies. They therefore argued that any
attempt to use this theory to reconstruct the histories of non-literate (i.e. leaving no historical documents)
peoples is entirely speculative and unscientific. They observed that the postulated progression, which
typically ended with a stage of civilization identical to that of modern Europe, is ethnocentric. They also
pointed out that the theory assumes that societies are clearly bounded and distinct, when in fact cultural traits
and forms often cross social boundaries and diffuse among many different societies (and is thus an important
mechanism of change).Boas in his culture history approach focused on anthropological fieldwork in an
attempt to identify factual processes instead of what he criticized as speculative stages of growth. His
approach was a major influence on the American anthropology in the first half of the 20th century, and
marked a retreat from high-level generalization and "systems building". The contribution to cultural
anthropology by Boas is extraordinary, if not controversial (Kiesing,'Cultural Anthropology',c.'98).
[edit] Global Change

Later critics observed that this assumption of firmly bounded societies was proposed precisely at the
time when European powers were colonizing non-Western societies, and was thus self-serving. Many
anthropologists and social theorists now consider unilineal cultural and social evolution a Western myth
seldom based on solid empirical grounds. Critical theorists argue that notions of social evolution are simply
justifications for power by the elites of society. Finally, the devastating World Wars that occurred between
1914 and 1945 crippled Europe's self-confidence. After millions of deaths, genocide, and the destruction of
Europe's industrial infrastructure, the idea of progress seemed dubious at best.
[edit] Major Objections & Concerns

Thus modern socio-cultural evolutionism rejects most of classical social evolutionism due to various
theoretical problems:
1. The theory was deeply ethnocentric--it makes heavy value judgements on different societies;
with Western civilization seen as the most valuable.
2. It assumed all cultures follow the same path or progression and have the same goals.
3. It equated civilization with material culture (technology, cities, etc.)
4. It equated evolution with progress or fitness, based on deep misunderstandings of
evolutionary theory.
5. It is greatly contradicted by evidence. Some (but not all) supposedly primitive societies are
arguably more peaceful and equitable / democratic than many modern societies.
Because social evolution was posited as a scientific theory, it was often used to support unjust and
often racist social practices—particularly colonialism, slavery, and the unequal economic conditions present
within industrialized Europe.
[edit] See also

• Multilineal evolution
• World-systems theory
[edit] References
1. ^ http://radicalacademy.com/adiphilpositivism.htm
2. ^ http://www.bolender.com/Dr.%20Ron/SOC4044%20Sociological%20Theory/Class
%20Sessions/Sociological%20Theory/Spencer,%20Herbert/spencer,_herbert.htm
3. ^ http://www.marxists.org/reference/archive/morgan-lewis/ancient-society/ch03.htm
Retrieved from "http://en.wikipedia.org/wiki/Unilineal_evolution"
Categories: Anthropology | Theories of history | Sociocultural evolution

W000
Horse

For other uses, see Horse (disambiguation).
Domestic horse
Conservation status
Domesticated
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Subclass: Theria
Infraclass: Eutheria
Order: Perissodactyla
Family: Equidae
Genus: Equus
Species: E. ferus
Subspecies: E. f. caballus
Trinomial name
Equus ferus caballus

Linnaeus, 1758[1]
Synonyms
48[2]
The horse (Equus ferus caballus)[2][3] is a hooved (ungulate) mammal, a subspecies of the family
Equidae. The horse has evolved over the past 45 to 55 million years from a small multi-toed creature into the
large, single-toed animal of today. Humans began to domesticate horses around 4000 BC, and their
domestication is believed to have been widespread by 3000 BC. Although most horses today are
domesticated, there are still endangered populations of the Przewalski's Horse, the only remaining true wild
horse, as well as more common populations of feral horses which live in the wild but are descended from
domesticated ancestors. There is an extensive, specialized vocabulary used to describe equine-related
concepts, covering everything from anatomy to life stages, size, colors, markings, breeds, locomotion, and
behaviour.
Horses' anatomy enables them to make use of speed to escape predators and they have a well-
developed sense of balance and a strong fight-or-flight instinct. Related to this need to flee from predators in
the wild is an unusual trait: horses are able to sleep both standing up and lying down. Female horses, called
mares, carry their young for approximately 11 months, and a young horse, called a foal, can stand and run
shortly following birth. Most domesticated horses begin training under saddle or in harness between the ages
of two and four. They reach full adult development by age five, and have an average lifespan of between 25
and 30 years.
Horse breeds are loosely divided into three categories based on general temperament: spirited "hot
bloods" with speed and endurance; "cold bloods", such as draft horses and some ponies, suitable for slow,
heavy work; and "warmbloods", developed from crosses between hot bloods and cold bloods, often focusing
on creating breeds for specific riding purposes, particularly in Europe. There are over 300 breeds of horses in
the world today, developed for many different uses.
Horses and humans interact in a wide variety of sport competitions and non-competitive recreational
pursuits, as well as in working activities such as police work, agriculture, entertainment, and therapy. Horses
were historically used in warfare, from which a wide variety of riding and driving techniques developed, using
many different styles of equipment and methods of control. Many products are derived from horses, including
meat, milk, hide, hair, bone, and pharmaceuticals extracted from the urine of pregnant mares. Humans
provide domesticated horses with food, water and shelter, as well as attention from specialists such as
veterinarians and farriers.
Contents
[hide]
• 1 Biology
• 1.1 Lifespan and life stages
• 1.2 Size and measurement
• 1.2.1 Ponies
• 1.3 Colors and markings
• 1.4 Reproduction and development
• 1.5 Anatomy
• 1.5.1 Skeletal system
• 1.5.2 Hooves
• 1.5.3 Teeth
• 1.5.4 Digestion
• 1.5.5 Senses
• 1.6 Movement
• 1.7 Behavior
• 1.7.1 Intelligence and learning
• 1.7.2 Temperament
• 1.7.3 Sleep patterns
• 2 Taxonomy and evolution
• 2.1 Wild species surviving into modern times
• 2.2 Other modern equids
Biology
Main article: Equine anatomy
Parts of a horse
Horse anatomy is described by a large number of specific terms, as illustrated by the chart to the
right. Specific terms also describe various ages, colors and breeds.
Lifespan and life stages
Depending on breed, management and environment, the domestic horse today has a life expectancy
of 25 to 30 years.[4] It is uncommon, but a few animals live into their 40s and, occasionally, beyond.[5] The
oldest verifiable record was "Old Billy", a 19th-century horse that lived to the age of 62.[4] In modern times,
Sugar Puff, who had been listed in the Guinness Book of World Records as the world's oldest living pony,
died in 2007, aged 56.[6]
Regardless of a horse's actual birth date, for most competition purposes an animal is considered a
year older on January 1 of each year in the northern hemisphere[4][7] and August 1 in the southern
hemisphere.[8] The exception is in endurance riding, where the minimum age to compete is based on the
animal's calendar age.[9] A very rough estimate of a horse's age can be made from looking at its teeth.[4]
The following terminology is used to describe horses of various ages:
• Foal: a horse of either sex less than one year old. A nursing foal is sometimes called a
suckling and a foal that has been weaned is called a weanling.[10] Most domesticated foals are
weaned at 5 to 7 months of age, although foals can be weaned at 4 months with no adverse effects.
[11]
• Yearling: a horse of either sex that is between one and two years old.[12]
• Colt: a male horse under the age of four.[13] A common terminology error is to call any
young horse a "colt", when the term actually only refers to young male horses.[14]
• Filly: a female horse under the age of four.[10]
• Mare: a female horse four years old and older.[15]
• Stallion: a non-castrated male horse four years old and older.[16] Some people, particularly
in the UK, refer to a stallion as a "horse".[17]
• Gelding: a castrated male horse of any age.[10]
In horse racing, these definitions may differ: For example, in the British Isles, Thoroughbred horse
racing defines colts and fillies as less than five years old.[18] However, for Australian Thoroughbred racing,
colts and fillies are less than four years old.[19]
Size and measurement

See also: Hand (length)
The height of horses is measured at the highest point of the withers, where the neck meets the back.
This point was chosen as it is a stable point of the anatomy, unlike the head or neck, which move up and
down.
The English-speaking world measures the height of horses in hands (abbreviated "h" or "hh", for
"hands high") and inches. One hand is equal to 101.6 millimetres (4 in). The height is expressed as the
number of full hands, followed by a decimal point, then the number of additional inches. Thus, a horse
described as "15.2 h" is 15 hands (60 inches (152.4 cm)) plus 2 inches (5.1 cm), for a total of 62 inches
(157.5 cm) in height.[20]
Size varies greatly among horse breeds, as with this full-sized horse and a miniature horse.
The size of horses varies by breed, but also is influenced by nutrition. Light riding horses usually
range in height from 14 to 16 hands (56 to 64 inches, 142 to 163 cm) and can weigh from 380 to 550
kilograms (840 to 1,200 lb).[21] Larger riding horses usually start at about 15.2 hands (62 inches, 157 cm)
and often are as tall as 17 hands (68 inches, 173 cm), weighing from 500 to 600 kilograms (1,100 to 1,300
lb).[22] Heavy or draft horses are usually at least 16 to 18 hands (64 to 72 inches, 163 to 183 cm) high and
can weigh from about 700 to 1,000 kilograms (1,500 to 2,200 lb).[23]
The largest horse in recorded history was probably a Shire horse named Mammoth, who was born in
1848. He stood 21.2½ hands high (86.5 in/220 cm), and his peak weight was estimated at 1,500 kilograms
(3,300 lb).[24] The current record holder for the world's smallest horse is Thumbelina, a fully mature
miniature horse affected by dwarfism. She is 17 inches (43 cm) tall and weighs 57 pounds (26 kg).[25]
Ponies
Main article: Pony
The general rule for height between a horse and a pony at maturity is 14.2 hands (58 inches,
147 cm). An animal 14.2 h or over is usually considered to be a horse and one less than 14.2 h a pony.[26]
However, there are many exceptions to the general rule. In Australia, ponies measure under 14 hands
(56 inches, 142 cm).[27] The International Federation for Equestrian Sports, which uses metric
measurements, defines the cutoff between horses and ponies at 148 centimetres (58.27 in) (just over 14.2 h)
without shoes and 149 centimetres (58.66 in) (just over 14.2½ h) with shoes.[28] Some breeds which
typically produce individuals both under and over 14.2 h consider all animals of that breed to be horses
regardless of their height.[29] Conversely, some pony breeds may have features in common with horses, and
individual animals may occasionally mature at over 14.2 h, but are still considered to be ponies.[30]
The distinction between a horse and pony is not simply a difference in height, but other aspects of
phenotype or appearance, such as conformation and temperament. Ponies often exhibit thicker manes, tails,
and overall coat. They also have proportionally shorter legs, wider barrels, heavier bone, shorter and thicker
necks, and short heads with broad foreheads. They may have calmer temperaments than horses and also a
high level of equine intelligence that may or may not be used to cooperate with human handlers.[26] In fact,
small size, by itself, is sometimes not a factor at all. While the Shetland pony stands on average 10 hands
(40 inches, 102 cm),[31] the Falabella and other miniature horses, which can be no taller than 30 inches (76
cm), the size of a medium-sized dog, are classified by their respective registries as very small horses rather
than as ponies.[32]
Colors and markings
Bay (left) and chestnut (sometimes called "sorrel") are two of the most common coat colors, seen in
almost all breeds.
Main articles: Equine coat color, Equine coat color genetics, and Horse markings
Horses exhibit a diverse array of coat colors and distinctive markings, described with a specialized
vocabulary. Often, a horse is classified first by its coat color, before breed or sex.[33] Horses of the same
color may be distinguished from one another by white markings,[34] which, along with various spotting
patterns, are inherited separately from coat color.[35]
Many genes that create horse coat colors have been identified, although research continues to
further identify factors that result in specific traits. One of the first genetic relationships to be understood was
that between recessive "red" (chestnut) and dominant "black", which is controlled by the "red factor" or
extension gene. Additional alleles control spotting, graying, suppression or dilution of color, and other effects
that create the dozens of possible coat colors found in horses.[36]
Chestnut, bay, and black are the basic equine coat colors. These colors are modified by at least ten
other genes to create all other colors, including dilutions such as palomino and spotting patterns such as
pinto.[36] Horses which are white in coat color are often mislabeled as "white" horses. However, a horse that
looks white is usually a middle-aged or older gray. Grays are born a darker shade, get lighter as they age,
and usually have black skin underneath their white hair coat (with the exception of pink skin under white
markings). The only horses properly called white are born with a white hair coat and have predominantly pink
skin, a fairly rare occurrence.[37] There are no truly "albino" horses having both pink skin and red eyes.[38]
Reproduction and development

Main article: Horse breeding
Gestation lasts for approximately 335–340 days[39] and usually results in one foal. Twins are rare.
[40] Horses are a precocial species, and foals are capable of standing and running within a short time
following birth.[41]
Horses, particularly colts, sometimes are physically capable of reproduction at about 18 months, but
domesticated horses are rarely allowed to breed before the age of three, especially females.[39] Horses four
years old are considered mature, although the skeleton normally continues to develop until the age of six;
maturation also depends on the horse's size, breed, sex, and quality of care. Also, if the horse is larger, its
bones are larger; therefore, not only do the bones take longer to actually form bone tissue, but the epiphyseal
plates are also larger and take longer to convert from cartilage to bone. These plates convert after the other
parts of the bones, and are crucial to development.[42]
Depending on maturity, breed, and work expected, horses are usually put under saddle and trained
to be ridden between the ages of two and four.[43] Although Thoroughbred race horses are put on the track
at as young as two years old in some countries,[44] horses specifically bred for sports such as dressage are
generally not put under saddle until they are three or four years old, because their bones and muscles are not
solidly developed.[45] For endurance riding competition, horses are not deemed mature enough to compete
until they are a full 60 calendar months (5 years) old.[9]
Anatomy
Main articles: Equine anatomy, Muscular system of the horse, Respiratory system of the horse, and
Circulatory system of the horse
Skeletal system
Main article: Skeletal system of the horse
The skeletal system of a modern horse
Horses have a skeleton that averages 205 bones.[46] A significant difference between the horse
skeleton and that of a human, is the lack of a collarbone—the horse's forelimbs are attached to the spinal
column by a powerful set of muscles, tendons, and ligaments that attach the shoulder blade to the torso. The
horse's legs and hooves are also unique structures. Their leg bones are proportioned differently from those of
a human. For example, the body part that is called a horse's "knee" is actually made up of the carpal bones
that correspond to the human wrist. Similarly, the hock contains bones equivalent to those in the human
ankle and heel. The lower leg bones of a horse correspond to the bones of the human hand or foot, and the
fetlock (incorrectly called the "ankle") is actually the proximal sesamoid bones between the cannon bones (a
single equivalent to the human metacarpal or metatarsal bones) and the proximal phalanges, located where
one finds the "knuckles" of a human. A horse also has no muscles in its legs below the knees and hocks,
only skin, hair, bone, tendons, ligaments, cartilage, and the assorted specialized tissues that make up the
hoof.[47]
Hooves
Main articles: Horse hoof, Horseshoe, and Farrier
The critical importance of the feet and legs is summed up by the traditional adage, "no foot, no
horse".[48] The horse hoof begins with the distal phalanges, the equivalent of the human fingertip or tip of the
toe, surrounded by cartilage and other specialized, blood-rich soft tissues such as the laminae. The exterior
hoof wall and horn of the sole is made of essentially the same material as a human fingernail.[49] The end
result is that a horse, weighing on average 500 kilograms (1,100 lb),[50] travels on the same bones as would
a human on tiptoe.[51] For the protection of the hoof under certain conditions, some horses have horseshoes
placed on their feet by a professional farrier. The hoof continually grows, and needs to be trimmed (and
horseshoes reset, if used) every five to eight weeks.[52]
Teeth
Main article: Horse teeth
Horses are adapted to grazing. In an adult horse, there are 12 incisors, adapted to biting off the grass
or other vegetation, at the front of the mouth. There are 24 teeth adapted for chewing, the premolars and
molars, at the back of the mouth. Stallions and geldings have four additional teeth just behind the incisors, a
type of canine teeth that are called "tushes". Some horses, both male and female, will also develop one to
four very small vestigial teeth in front of the molars, known as "wolf" teeth, which are generally removed
because they can interfere with the bit. There is an empty interdental space between the incisors and the
molars where the bit rests directly on the bars (gums) of the horse's mouth when the horse is bridled.[53]
The incisors show a distinct wear and growth pattern as the horse ages, as well as change in the
angle at which the chewing surfaces meet. The teeth continue to erupt throughout life as they are worn down
by grazing, so a very rough estimate of a horse's age can be made by an examination of its teeth, although
diet and veterinary care can affect the rate of tooth wear.[4]
Digestion
Main articles: Equine digestive system and Equine nutrition
Horses are herbivores with a digestive system adapted to a forage diet of grasses and other plant
material, consumed steadily throughout the day. Therefore, compared to humans, they have a relatively
small stomach but very long intestines to facilitate a steady flow of nutrients. A 450-kilogram (990 lb) horse
will eat 7 to 11 kilograms (15 to 24 lb) of food per day and, under normal use, drink 38 litres (8.4 imp gal;
10 US gal) to 45 litres (9.9 imp gal; 12 US gal) of water. Horses are not ruminants, so they have only one
stomach, like humans, but unlike humans, they can also digest cellulose from grasses due to the presence of
a "hind gut" called the cecum, or "water gut", which food goes through before reaching the large intestine.
Unlike humans, horses cannot vomit, so digestion problems can quickly cause colic, a leading cause of
death.[54]
Senses
A horse's eye
See also: Equine vision
The horse's senses are generally superior to those of a human. As prey animals, they must be aware
of their surroundings at all times.[55] They have the largest eyes of any land mammal,[56] and are lateral-
eyed, meaning that their eyes are positioned on the sides of their heads.[57] This means that horses have a
range of vision of more than 350°, with approximately 65° of this being binocular vision and the remaining
285° monocular vision.[56] Horses have excellent day and night vision, but they have two-color, or
dichromatic vision; their color vision is somewhat like red-green color blindness in humans, where certain
colors, especially red and related colors, appear more green.[58]
Their hearing is good,[55] and the pinna of each ear can rotate up to 180°, giving the potential for
360° hearing without having to move the head.[59] Their sense of smell, while much better than that of
humans, is not their strongest asset; they rely to a greater extent on vision.[55]
Horses have a great sense of balance, due partly to their ability to feel their footing and partly to
highly developed proprioceptive abilities (the unconscious sense of where the body and limbs are at all
times).[60] A horse's sense of touch is well developed. The most sensitive areas are around the eyes, ears,
and nose.[61] Horses sense contact as subtle as an insect landing anywhere on the body.[62]
Horses have an advanced sense of taste that allows them to sort through fodder to choose what they
would most like to eat,[63] and their prehensile lips can easily sort even the smallest grains. Horses generally
will not eat poisonous plants. However, there are exceptions and horses will occasionally eat toxic amounts
of poisonous plants even when there is adequate healthy food.[64]
Movement
The gallop
Main articles: Horse gait, Trot (horse gait), Canter, and Ambling
All horses move naturally with four basic gaits: the four-beat walk, which averages 6.4 kilometres per
hour (4.0 mph); the two-beat trot or jog at 13 to 19 kilometres per hour (8.1 to 12 mph) (faster for harness
racing horses); the canter or lope, a three-beat gait that is 19 to 24 kilometres per hour (12 to 15 mph); and
the gallop.[65] The gallop averages 40 to 48 kilometres per hour (25 to 30 mph),[66] but the world record for
a horse galloping over a short, sprint distance is 88 kilometres per hour (55 mph).[67] Besides these basic
gaits, some horses perform a two-beat pace, instead of the trot.[68] There also are several four-beat
"ambling" gaits that are approximately the speed of a trot or pace, though smoother to ride. These include the
lateral rack, running walk, and tölt as well as the diagonal fox trot.[69] Ambling gaits are often genetic in
some breeds, known collectively as gaited horses.[70] Often, gaited horses replace the trot with one of the
ambling gaits.[71]
Behavior
Main articles: Horse behavior and Stable vices
Horses are prey animals with a strong fight-or-flight instinct. Their first response to threat is to startle
and usually flee, although they will stand their ground and defend themselves when flight is not possible, or if
their young are threatened. They also tend to be curious; when startled, they will often hesitate an instant to
ascertain the cause of their fright, and may not always flee from something that they perceive as non-
threatening. Most light horse riding breeds were developed for speed, agility, alertness and endurance;
natural qualities that extend from their wild ancestors. However, through selective breeding, some breeds of
horses are quite docile, particularly certain draft horses.[72] Horses are herd animals, with a clear hierarchy
of rank, led by a dominant animal (usually a mare). They are also social creatures who are able to form
companionship attachments to their own species and to other animals, including humans. They communicate
in various ways, including vocalizations such as nickering or whinnying, mutual grooming, and body
language. Many horses will become difficult to manage if they are isolated, but with training, horses can learn
to accept a human as a companion, and thus be comfortable away from other horses.[73] However, when
confined with insufficient companionship, exercise, or stimulation, individuals may develop stable vices, an
assortment of bad habits, mostly psychological in origin, that include wood chewing, wall kicking, "weaving"
(rocking back and forth), and other problems.[74]
Intelligence and learning
In the past, horses were considered unintelligent, with no abstract thinking ability, unable to
generalize, and driven primarily by a herd mentality. However, modern studies show that they perform a
number of cognitive tasks on a daily basis, with mental challenges that include food procurement and social
system identification. They also have good spatial discrimination abilities.[75] Studies have assessed equine
intelligence in the realms of problem solving, learning speed, and knowledge retention. Results show that
horses excel at simple learning, but also are able to solve advanced cognitive challenges that involve
categorization and concept learning. They learn from habituation, desensitization, Pavlovian conditioning,
and operant conditioning. They respond to and learn from both positive and negative reinforcement.[75]
Recent studies even suggest horses are able to count if the quantity involved is less than four.[76]
Domesticated horses tend to face greater mental challenges than wild horses, because they live in
artificial environments that stifle instinctual behaviour while learning tasks that are not natural.[75] Horses are
creatures of habit that respond and adapt well to regimentation, and respond best when the same routines
and techniques are used consistently. Some trainers believe that "intelligent" horses are reflections of
intelligent trainers who effectively use response conditioning techniques and positive reinforcement to train in
the style that fits best with an individual animal's natural inclinations. Others who handle horses regularly
note that personality also may play a role separate from intelligence in determining how a given animal
responds to various experiences.[77]
Temperament
Main articles: Draft horse, Warmblood, and Oriental horse
Horses are mammals, and as such are "warm-blooded" creatures, as opposed to cold-blooded
reptiles. However, these words have developed a separate meaning in the context of equine terminology,
used to describe temperament, not body temperature. For example, the "hot-bloods", such as many race
horses, exhibit more sensitivity and energy,[78] while the "cold-bloods", such as most draft breeds, are
quieter and calmer.[79] Sometimes "hot-bloods" are classified as "light horses" or "riding horses",[80] with the
"cold-bloods" classified as "draft horses" or "work horses".[81]
Illustration of hotbloods, warmbloods and coldblood breeds

"Hot blooded" breeds include "oriental horses" such as the Akhal-Teke, Barb, Arabian horse and
now-extinct Turkoman horse, as well as the Thoroughbred, a breed developed in England from the older
oriental breeds.[78] Hot bloods tend to be spirited, bold, and learn quickly. They are bred for agility and
speed.[82] They tend to be physically refined—thin-skinned, slim, and long-legged.[83] The original oriental
breeds were brought to Europe from the Middle East and North Africa when European breeders wished to
infuse these traits into racing and light cavalry horses.[84][85]
Muscular, heavy draft horses are known as "cold bloods", as they are bred not only for strength, but
also to have the calm, patient temperament needed to pull a plow or a heavy carriage full of people.[79] They
are sometimes nicknamed "gentle giants".[86] Well-known draft breeds include the Belgian and the
Clydesdale.[86] Some, like the Percheron are lighter and livelier, developed to pull carriages or to plow large
fields in drier climates.[87] Others, such as the Shire, are slower and more powerful, bred to plow fields with
heavy, clay-based soils.[88] The cold-blooded group also includes some pony breeds.[89]
"Warmblood" breeds, such as the Trakehner or Hanoverian, developed when European carriage and
war horses were crossed with Arabians or Thoroughbreds, producing a riding horse with more refinement
than a draft horse, but greater size and milder temperament than a lighter breed.[90] Certain pony breeds
with warmblood characteristics have been developed for smaller riders.[91] Warmbloods are considered a
"light horse" or "riding horse".[80]
Today, the term "Warmblood" refers to a specific subset of sport horse breeds that are used for
competition in dressage and show jumping.[92] Strictly speaking, the term "warm blood" refers to any cross
between cold-blooded and hot-blooded breeds.[93] Examples include breeds such as the Irish Draught or the
Cleveland Bay. The term was once used to refer to breeds of light riding horse other than Thoroughbreds or
Arabians, such as the Morgan horse.[82]
Sleep patterns
When horses lie down to sleep, others in the herd remain standing, awake or in a light doze, keeping
watch.
See also: Horse sleep patterns and Sleep in non-humans
Horses are able to sleep both standing up and lying down. In an adaptation from life in the wild,
horses are able to enter light sleep by using a "stay apparatus" in their legs, allowing them to doze without
collapsing.[94] Horses sleep better when in groups because some animals will sleep while others stand
guard to watch for predators. A horse kept alone will not sleep well because its instincts are to keep a
constant eye out for danger.[95]
Unlike humans, horses do not sleep in a solid, unbroken period of time, but take many short periods
of rest. Horses spend four to fifteen hours a day in standing rest, and from a few minutes to several hours
lying down. Total sleep time in a 24-hour period may range from several minutes to a couple of hours,[95]
mostly in short intervals of about 15 minutes each.[96]
Horses must lie down to reach REM sleep. They only have to lie down for an hour or two every few
days to meet their minimum REM sleep requirements.[95] However, if a horse is never allowed to lie down,
after several days it will become sleep-deprived, and in rare cases may suddenly collapse as it involuntarily
slips into REM sleep while still standing.[97] This condition differs from narcolepsy, although horses may also
suffer from that disorder.[98]
Taxonomy and evolution
From left to right: Size development, biometrical changes in the cranium, reduction of toes (left
forefoot)
Main articles: Evolution of the horse, Equus (genus), and Equidae
The horse adapted to survive in areas of wide-open terrain with sparse vegetation, surviving in an
ecosystem where other large grazing animals, especially ruminants, could not.[99] Horses and other equids
are odd-toed ungulates of the order Perissodactyla, a group of mammals that was dominant during the
Tertiary period. In the past, this order contained 14 families, but only three—Equidae (the horse and related
species), the tapir, and the rhinoceros—have survived to the present day.[100] The earliest known member of
the Equidae family was the Hyracotherium, which lived between 45 and 55 million years ago, during the
Eocene period. It had 4 toes on each front foot, and 3 toes on each back foot.[101] The extra toe on the front
feet soon disappeared with the Mesohippus, which lived 32 to 37 million years ago.[102] Over time, the extra
side toes shrank in size until they vanished. All that remains of them in modern horses is a set of small
vestigial bones on the leg below the knee,[103] known informally as splint bones.[104] Their legs also
lengthened as their toes disappeared until they were a hooved animal capable of running at great speed.
[103] By about 5 million years ago, the modern Equus had evolved.[105] Equid teeth also evolved from
browsing on soft, tropical plants to adapt to browsing of drier plant material, then to grazing of tougher plains
grasses. Thus proto-horses changed from leaf-eating forest-dwellers to grass-eating inhabitants of semi-arid
regions worldwide, including the steppes of Eurasia and the Great Plains of North America.
By about 15,000 years ago, Equus ferus was a widespread holarctic species. Horse bones from this
time period, the late Pleistocene, are found in Europe, Eurasia, Beringia, and North America.[106] Yet
between 10,000 and 7,600 years ago, the horse became extinct in North America and rare elsewhere.[107]
[108][109] The reasons for this extinction are not fully known, but one theory notes that extinction in North
America paralleled human arrival.[110] Another theory points to climate change, noting that approximately
12,500 years ago, the grasses characteristic of a steppe ecosystem gave way to shrub tundra, which was
covered with unpalatable plants.[111]
Wild species surviving into modern times
A small herd of Przewalski's Horses

Main article: Wild horse
A truly wild horse is a species or subspecies with no ancestors that were ever domesticated.
Therefore, most "wild" horses today are actually feral horses, animals that escaped or were turned loose from
domestic herds and the descendants of those animals.[112] Only one truly wild horse species (Equus ferus)
with two subspecies, the Tarpan and the Przewalski's Horse, survived into recorded history.
The only true wild horse alive today is the Przewalski's Horse (Equus ferus przewalskii), named after
the Russian explorer Nikolai Przhevalsky. It is a rare Asian animal, also known as the Mongolian Wild Horse;
Mongolian people know it as the taki, and the Kyrgyz people call it a kirtag. The species was presumed
extinct in the wild between 1969 and 1992, while a small breeding population survived in zoos around the
world. In 1992, it was reestablished in the wild due to the conservation efforts of numerous zoos.[113] Today,
a small wild breeding population exists in Mongolia.[114][115] There are additional animals still maintained at
zoos throughout the world.
The Tarpan or European Wild Horse (Equus ferus ferus) was found in Europe and much of Asia. It
survived into the historical era, but became extinct in 1909, when the last captive died in a Russian zoo.[116]
Thus, the genetic line was lost. Attempts have been made to recreate the Tarpan,[116][117][118] which
resulted in horses with outward physical similarities, but nonetheless descended from domesticated
ancestors and not true wild horses.
Periodically, populations of horses in isolated areas are speculated to be relic populations of wild
horses, but generally have been proven to be feral or domestic. For example, the Riwoche horse of Tibet was
proposed as such,[115] but testing did not reveal genetic differences with domesticated horses,[119]
Similarly, the Sorraia of Spain was proposed as a direct descendant of the Tarpan based on shared
characteristics,[120][121] but genetic studies have shown that the Sorraia is more closely related to other
horse breeds and that the outward similarity is an unreliable measure of relatedness.[120][122]
Other modern equids

Main article: Equus (genus)
Besides the horse, there are seven other species of genus Equus in the Equidae family. These are
the ass or donkey, Equus asinus; the mountain zebra, Equus zebra; plains zebra, Equus burchelli; Grévy's
zebra, Equus grevyi; the kiang, Equus kiang; and the onager, Equus hemionus.[123]
Horses can crossbreed with other members of their genus. The most common hybrid is the mule, a
cross between a "jack" (male donkey) and a mare. A related hybrid, a hinny, is a cross between a stallion and
a jenny (female donkey).[124] Other hybrids include the zorse, a cross between a zebra and a horse.[125]
With rare exceptions, most hybrids are sterile and cannot reproduce.[126]
Domestication
Main article: Domestication of the horse
Domestication of the horse most likely took place in central Asia prior to 3500 BC. Two major
sources of information are used to determine where and when the horse was first domesticated and how the
domesticated horse spread around the world. The first source is based on palaeological and archaeological
discoveries, the second source is a comparison of DNA obtained from modern horses to that from bones and
teeth of ancient horse remains.
The earliest archaeological evidence for the domestication of the horse comes from sites in Ukraine
and Kazakhstan, dating to approximately 3500–4000 BC.[127][128] By 3000 BC, the horse was completely
domesticated and by 2000 BC there was a sharp increase in the number of horse bones found in human
settlements in northwestern Europe, indicating the spread of domesticated horses throughout the continent.
[129] The most recent, but most irrefutable evidence of domestication comes from sites where horse remains
were interred with chariots in graves of the Sintashta and Petrovka cultures c. 2100 BC.[130]
Domestication is also studied by using the genetic material of present day horses and comparing it
with the genetic material present in the bones and teeth of horse remains found in archaeological and
palaeological excavations. The variation in the genetic material shows that very few wild stallions contributed
to the domestic horse,[131][132] while many mares were part of early domesticated herds.[122][133][134]
This is reflected in the difference in genetic variation between the DNA that is passed on along the paternal,
or sire line (Y-chromosome) versus that passed on along the maternal, or dam line (mitochondrial DNA).
There are very low levels of Y-chromosome variability,[131][132] but a great deal of genetic variation in
mitochondrial DNA.[122][133][134] There is also regional variation in mitochondrial DNA due to the inclusion
of wild mares in domestic herds.[122][133][134][135] Another characteristic of domestication is an increase in
coat color variation.[136] In horses, this increased dramatically between 5000 and 3000 BC.[137]
Before the availability of DNA techniques to resolve the questions related to the domestication of the
horse, various hypothesis were proposed. One classification was based on body types and conformation,
suggesting the presence of four basic prototypes that had adapted to their environment prior to
domestication.[138] Another hypothesis held that the four prototypes originated from a single wild species
and that all different body types were entirely a result of selective breeding after domestication.[139]
However, the lack of a detectable substructure in the horse has resulted in a rejection of both hypotheses.
Feral populations
Main article: Feral horse
Feral horses are born and live in the wild, but are descended from domesticated animals.[112] Many
populations of feral horses exist throughout the world.[140][141] Studies of feral herds have provided useful
insights into the behavior of prehistoric horses,[142] as well as greater understanding of the instincts and
behaviors that drive horses that live in domesticated conditions.[143]
Breeds
Main article: Horse breed, List of horse breeds, and Horse breeding
Horse breeds are groups of horses with distinctive characteristics that are transmitted consistently to
their offspring, such as conformation, color, performance ability, or disposition. These inherited traits result
from a combination of natural crosses and artificial selection methods. Horses have been selectively bred
since their domestication. Breeds developed due to a need for "form to function", the necessity to develop
certain characteristics in order to perform a particular type of work.[144] Thus, powerful but refined breeds
such as the Andalusian developed as riding horses that also had a great aptitude for dressage,[144] while
heavy draft horses such as the Clydesdale developed out of a need to perform demanding farm work and pull
heavy wagons.[145] Other horse breeds developed specifically for light agricultural work, carriage and road
work, various sport disciplines, or simply as pets.[146] Some breeds developed through centuries of
crossings with other breeds, while others, such as Tennessee Walking Horses and Morgans, descended
from a single foundation sire. There are more than 300 horse breeds in the world today.[147]
However, the concept of purebred bloodstock and a controlled, written breed registry only became of
significant importance in modern times. Sometimes purebred horses are called Thoroughbreds, which is
incorrect; "Thoroughbred" is a specific breed of horse, while a "purebred" is a horse (or any other animal)
with a defined pedigree recognized by a breed registry.[148] An early example of people who practiced
selective horse breeding were the Bedouin, who had a reputation for careful practices, keeping extensive
pedigrees of their Arabian horses and placing great value upon pure bloodlines.[149] These pedigrees were
originally transmitted via an oral tradition.[150] In the 14th century, Carthusian monks of southern Spain kept
meticulous pedigrees of bloodstock lineages still found today in the Andalusian horse.[151] One of the
earliest formal registries was General Stud Book for Thoroughbreds, which began in 1791 and traced back to
the foundation bloodstock for the breed.[152]
Interaction with humans

Worldwide, horses play a role within human cultures and have done so for millennia. Horses are
used for leisure activities, sports, and working purposes. The Food and Agriculture Organization (FAO)
estimates that in 2008, there were almost 59,000,000 horses in the world, with around 33,500,000 in the
Americas, 13,800,000 in Asia and 6,300,000 in Europe and smaller portions in Africa and Oceania. There are
estimated to be 9,500,000 horses in the United States alone.[153] The American Horse Council estimates
that horse-related activities have a direct impact on the economy of the United States of over $39 billion, and
when indirect spending is considered, the impact is over $102 billion.[154] In a 2004 "poll" conducted by
Animal Planet, more than 50,000 viewers from 73 countries voted for the horse as the world's 4th favorite
animal.[155]
Communication between human and horse is paramount in any equestrian activity;[156] to aid this
process horses are usually ridden with a saddle on their backs to assist the rider with balance and
positioning, and a bridle or related headgear to assist the rider in maintaining control.[157] Sometimes horses
are ridden without a saddle,[158] and occasionally, horses are trained to perform without a bridle or other
headgear.[159] Many horses are also driven, which requires a harness, bridle, and some type of vehicle.
[160]
Sport
A horse and rider in dressage competition at the Olympics

Main articles: Equestrianism, Horse racing, Horse training, and Horse tack
Historically, equestrians honed their skills through games and races. Equestrian sports provided
entertainment for crowds and honed the excellent horsemanship that was needed in battle. Many sports,
such as dressage, eventing and show jumping, have origins in military training, which were focused on
control and balance of both horse and rider. Other sports, such as rodeo, developed from practical skills such
as those needed on working ranches and stations. Sport hunting from horseback evolved from earlier
practical hunting techniques.[156] Horse racing of all types evolved from impromptu competitions between
riders or drivers. All forms of competition, requiring demanding and specialized skills from both horse and
rider, resulted in the systematic development of specialized breeds and equipment for each sport. The
popularity of equestrian sports through the centuries has resulted in the preservation of skills that would
otherwise have disappeared after horses stopped being used in combat.[161]
Horses are trained to be ridden or driven in a variety of sporting competitions. Examples include
show jumping, dressage, three-day eventing, competitive driving, endurance riding, gymkhana, rodeos, and
fox hunting.[162] Horse shows, which have their origins in medieval European fairs, are held around the
world. They host a huge range of classes, covering all of the mounted and harness disciplines, as well as "In-
hand" classes where the horses are led, rather than ridden, to be evaluated on their conformation. The
method of judging varies with the discipline, but winning usually depends on style and ability of both horse
and rider.[163] Sports such as polo do not judge the horse itself, but rather use the horse as a partner for
human competitors as a necessary part of the game. Although the horse requires specialized training to
participate, the details of its performance are not judged, only the result of the rider's actions—be it getting a
ball through a goal or some other task.[164] Examples of these sports of partnership between human and
horse include jousting, in which the main goal is for one rider to unseat the other,[165] and buzkashi, a team
game played throughout Central Asia, the aim being to capture a goat carcass while on horseback.[164]
Horse racing is an equestrian sport and major international industry, watched in almost every nation
of the world. There are three types: "flat" racing; steeplechasing, i.e. racing over jumps; and harness racing,
where horses trot or pace while pulling a driver in a small, light cart known as a sulky.[166] A major part of
horse racing's economic importance lies in the gambling associated with it.[167]
Work
A mounted police officer in Poland

There are certain jobs that horses do very well, and no technology has yet developed to fully replace
them. For example, mounted police horses are still effective for certain types of patrol duties and crowd
control.[168] Cattle ranches still require riders on horseback to round up cattle that are scattered across
remote, rugged terrain.[169] Search and rescue organizations in some countries depend upon mounted
teams to locate people, particularly hikers and children, and to provide disaster relief assistance.[170] Horses
can also be used in areas where it is necessary to avoid vehicular disruption to delicate soil, such as nature
reserves. They may also be the only form of transport allowed in wilderness areas. Horses are quieter than
motorized vehicles. Law enforcement officers such as park rangers or game wardens may use horses for
patrols, and horses or mules may also be used for clearing trails or other work in areas of rough terrain where
vehicles are less effective.[171]
Although machinery has replaced horses in many parts of the world, an estimated 100 million horses,
donkeys and mules are still used for agriculture and transportation in less developed areas. This number
includes around 27 million working in Africa alone.[172] Some land management practices such as
cultivating and logging can be efficiently performed with horses. In agriculture, less fossil fuel is used and
increased environmental conservation occurs over time with the use of draft animals such as horses.[173]
[174] Logging with horses and can result in reduced damage to soil structure and less damage to trees due
to more selective logging.[175]
Entertainment and culture

See also: Horses in art and Horse worship
Modern horses are often used to reenact many of their historical work purposes. Horses are used,
complete with equipment that is authentic or a meticulously recreated replica, in various live action historical
reenactments of specific periods of history, especially recreations of famous battles.[176] Horses are also
used to preserve cultural traditions and for ceremonial purposes. Countries such as the United Kingdom still
use horse-drawn carriages to convey royalty and other VIPs to and from certain culturally significant events.
[177] Public exhibitions are another example, such as the Budweiser Clydesdales, seen in parades and other
public settings, a team of draft horses that pull a beer wagon similar to that used before the invention of the
modern motorized truck.[178]
Horses are frequently seen in television and films. They are used both as main characters, in films
such as Seabiscuit, and Dreamer, and as visual elements that assure the accuracy of historical stories.[179]
Both live horses and iconic images of horses are used in advertising to promote a variety of products.[180]
The horse frequently appears in coats of arms in heraldry. The horse can be represented as standing,
walking (passant), trotting, running (courant), rearing (rampant or forcine) or springing (salient). The horse
may be saddled and bridled, harnessed, or without any apparel whatsoever.[181] The horse also appears in
the 12-year cycle of animals in the Chinese zodiac related to the Chinese calendar. According to Chinese
folklore, each animal is associated with certain personality traits, and those born in the year of the horse are
intelligent, independent, and free-spirited.[182]
Therapeutic use
See also: Hippotherapy and Therapeutic horseback riding
People of all ages with physical and mental disabilities obtain beneficial results from association with
horses. Therapeutic riding is used to mentally and physically stimulate disabled persons and help them
improve their lives through improved balance and coordination, increased self-confidence, and a greater
feeling of freedom and independence.[183] The benefits of equestrian activity for people with disabilities has
also been recognized with the addition of equestrian events to the Paralympic Games and recognition of
para-equestrian events by the International Federation for Equestrian Sports (FEI).[184] Hippotherapy and
therapeutic horseback riding are names for different physical, occupational, and speech therapy treatment
strategies that utilize equine movement. In hippotherapy, a therapist uses the horse's movement to improve
their patient's cognitive, coordination, balance, and fine motor skills, whereas therapeutic horseback riding
uses specific riding skills.[185]
Horses also provide psychological benefits to people whether they actually ride or not. "Equine-
assisted" or "equine-facilitated" therapy is a form of experiential psychotherapy that uses horses as
companion animals to assist people with mental illness, including anxiety disorders, psychotic disorders,
mood disorders, behavioral difficulties, and those who are going through major life changes.[186] There are
also experimental programs using horses in prison settings. Exposure to horses appears to improve the
behavior of inmates and help reduce recidivism when they leave.[187]
Warfare
Main article: Horses in warfare
Turkish cavalry, 1917
Horses in warfare have been seen for most of recorded history. The first archaeological evidence of
horses used in warfare dates to between 4000 to 3000 BC,[188] and the use of horses in warfare was
widespread by the end of the Bronze Age.[189][190] Although mechanization has largely replaced the horse
as a weapon of war, horses are still seen today in limited military uses, mostly for ceremonial purposes, or for
reconnaissance and transport activities in areas of rough terrain where motorized vehicles are ineffective.
Horses have been used in the 21st century by the Janjaweed militias in the War in Darfur.[191]
Products
Horses are raw material for many products made by humans throughout history, including
byproducts from the slaughter of horses as well as materials collected from living horses.
Products collected from living horses include mare's milk, used by people with large horse herds,
such as the Mongols, who let it ferment to produce kumis.[192] Horse blood was once used as food by the
Mongols and other nomadic tribes, who found it a convenient source of nutrition when traveling. Drinking
their own horses' blood allowed the Mongols to ride for extended periods of time without stopping to eat.[192]
Today, the drug Premarin is a mixture of estrogens extracted from the urine of pregnant mares (pregnant
mares' urine). It is a widely used drug for hormone replacement therapy.[193] The tail hair of horses can be
used for making bows for string instruments such as the violin, viola, cello, and double bass.[194]
Horse meat has been used as food for humans and carnivorous animals throughout the ages. It is
eaten in many parts of the world, though consumption is taboo in some cultures.[195] Horsemeat has been
an export industry in the United States and other countries,[195] though legislation has periodically been
introduced in the United States Congress which would end export from the United States.[196] Horsehide
leather has been used for boots, gloves, jackets,[197] baseballs,[198] and baseball gloves. Horse hooves
can also be used to produce animal glue.[199] Horse bones can be used to make implements.[200]
Specifically, in Italian cuisine, the horse tibia is sharpened into a probe called a spinto, which is used to test
the readiness of a (pig) ham as it cures.[201] In Asia, the saba is a horsehide vessel used in the production of
kumis.[202]
Care
Checking teeth and other physical examinations are an important part of horse care
Main article: Horse care
See also: Equine nutrition, Horse grooming, Veterinary medicine, and Farrier
Horses are grazing animals, and their major source of nutrients is good-quality forage from hay or
pasture.[203] They can consume approximately 2% to 2.5% of their body weight in dry feed each day.
Therefore, a 450-kilogram (990 lb) adult horse could eat up to 11 kilograms (24 lb) of food.[204] Sometimes,
concentrated feed such as grain is fed in addition to pasture or hay, especially when the animal is very
active.[205] When grain is fed, equine nutritionists recommend that 50% or more of the animal's diet by
weight should still be forage.[206]
Horses require a plentiful supply of clean water, a minimum of 10 US gallons (38 L) to 12 US gallons
(45 L) per day.[207] Although horses are adapted to live outside, they require shelter from the wind and
precipitation, which can range from a simple shed or shelter to an elaborate stable.[208]
Horses require routine hoof care from a farrier, as well as vaccinations to protect against various
diseases, and dental examinations from a veterinarian or a specialized equine dentist.[209] If horses are kept
inside in a barn, they require regular daily exercise for their physical health and mental well-being.[210]
When turned outside, they require well-maintained, sturdy fences to be safely contained.[211] Regular
grooming is also helpful to help the horse maintain good health of the hair coat and underlying skin.[212]
See also
Horses portal
• List of horse breeds

• Glossary of equestrian terms
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[hide]v · d · eExtant Perissodactyla (Odd-toed ungulates) species by suborder
Kingdom Animalia · Phylum Chordata · Class Mammalia · Infraclass Eutheria · Superorder

Laurasiatheria
Hippomorpha
Subgenus Equus: Wild horse (E. ferus) · Domestic

Horse (E. ferus caballus)
Equidae Subgenus Asinus: African Wild Ass (E. africanus) · Donkey
Equus
(Horse family) (E. asinus) · Onager (E. hemionus) · Kiang (E. kiang)
(including Zebras)
Subgenus Dolichohippus: Grévy's Zebra (E. grevyi)
Subgenus Hippotigris: Plains Zebra (E. quagga) · Mountain
Zebra (E. zebra)
Ceratomorpha
Rhinocerotidae Rhinoceros Indian Rhinoceros (R. unicornis) · Javan

Rhinoceros (R. sondaicus)
Dicerorhinus Sumatran Rhinoceros (D. sumatrensis)

(Rhinoceroses)
Ceratotherium White Rhinoceros (C. simum)
Diceros Black Rhinoceros (D. bicornis)
Tapiridae Baird's Tapir (T. bairdii) · Malayan Tapir (T. indicus) ·

(Tapirs) Tapirus Mountain Tapir (T. pinchaque) · Black Lowland Tapir (T.
pygmaeus) · South American Tapir (T. terrestris)
Category
[hide]v · d · eEquine
Equine Equine anatomy · Equine nutrition ·

science and Horse behavior · Horse care · Horse breeding ·
management Equine conformation · Equine coat color · Horse
gait
Glossary of equestrian terms · Horse
Equestrianism tack · Bit · Bridle · Saddle · Harness · English
and sport riding · Western riding · Driving · Horse training ·
Horse racing · Equestrian at the Summer
Olympics · Horse show · Equitation
Domestication · In warfare · In the Middle

Evolution and Ages · Horses in East Asian warfare · History of
history the horse in South Asia · Horses in the
Napoleonic Wars · Horses in World War I ·
Horses in World War II
List of horse breeds ·

Wild horse · Feral horse ·
Horses Stock horse · Gaited horse ·
Draft horse · Warmblood ·
Horse breeds,
Sport horse
types
and other Equidae
Other Donkey · Zebra ·
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Evolvability

Evolvability is defined as the ability of a population of organisms to generate genetic diversity and
evolve through natural selection.[1][2]
In order for a biological organism to evolve by natural selection, there must be a certain minimum
probability that new, heritable variants are beneficial. Random mutations, unless they occur in DNA
sequences with no function, are expected to be mostly detrimental. Beneficial mutations are always rare, but
if they are too rare, then adaptation cannot occur. Random mutations seem to be beneficial more often than
random changes to a typical computer program are.[3] This means that biological genomes are structured in
ways that make beneficial changes less unlikely than they would otherwise be. This has been taken as
evidence that evolution has created not just fitter organisms, but populations of organisms that are better
able to evolve.
Contents
[hide]
• 1 Alternative definitions
• 1.1 Example
• 2 Generating more variation
• 3 Enhancement of Selection
• 4 Robustness and evolvability
• 5 Exploration ahead of time
• 6 Modularity
• 7 Evolution of evolvability
• 8 References
[edit] Alternative definitions

Wagner (2005) describes two definitions of evolvability. According to the first definition, a biological
system is evolvable
• if its properties show heritable genetic variation, and
• if natural selection can thus change these properties.
According to the second definition, a biological system is evolvable
• if it can acquire novel functions through genetic change, functions that help the organism
survive and reproduce.
These definitions can be applied on all levels of biological organisation, from macromolecules to
mammals. Not all systems that are evolvable in the first sense are evolvable in the second sense. (See
example below from Wagner (2005)).
Pigliucci[4] recognizes three classes of definition, depending on timescale. The first corresponds to
Wagner's first, and represents the very short timescales that are described by quantitative genetics. He
divides Wagner's second definition into two categories, one representing the intermediate timescales that
can be studied using population genetics, and one representing exceedingly rare long-term innovations of
form.
[edit] Example
Consider an enzyme with multiple alleles in the population. Each allele catalyzes the same reaction,
but with a different level of activity. However, even after millions of years of evolution, exploring many
sequences with similar function, no mutation might exist that gives this enzyme the ability to catalyze a
different reaction. Thus, although the enzyme’s activity is evolvable in the first sense, that does not mean that
the enzyme's function is evolvable in the second sense. However, every system evolvable in the second
sense must also be evolvable in the first.
[edit] Generating more variation

More heritable phenotypic variation means more evolvability. While mutation is the ultimate source of
heritable variation, its permutations and combinations also make a big difference. Sexual reproduction
generates more variation (and thereby evolvability) relative to asexual reproduction (see evolution of sexual
reproduction). Evolvability is further increased by generating more variation when an organism is stressed,
and thus likely to be less well adapted, but less variation when an organism is doing well. The amount of
variation generated can be adjusted in many different ways, for example via the mutation rate, via the
probability of sexual vs. asexual reproduction, via the probability of outcrossing vs. inbreeding, and via
dispersal.
[edit] Enhancement of Selection

Rather than creating more phenotypic variation, some mechanisms increase the intensity and
effectiveness with which selection acts on existing phenotypic variation. For example:
• Mating rituals that allow sexual selection on "good genes", and so intensify natural selection
• Large population size
• Recombination decreasing the importance of the Hill-Robertson effect, where different
genotypes contain different adaptive mutations. Recombination brings the two alleles together,
creating a super-genotype in place of two competing lineages.
• Shorter generation time
[edit] Robustness and evolvability

Robustness will not increase evolvability in the first sense. In organisms with a high level of
robustness, mutations will have smaller phenotypic effects than in organisms with a low level of robustness.
Thus, robustness reduces the amount of heritable genetic variation on which selection can act. However,
robustness may allow exploration of large regions of genotype space, increasing robustness according to the
second sense.[5][6]
For example, one reason many proteins are less robust to mutation is that they have marginal
thermodynamic stability, and most mutations reduce this stability further. Proteins that are more thermostable
can tolerate a wider range of mutations, and are more evolvable.[7]
[edit] Exploration ahead of time

When mutational robustness exists, many mutants will persist in a cryptic state. Mutations tend to fall
into two categories, having either a very bad effect or very little effect: few mutations fall somewhere in
between.[8] Sometimes, these mutations will not be completely invisible, but still have rare effects, with very
low penetrance. When this happens, natural selection weeds out the really bad mutations, while leaving the
other mutations relatively unaffected.[9] While evolution has no "foresight" to know which environment will be
encountered in the future, some mutations cause major disruption to a basic biological process, and will
never be adaptive in any environment. Screening these out in advance leads to preadapted stocks of cryptic
genetic variation.
Another way that phenotypes can be explored, prior to strong genetic commitment, is through
learning. An organism that learns gets to "sample" several different phenotypes during its early development,
and later sticks to whatever worked best. Later in evolution, the optimal phenotype can be genetically
assimilated so it becomes the default behavior rather than a rare behavior. This is known as the Baldwin
effect, and it can increase evolvability.[10][11]
Learning biases phenotypes in a beneficial direction. But an exploratory flattening of the fitness
landscape can also increase evolvability even when it has no direction, for example when the flattening is a
result of random errors in molecular and/or developmental processes. This increase in evolvability can
happen when evolution is faced with crossing a "valley" in an adaptive landscape. This means that two
mutations exist that are deleterious by themselves, but beneficial in combination. These combinations can
evolve more easily when the landscape is first flattened, and the discovered phenotype is then fixed by
genetic assimilation.[12][13][14]
[edit] Modularity
If every mutation affected every trait, then a mutation that was an improvement for one trait would be
a disadvantage for other traits. This means that almost no mutations would be beneficial overall. But if
pleiotropy is restricted to within functional modules, then mutations affect only one trait at a time, and
adaptation is much easier.
[edit] Evolution of evolvability

While variation yielding high evolvability could be useful in the long term, in the short term most of
that variation is likely to be deleterious. For example, naively it would seem that increasing the mutation rate
via a mutator allele would increase evolvability. But as an extreme example, if the mutation rate is too high
then all individuals will be dead or at least carry a heavy mutation load. Short-term selection for low variation
most of the time is usually thought likely to be more powerful than long-term selection for evolvability, making
it difficult for natural selection to cause the evolution of evolvability.
When recombination is low, mutator alleles may still sometimes hitchhike on the success of adaptive
mutations that they cause. In this case, selection can take place at the level of the lineage.[15] This may
explain why mutators are often seen during experimental evolution of microbes. Mutator alleles can also
evolve more easily when they only increase mutation rates in nearby DNA sequences, not across the whole
genome: this is known as a contingency locus.
The evolution of evolvability is less controversial if it occurs via the evolution of sexual reproduction,
or via the tendency of variation-generating mechanisms to become more active when an organism is
stressed. The yeast prion [PSI+] may also be an example of the evolution of evolvability through evolutionary
capacitance.[16][17] An evolutionary capacitor is a switch that turns genetic variation on and off. This is very
much like bet-hedging the risk that a future environment will be similar or different.[18] Theoretical models
also predict the evolution of evolvability via modularity.[19]
[edit] References
1. ^ Colegrave N, Collins S (May 2008). "Experimental evolution: experimental evolution and
evolvability". Heredity 100 (5): 464–70. doi:10.1038/sj.hdy.6801095. PMID 18212804.
2. ^ Kirschner M, Gerhart J (1998). "Evolvability". Proceedings of the National Academy of
Sciences of the United States of America 95 (15): 8420–8427. doi:10.1073/pnas.95.15.8420.
PMID 9671692.
3. ^ Wagner GP, Alternberg L (1996). "Complex adaptations and the evolution of evolvability".
Evolution 50 (3): 967–976. doi:10.2307/2410639. http://jstor.org/stable/2410639.
4. ^ Pigliucci M (2008). "Is evolvability evolvable?". Nature Reviews Genetics 9 (1): 75–82.
doi:10.1038/nrg2278. PMID 18059367.
5. ^ Masel J, Trotter MV (2010). "Robustness and evolvability". Trends in Genetics 26 (9): 406–
414. doi:10.1016/j.tig.2010.06.002. PMID 20598394.
6. ^ Wagner A (2005). Robustness and evolvability in living systems . Princeton Studies in
Complexity. Princeton University Press. ISBN 0691122407.
7. ^ Bloom JD, Labthavikul ST, Otey, CR, Arnold FH (2006). "Protein stability promotes
evolvability". Proceedings of the National Academy of Sciences of the United States of America 103
(15): 5869–5874. doi:10.1073/pnas.0510098103. PMID 16581913. PMC 1458665.
http://www.pnas.org/cgi/content/abstract/103/15/5869.
8. ^ Eyre-Walker A, Keightley, PD (2007). "The distribution of fitness effects of new mutations".
9. ^ Masel, Joanna (March 2006). "Cryptic Genetic Variation Is Enriched for Potential
Adaptations". Genetics (Genetics Society of America) 172 (3): 1985–1991.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=1456269.
10.^ Hinton GE, Nowlan SJ (1987). "How learning can guide evolution". Complex Systems 1:
495–502.
11.^ Borenstein E, Meilijson I, Ruppin E (2006). "The effect of phenotypic plasticity on evolution
in multipeaked fitness landscapes". Journal of Evolutionary Biology 19 (5): 1555–1570.
doi:10.1111/j.1420-9101.2006.01125.x. PMID 16910985.
12.^ Kim Y (2007). "Rate of adaptive peak shifts with partial genetic robustness". Evolution 61
(8): 1847–1856. doi:10.1111/j.1558-5646.2007.00166.x. PMID 17683428.
13.^ Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E (2008). "The look-ahead
effect of phenotypic mutations". Biology Direct 3: 18. doi:10.1186/1745-6150-3-18. PMID 18479505.
PMC 2423361. http://www.biology-direct.com/content/3/1/18.
14.^ Griswold CK, Masel J (2009). "Complex adaptations can drive the evolution of the capacitor
[PSI+, even with realistic rates of yeast sex"]. PLoS Genetics 5 (6): e1000517.
doi:10.1371/journal.pgen.1000517. PMID 19521499. PMC 2686163.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000517.
15.^ Eshel I (1973). "Clone-selection and optimal rates of mutation". Journal of Applied
Probability 10 (4): 728–738. doi:10.2307/3212376. http://jstor.org/stable/3212376.
16.^ Masel J, Bergman A, (2003). "The evolution of the evolvability properties of the yeast prion
[PSI+]". Evolution 57 (7): 1498–1512. PMID 12940355.
17.^ Lancaster AK, Bardill JP, True HL, Masel J (2010). "The Spontaneous Appearance Rate of
the Yeast Prion [PSI+ and Its Implications for the Evolution of the Evolvability Properties of the [PSI+]
System"]. Genetics 184 (2): 393–400. doi:10.1534/genetics.109.110213. PMID 19917766.
18.^ King O, Masel J (2007). "The evolution of bet-hedging adaptations to rare scenarios".
Theoretical Population Biology 72 (4): 560–575. doi:10.1016/j.tpb.2007.08.006. PMID 17915273.
19.^ Draghi J, Wagner G (2008). "Evolution of evolvability in a developmental model".
Theoretical Population Biology 62: 301–315.


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Evolvability"
Categories: Evolutionary biology
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Islamic creationism

challenged and removed. (March 2007)
This article may contain original research. Please improve it by verifying the claims
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Islamic creationism is the belief that the universe (including humanity) was created by Allah as
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Contents
[hide]
• 1 Islam and human evolution - A history
• 1.1 Struggle for existence
• 1.2 Transmutation of species
• 1.3 Ahmadiyya views
• 2 Prevalence
• 3 Theology
• 3.1 Universal creation
• 4 References
[edit] Islam and human evolution - A history
[edit] Struggle for existence
The Mu'tazili scientist and philosopher al-Jahiz (c. 776-869) was the first of the Muslim biologists and
philosophers to develop an early theory of evolution. He speculated on the influence of the environment on
animals, considered the effects of the environment on the likelihood of an animal to survive, and first
described the struggle for existence, a precursor to natural selection.[1][2][3] Al-Jahiz's ideas on the struggle
for existence in the Book of Animals have been summarized as follows:
"Animals engage in a struggle for existence; for resources, to avoid being eaten and to breed.
Environmental factors influence organisms to develop new characteristics to ensure survival,
thus transforming into new species. Animals that survive to breed can pass on their successful
characteristics to offspring."[citation needed]
In Chapter 47 of his India, entitled "On Vasudeva and the Wars of the Bharata," Abu Rayhan Biruni
attempted to give a naturalistic explanation as to why the struggles described in the Mahabharata "had to
take place." He explains it using natural processes that include biological ideas related to evolution, which
has led several scholars to compare his ideas to Darwinism and natural selection. This is due to Biruni
describing the idea of artificial selection and then applying it to nature:[4]
"The agriculturist selects his corn, letting grow as much as he requires, and tearing out the
remainder. The forester leaves those branches which he perceives to be excellent, whilst he
cuts away all others. The bees kill those of their kind who only eat, but do not work in their
beehive. Nature proceeds in a similar way; however, it does not distinguish for its action is under
all circumstances one and the same. It allows the leaves and fruit of the trees to perish, thus
preventing them from realising that result which they are intended to produce in the economy of
nature. It removes them so as to make room for others."
In the 13th century, Nasir al-Din al-Tusi explains how the elements evolved into minerals, then
plants, then animals, and then humans. Tusi then goes on to explain how hereditary variability was an
important factor for biological evolution of living things:[5]
"The organisms that can gain the new features faster are more variable. As a result, they gain
advantages over other creatures. [...] The bodies are changing as a result of the internal and
external interactions."
Tusi discusses how organisms are able to adapt to their environments:[5]

"Look at the world of animals and birds. They have all that is necessary for defense, protection
and daily life, including strengths, courage and appropriate tools [organs] [...] Some of these
organs are real weapons, [...] For example, horns-spear, teeth and claws-knife and needle, feet
and hoofs-cudgel. The thorns and needles of some animals are similar to arrows. [...] Animals
that have no other means of defense (as the gazelle and fox) protect themselves with the help of
flight and cunning. [...] Some of them, for example, bees, ants and some bird species, have
united in communities in order to protect themselves and help each other."
Tusi then explains how humans evolved from advanced animals:[5]

"Such humans [probably anthropoid apes] live in the Western Sudan and other distant corners
of the world. They are close to animals by their habits, deeds and behavior. [...] The human has
features that distinguish him from other creatures, but he has other features that unite him with
the animal world, vegetable kingdom or even with the inanimate bodies."
[edit] Transmutation of species

Al-Dinawari (828-896), considered the founder of Arabic botany for his Book of Plants, discussed
plant evolution from its birth to its death, describing the phases of plant growth and the production of flowers
and fruit.[6]
Material in Ibn Miskawayh's al-Fawz al-Asghar and the Brethren of Purity's Encyclopedia of the
Brethren of Purity (The Epistles of Ikhwan al-Safa) has been criticized as overenthusiastic.[7] Muhammad
Hamidullah describes their evolutionary ideas as follows:
"[These books] state that God first created matter and invested it with energy for development.
Matter, therefore, adopted the form of vapour which assumed the shape of water in due time.
The next stage of development was mineral life. Different kinds of stones developed in course of
time. Their highest form being mirjan (coral). It is a stone which has in it branches like those of a
tree. After mineral life evolves vegetation. The evolution of vegetation culminates with a tree
which bears the qualities of an animal. This is the date-palm. It has male and female genders. It
does not wither if all its branches are chopped but it dies when the head is cut off. The date-
palm is therefore considered the highest among the trees and resembles the lowest among
animals. Then is born the lowest of animals. It evolves into an ape. This is not the statement of
Darwin. This is what Ibn Maskawayh states and this is precisely what is written in the Epistles of
Ikhwan al-Safa. The Muslim thinkers state that ape then evolved into a lower kind of a barbarian
man. He then became a superior human being. Man becomes a saint, a prophet. He evolves
into a higher stage and becomes an angel. The one higher to angels is indeed none but God.
Everything begins from Him and everything returns to Him."[8]
English translations of the Encyclopedia of the Brethren of Purity were available from 1812.[9]
In the 14th century, Ibn Khaldun further developed the evolutionary ideas found in the Encyclopedia
of the Brethren of Purity. The following statements from his 1377 work, the Muqaddimah, express
evolutionary ideas:
"We explained there that the whole of existence in (all) its simple and composite worlds is
arranged in a natural order of ascent and descent, so that everything constitutes an
uninterrupted continuum. The essences at the end of each particular stage of the worlds are by
nature prepared to be transformed into the essence adjacent to them, either above or below
them. This is the case with the simple material elements; it is the case with palms and vines,
(which constitute) the last stage of plants, in their relation to snails and shellfish, (which
constitute) the (lowest) stage of animals. It is also the case with monkeys, creatures combining
in themselves cleverness and perception, in their relation to man, the being who has the ability
to think and to reflect. The preparedness (for transformation) that exists on either side, at each
stage of the worlds, is meant when (we speak about) their connection.[10]
Plants do not have the same fineness and power that animals have. Therefore, the sages rarely
turned to them. Animals are the last and final stage of the three permutations. Minerals turn into
plants, and plants into animals, but animals cannot turn into anything finer than themselves."[11]
Numerous other Islamic scholars and scientists, including the polymaths Ibn al-Haytham and Al-
Khazini, discussed and developed these ideas. Translated into Latin, these works began to appear in the
West after the Renaissance and may have had an impact on Western philosophy and science.[citation
needed]
[edit] Ahmadiyya views

Main article: Ahmadiyya views of evolution
The Ahmadiyya Muslim Movement are the only denomination of Islam that universally accept
Evolution, albeit divinely designed, and actively promote it.[12] Over the course of several decades the
movement has issued various publications in support of the scientific concepts behind Evolution and
frequently engage in promoting how it contends with religious scripture.
[edit] Prevalence
Evolutionary ideas have existed in the Muslim world ever since they were expressed by the Afro-
Arab biologist Al-Jahiz (c. 776-869), who first described the struggle for existence, a precursor to natural
selection.[1][2] Many other medieval Islamic philosophers and biologists later expressed evolutionary ideas,
including Ibn Miskawayh, the Brethren of Purity,[8] Abu Rayhan Biruni,[13] Nasir al-Din Tusi[5] and Ibn
Khaldun.[14][15]
Little is known about general societal views of evolution in Muslim countries. A 2007 study of
religious patterns found that only 8% of Egyptians, 11% of Malaysians, 14% of Pakistanis, 16% of
Indonesians, and 22% of Turks agree that Darwin's theory is probably or most certainly true, and a 2006
survey reported that about 25% of Turkish adults agreed that human beings evolved from earlier animal
species. In contrast, the 2007 study found that only 28% of Kazakhs thought that evolution is false; this
fraction is much lower than the roughly 40% of U.S. adults with the same opinion (this could be due to the
fact that Kazakhstan is a former republic of the USSR, where atheism was explicitly endorsed and
promoted).[16]
In Turkey, polemics against the theory of evolution have been waged by the Nurculuk movement of
Said Nursi since the late 1970s. At present, its main exponent[17] is the writer Harun Yahya (pseudonym of
Adnan Oktar) who uses the Internet as one of the main methods for the propagation of his ideas.[18] His BAV
(Bilim Araştırma Vakfı/ Science Research Foundation) organizes conferences with leading American
creationists. Another leading Turkish advocate of Islamic creationism is Fethullah Gülen. Due to the lack of a
detailed account of creation in the Qur'an, aspects other than the literal truth of the scripture are emphasized
in the Islamic debate. The most important concept is the idea that there is no such thing as a random event,
and that everything happens according to God's will. This does not mean that God has to interfere with the
universe. Hence the ideas of some Islamic creationists are closer to Intelligent design than to Young Earth
Creationism. According to Guardian some British Muslim students quote the Qu'ran in scientific exams and
fail as a result.[19] At a conference in the UK in January, 2004, entitled Creationism: Science and Faith in
Schools, Dr Khalid Anees, president of the Islamic Society of Britain stated that "Muslims interpret the world
through both the Koran and what is tangible and seen. There is no contradiction between what is revealed in
the Koran and natural selection and survival of the fittest."[20]
[edit] Theology
See also: Qur'an and science
The Qur'an does not contain a complete set out a chronology of creation,[21] other than declaring
that it took six days, and that "days" might have been interpreted not just as literal twenty-four hour periods
but as stages or other periods of time to complete (it is rather a relative quantity of time),[21][22] and
therefore is not subject to the same level of debate as some interpretators of the Bible regarding scientific
evidence and chronology. Skeptics point out there is no explicit mention of the extinction of whole species
long before the creation of man in the Qur'an, whilst its inspiration is defended on the grounds that it is not a
book of science. The Bible is held by Muslims to contain errors and therefore has not presented the same
level of difficulty in the Islamic world as in some sections of Christianity outlined above. However, in recent
years, a movement has begun to emerge in some Muslim countries promoting themes that have been
characteristic of Christian creationists and Bible literalists in the past. A few oppose this citing the lack of
compatibility between the two and that the Qur'an contradicts the Bible in numerous passages.[19][23][24]
Khalid Anees, president of the Islamic Society of Britain, at a conference, Creationism: Science and Faith in
Schools, made points including the following:[20]
"Islam also has its own school of Evolutionary creationism/Theistic evolutionism, which holds
that mainstream scientific analysis of the origin of the universe is supported by the Qur'an. Many
Muslims believe in evolutionary creationism, especially among Sunni and Shia Muslims and the
Liberal movements within Islam. Among scholars of Islam İbrahim Hakkı of Erzurum who lived in
Erzurum then Ottoman Empire now Republic of Turkey in 18th century is famous of stating
'between plants and animals there is sponge, and, between animals and humans there is
monkey'."[25]
[edit] Universal creation

There are several verses in the Qur'an which some modern writers have interpreted as being
compatible with the expansion of the universe, Big Bang and Big Crunch theories:[26][27][28]
"Do not the Unbelievers see that the skies (space) and the earth were joined together, then We
clove them asunder and We created every living thing out of the water. Will they not then
believe?"[Qur'an 21:30]
"Then turned He to the sky (space) when it was smoke, and said unto it and unto the earth:
Come both of you, willingly or loth. They said: We come, obedient." [Qur'an 41:11]
"With power and skill did We construct the Firmament: for it is We Who create the vastness of
space."[Qur'an 51:47]
"On the day when We will roll up the sky (space) like the rolling up of the scroll for writings, as
We originated the first creation, (so) We shall reproduce it; a promise (binding on Us); surely We
will bring it about."[Qur'an 21:104]
[edit] References
1. ^ a b Conway Zirkle (1941). Natural Selection before the "Origin of Species", Proceedings of
the American Philosophical Society 84 (1), p. 71-123.
2. ^ a b Mehmet Bayrakdar (Third Quarter, 1983). "Al-Jahiz And the Rise of Biological
Evolutionism", The Islamic Quarterly. London.
3. ^ Paul S. Agutter & Denys N. Wheatley (2008). Thinking about Life: The History and
Philosophy of Biology and Other Sciences. Springer. p. 43. ISBN 1402088655
4. ^ Jan Z. Wilczynski (December 1959). "On the Presumed Darwinism of Alberuni Eight
Hundred Years before Darwin". Isis 50 (4): 459–466 [459–61]. doi:10.1086/348801
5. ^ a b c d Farid Alakbarov (Summer 2001). A 13th-Century Darwin? Tusi's Views on Evolution,
Azerbaijan International 9 (2).
6. ^ Fahd, Toufic. "Botany and agriculture". pp. 815. , in (Morelon & Rashed 1996)
7. ^ Footnote 27a to Chapter 6, Part 5 in Khaldūn, Ibn. The Muqaddimah. Franz Rosenthal
(trans.). http://www.muslimphilosophy.com/ik/Muqaddimah/.
8. ^ a b Muhammad Hamidullah and Afzal Iqbal (1993), The Emergence of Islam: Lectures on
the Development of Islamic World-view, Intellectual Tradition and Polity , p. 143-144. Islamic
Research Institute, Islamabad.
9. ^ "Ikhwan as-Safa and their Rasa'il: A Critical Review of a Century and a Half of Research",
by A. L. Tibawi, as published in volume 2 of The Islamic Quarterly in 1955; pgs. 28-46
10.^ Muqaddimah, Chapter 6, Part 5
11.^ Muqaddimah, Chapter 6, Part 29
12.^ Jesus and the Indian Messiah – 13. Every Wind of Doctrine
13.^ Jan Z. Wilczynski (December 1959). "On the Presumed Darwinism of Alberuni Eight
Hundred Years before Darwin". Isis 50 (4): 459–466. doi:10.1086/348801
16.^ Hameed S (2008). "Bracing for Islamic creationism". Science 322 (5908): 1637–8.
doi:10.1126/science.1163672. PMID 19074331.
17.^ "Seeing the light -- of science". salon.com.
http://www.salon.com/books/int/2007/01/02/numbers/index3.html. Retrieved 2009-01-06.
18.^ Darwinism's Contradiction with Religion, Why Darwinism is Incompatible With the Qur'an,
Harun Yahya
19.^ a b Campbell, Duncan (2006-02-21). "Academics fight rise of creationism at universities".
Guardian. http://education.guardian.co.uk/higher/news/story/0,,1714171,00.html. Retrieved 2008-07-
19.
20.^ a b Papineau, David (2004-01-07). "Creationism: Science and Faith in Schools". Guardian.
http://education.guardian.co.uk/conferences/story/0,,1117752,00.html. Retrieved 2008-07-18.
21.^ a b "The Origin of Life: An Islamic perspective". Islam for Today.
http://www.islamfortoday.com/emerick16.htm. Retrieved 2007-03-14.
22.^ "Your Guardian Lord is Allah, Who created the heavens and the earth in six days", Qur'an,
Surah 7:54
23.^ Sayin, Ümit; Kence, Aykut (1999). "Islamic Scientific Creationism: A New Challenge in
Turkey". National Center for Science Education. http://ncse.com/rncse/19/6/islamic-scientific-
creationism. Retrieved 2009-11-12.
24.^ Koning, Danielle (2006). "Anti-evolutionism amongst Muslim students" (PDF). ISIM Review
18: 48. http://www.isim.nl/files/Review_18/Review_18-48.pdf. Retrieved 2007-03-14.
25.^ Erzurumi, İ. H. (1257). Marifetname
26.^ Harun Yahya, The Big Bang Echoes through the Map of the Galaxy
27.^ Maurice Bucaille (1990), The Bible the Qur'an and Science, "The Quran and Modern
Science", ISBN 8171011322.
28.^ A. Abd-Allah, The Qur'an, Knowledge, and Science, University of Southern California.

• Science in the Quran, by Ashraf Salmawi
• The Muslim Responses to Evolution by Abdul Majid
• Quran Evolution and Intelligent Design, by Iyad Hijazi & Sylvia Nemmers
• In the Muslim world, creationism is on the rise Boston.com
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W000
Whale
This article is about a marine mammal. For other uses, see Whale (disambiguation).
Whale
Humpback whale
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Subclass: Eutheria
Order: Cetacea
Whale (origin Old English hƿæl) is the common name for various marine mammals of the order
Cetacea.[1] The term whale sometimes refers to all cetaceans, but more often it excludes dolphins and
porpoises[2], which belong to suborder Odontoceti (toothed whales). This suborder also includes the sperm
whale, killer whale, pilot whale, and beluga whale. The other Cetacean suborder Mysticeti (baleen whales),
are filter feeders that eat small organisms caught by straining seawater through a comblike structure found in
the mouth called baleen. This suborder includes the blue whale, the humpback whale, the bowhead whale
and the minke whale. All Cetacea have forelimbs modified as fins, a tail with horizontal flukes, and nasal
openings (blowholes) on top of the head.
Whales range in size from the blue whale, the largest animal known to have ever existed[3] at 35 m
(115 ft) and 150 tonnes (150 LT; 170 ST), to various pygmy species, such as the pygmy sperm whale at
3.5 m (11 ft).
Whales collectively inhabit all the world's oceans and number in the millions, with annual population
growth rate estimates for various species ranging from 3-13%.[4] For centuries, whales have been hunted for
meat and as a source of raw materials. By the middle of the 20th century, however, industrial whaling had left
many species seriously endangered, leading to the end of whaling in all but a few countries.
Contents
[hide]
• 1 Taxonomy
• 2 Evolution
• 3 Anatomy
• 3.1 Blowhole(s)
• 3.2 Appendages
• 3.3 Dentition
• 3.4 Ears
• 4 Life history/behavior
• 4.2 Socialization
• 4.3 Sleep
• 4.4 Surfacing behavior
• 4.5 Lifespan
• 4.6 Vocalization
• 5 Ecology
• 5.1 Feeding
• 6 Relation to humans
• 6.1 Whaling
• 6.2 Bycatch
• 6.3 Naval sonar
Taxonomy
See also: List of whale species
Cetaceans are divided into two suborders:
• The largest suborder, Mysticeti (baleen whales) are characterized by baleen, a sieve-like
structure in the upper jaw made of keratin, which it uses to filter plankton from the water.
• Odontoceti (toothed whales) bear sharp teeth for hunting. Odontoceti also include dolphins
and porpoises.
Both cetaceans and artiodactyl are now classified under the super-order Cetartiodactyla which
includes both whales and hippopotamuses. Whales are the hippopotamus's closest living relatives.[5]
Evolution
Ambulocetus natans - a primitive whale

See also: Evolution of cetaceans
All cetaceans, including whales, dolphins and porpoises, are descendants of land-living mammals of
the Artiodactyl order (even-toed ungulates). Both descended from a common ancestor, the Indohyus (an
extinct semi-aquatic deer-like ungulate) from which they split around 54 million years ago.[6][7] Primitive
whales probably first took to the sea about 50 million years ago and became fully aquatic about 5-10 million
years later.[8]
Anatomy
Like all mammals, whales breathe air, are warm-blooded, nurse their young with milk from mammary
glands, and have body hair.[citation needed]
Beneath the skin lies a layer of fat called blubber, which stores energy and insulates the body.
Whales have a spinal column, a vestigial pelvic bone, and a four-chambered heart. The neck vertebrae are
typically fused, trading flexibility for stability during swimming.[ citation needed]
Blowhole(s)
Features of a blue whale

Whales breathe via blowholes; baleen whales have two and toothed whales have one. These are
located on the top of the head, allowing the animal to remain mostly submerged whilst breathing. Breathing
involves expelling excess water from the blowhole, forming an upward spout, followed by inhaling air into the
lungs. Spout shapes differ among species and can help with identification.
Appendages
The body shape is fusiform and the modified forelimbs, or fins, are paddle-shaped. The end of the tail
is composed of two flukes, which propel the animal by vertical movement, as opposed to the horizontal
movement of a fish tail. Although whales do not possess fully developed hind limbs, some (such as sperm
whales and baleen whales) possess discrete rudimentary appendages, which may even have feet and digits.
Most species have a dorsal fin.[citation needed]
Dentition
Toothed whales, such as the sperm whale, possess teeth with cementum cells overlying dentine
cells. Unlike human teeth, which are composed mostly of enamel on the portion of the tooth outside of the
gum, whale teeth have cementum outside the gum. Only in larger whales, where the cementum has been
worn away on the tip of the tooth, does enamel show.[9]
Instead of teeth, Baleen whales have a row of plates on the upper side of their jaws that resemble the
"teeth" of a comb.
Ears
The whale ear has specific adaptations to the marine environment. In humans, the middle ear works
as an impedance matcher between the outside air’s low impedance and the cochlear fluid’s high impedance.
In aquatic mammals such as whales, however, there is no great difference between the outer and inner
environments. Instead of sound passing through the outer ear to the middle ear, whales receive sound
through the throat, from which it passes through a low-impedance fat-filled cavity to the inner ear.[10]
Life history/behavior
Reproduction
Males are called 'bulls', females, 'cows' and newborns, 'calves'. Most species do not maintain fixed
partnerships and females have several mates each season.[11][12]
The female delivers usually a single calf tail-first to minimize the risk of drowning. Whale cows nurse
by actively squirting milk, so fatty that it has the consistency of toothpaste, into the mouths of their young.[13]
Nursing continues for more than a year in many species, and is associated with a strong bond between
mother and calf. Reproductive maturity occurs typically at seven to ten years. This mode of reproduction
produces few offspring, but increases survival probability.
Socialization
Whales are known to teach, learn, cooperate, scheme, and even grieve.[14]
Sleep
A Humpback Whale breaching.

Unlike most animals, whales are conscious breathers. All mammals sleep, but whales cannot afford
to become unconscious for long because they may drown. It is thought that only one hemisphere of the
whale's brain sleeps at a time, so they rest but are never completely asleep.[15]
Surfacing behavior
Main article: Whale surfacing behavior
Many whales exhibit behaviors such as breaching and tail slapping that expose large parts of their
bodies to the air.
Lifespan
Whale lifespans vary among species and are not well characterized. Whaling left few older
individuals to observe directly. R.M. Nowak of Johns Hopkins University estimated that humpback whales
may live as long as 77 years.[16] In 2007, a 19th century lance fragment was found in a bowhead whale off
Alaska, suggesting the individual could be between 115 and 130 years old.[17] Aspartic acid racemization in
the whale eye, combined with a harpoon fragment, indicated an age of 211 years for another male, which, if
true would make bowheads the longest-lived extant mammal species.[18][19] The accuracy of this technique
has been questioned because racemization did not correlate well with other dating methods.[20]
Vocalization
Humpback Whale "Song"
Recording of Humpback
Whales singing and Clicking.

Some species, such as the humpback whale, communicate using melodic sounds, known as whale
song. These sounds can be extremely loud, depending on the species. Sperm whales have only been heard
making clicks, while toothed whales (Odontoceti) use echolocation that can generate about 20,000 watts of
sound (+73 dBm or +43 dBw[21]) and be heard for many miles. Whale vocalization is likely to serve many
purposes, including echolocation, mating, and identification.[citation needed]
Ecology
Feeding
Whales are generally classed as predators, but their food ranges from microscopic plankton to very
large animals.
Toothed whales eat fish and squid which they hunt by use of echolocation. Orcas sometimes eat
other marine mammals, including whales.
Baleen whales such as humpbacks and blues feed only in arctic waters, eating mostly krill. They
imbibe enormous amounts of seawater which they expel through their baleen plates. The water is then
expelled and the krill is retained on the plates and then swallowed.[13] Whales do not drink seawater but
indirectly extract water from their food by metabolizing fat.[13]
Relation to humans
Whaling
Main article: Whaling
Dutch whalers near Spitsbergen. Abraham Storck, 1690
World map of International Whaling Commission (IWC) members/non-members(member countries in

blue)
World population graph of Blue Whales (Balaenoptera musculus)
Some species of large whales are listed as endangered by multinational organizations such as
CITES along with governments and advocacy groups primarily due to whaling's impacts. They have been
hunted commercially for whale oil, meat, baleen and ambergris (a perfume ingredient from the intestine of
sperm whales) since the 17th century.[22] At its peak in 1846, 736 vessels and 70,000 people were involved
in the American whaling industry.[23] More than 2 million were taken in the early 20th century,[24] and by the
middle of the century, many populations were severely depleted.
The International Whaling Commission banned commercial whaling in 1986.[25] The ban is not
absolute, however, and some whaling continues under the auspices of scientific research[25] (sometimes not
proved[26]) or aboriginal rights; current whaling nations are Norway, Iceland and Japan and the aboriginal
communities of Siberia, Alaska and northern Canada.
Bycatch
Several species of small whales are caught as bycatch in fisheries for other species. In the Eastern
Tropical Pacific tuna fishery, thousands of dolphins drowned in purse-seine nets, until preventive measures
were introduced. Gear and deployment modifications, and eco-labelling (dolphin-safe or dolphin-friendly
brands of tuna), have contributed to a reduction in dolphin mortality by tuna vessels.[ citation needed] In many
countries, small whales are still hunted for food, oil, meat or bait.[ citation needed]
Naval sonar
See also: Marine Mammals and Sonar
Environmentalists speculate that advanced naval sonar endangers some cetaceans, including
whales. In 2003 British and Spanish scientists suggested in Nature that the effects of sonar trigger whale
beachings and to signs that such whales have experienced decompression sickness.[27] Responses in
Nature the following year discounted the explanation.[28]
Mass whale beachings occur in many species, mostly beaked whales that use echolocation for deep
diving. The frequency and size of beachings around the world, recorded over the last 1,000 years in religious
tracts and more recently in scientific surveys, have been used to estimate the population of various whale
species by assuming that the proportion of the total whale population beaching in any one year is constant.
Beached whales can give other clues about population conditions, especially health problems. For example,
bleeding around ears, internal lesions, and nitrogen bubbles in organ tissue suggest decompression
sickness.[14]
Following public concern, the U.S. Defense department was ordered by the 9 th Circuit Court to
strictly limit use of its Low Frequency Active Sonar during peacetime. Attempts by the UK-based Whale and
Dolphin Conservation Society to obtain a public inquiry into the possible dangers of the Royal Navy's
equivalent (the "2087" sonar launched in December 2004) failed as of 2008. The European Parliament has
requested that EU members refrain from using the powerful sonar system until an environmental impact
study has been carried out.
Other environmental disturbances

See also: Cetacean bycatch
Other human activities have been suggested by marine biologists to adversely impact whale
populations, such as collisions with ships and propellers, poisoning by waste contaminants and the
unregulated use of fishing gear that catches anything that swims into it.[ citation needed]
In mythology
Whale weather-vane atop the Nantucket Historical Association Whaling Museum displaying a Sperm
Whale.
Whales were little understood for most of human history as they spend up to 90% of the lives
underwater, only surfacing briefly to breathe.[29] They also include the largest animals on the planet, so it is
not surprising that many cultures, even those that have hunted them, hold them in awe and feature them in
their mythologies.
In China, Yu-kiang, a whale with the hands and feet of a man was said to rule the ocean.[30]
In the Tyrol region of Austria it was said that if a sunbeam were to fall on a maiden entering
womanhood, she would be carried away in the belly of a whale.[30]
Paikea, the youngest and favourite son of the chief Uenuku from the island of Mangaia in the present
day Cook Islands in New Zealand was said by the Kati Kuri people of Kaikoura to have come from the Pacific
Islands on the back of a whale many centuries before.[31] The novel and movie Whale Rider follow the trials
of a girl named Paikia, who lives in such a culture.
The whale features in Inuit creation myths. When ‘Big Raven', a deity in human form, found a
stranded whale, he was told by the Great Spirit where to find special mushrooms that would give him the
strength to drag the whale back to the sea and thus return order to the world.[32]
The Tlingit people of northern Canada said that the Orcas were created when the hunter Natsihlane
carved eight fish from yellow cedar, sang his most powerful spirit song and commanded the fish to leap into
the water.[32]
In Icelandic legend a man threw a stone at a fin whale and hit the blowhole, causing the whale to
burst. The man was told not to go to sea for twenty years but in the nineteenth year he went fishing and a
whale came and killed him.[32]
In East African legend King Sulemani asked God that He might permit him to feed all the beings on
earth. A whale came and ate until there was no corn left and then told Sulemani that he was still hungry and
that there were 70,000 more in his tribe. Sulemani then prayed to God for forgiveness and thanked the
creature for teaching him a lesson in humility.[32]
The King James Version of the Bible mentions whales four times: "And God created great whales"
(Genesis 1:21); "Am I a sea, or a whale, that thou settest a watch over me? (Job 7:12); "Thou art like a young
lion of the nations, and thou art as a whale in the seas (Ezekiel 32:2); and "For as Jonas [sic] was three days
and three nights in the whale's belly; so shall the Son of man be three days and three nights in the heart of
the earth" (Matthew 12:40). The story of Jonah being swallowed by a whale also is told in the Qur'an.[33]
Some cultures associate divinity with whales, such as among Ghanaians and Vietnamese, who
occasionally hold funerals for beached whales, a throwback to Vietnam's ancient sea-based Austro-asiatic
culture.[citation needed]
See also
• Atlantic Whale Foundation
• Baleen whale
• Beached whale
• Cetacea
• Cetacean bycatch
• Cetacean Conservation Center
• Cetacean intelligence
• Famous cetaceans (category)
• List of cetaceans
• List of dolphin species
• List of extinct cetaceans
• List of porpoise species
• Toothed whale
• Vocal learning
• Whale fall
• Whale meat
• Whale watching
References
1. ^ Brown, Lesley, ed (2007). Shorter Oxford English Dictionary. II (Sixth ed.). Oxford: Oxford
University press. pp. 3611.
2. ^ http://www.acsonline.org/education/taxonomy.html
3. ^ "What is the biggest animal ever to exist on Earth?". How Stuff Works.
http://science.howstuffworks.com/question687.htm. Retrieved 2007-05-29.
4. ^ "Whale Population Estimates". International Whaling Commission. March 2010.
http://www.iwcoffice.org/conservation/estimate.htm#table. Retrieved March 2010.
5. ^ Anon (25 January 2005). "Scientists find missing link between the whale and its closest
relative, the hippo". PhysOrg.com. PhysOrg.com. http://www.physorg.com/news2806.html. Retrieved
6 May 2010.
6. ^ Northeastern Ohio Universities Colleges of Medicine and Pharmacy. "Whales Descended
From Tiny Deer-like Ancestors". ScienceDaily.
7. ^ Dawkins, Richard (2004). The Ancestor's Tale. Boston: Houghton Mifflin Company. ISBN 0-
618-00583-8.
8. ^ "How whales learned to swim". BBC News. 2002-05-08.
http://news.bbc.co.uk/1/hi/sci/tech/1974869.stm. Retrieved 2006-08-20.
9. ^ "Common Characteristics of Whale Teeth" here
10.^ "How is that whale listening?". http://www.eurekalert.org/pub_releases/2008-02/iop-
hit020108.php. Retrieved February 4, 2008.
11.^ Blue Whale. Retrieved on October 5, 2009.
12.^ "Milk". Modern Marvels. The History Channel. 2008-01-07.
13.^ a b c Blue Whale. Retrieved on October 5, 2009.
14.^ a b Siebert, Charles (July 8, 2009). "Watching Whales Watching Us". New York Times
Magazine. http://www.nytimes.com/2009/07/12/magazine/12whales-t.html?pagewanted=all.
15.^ Anon. "Do whales and dolphins sleep?". How Stuff Works. Discovery Communications.
http://animals.howstuffworks.com/mammals/question643.htm. Retrieved 14 February 2010.
16.^ Anon (2005). "Humpback Whale". Animal Infor. Animal Info.
http://www.animalinfo.org/species/cetacean/meganova.htm#Maximum_age. Retrieved 25 February
2010.
17.^ Conroy, Erin (June, 2007). "Netted whale hit by lance a century ago". Associated Press.
18.^ "Bowhead Whales May Be the World's Oldest Mammals". 2008-02-15.
http://www.gi.alaska.edu/ScienceForum/ASF15/1529.html. Retrieved 2008-03-25.
19.^ George, J.C. et al. (1999). "Age and growth estimates of bowhead whales (Balaena
mysticetus) via aspartic acid racemization". Can. J. Zool. 77 (4): 571–580. doi:10.1139/cjz-77-4-571.
20.^ Brignole, Edward; McDowell, Julie. "Amino Acid Racemization". Today's chemist at work.
American Chemical Society. http://pubs.acs.org/subscribe/journals/tcaw/10/i02/html/02brignole.html.
Retrieved 25 February 2010.
21.^ dBm - dBw Watts conversion chart, Radio-Electronics.com
22.^ http://www.whaling.jp/english/history.html
23.^ Schneider, D.R. (1980). Saving the Whales--A Bwana Doc Adventure. Bwana Doc
Adventures. p. 43. ISBN 0982077602.
24.^ Desonie, Dana (2008). Polar Regions: Human Impacts. Infobase Publishing. p. 154.
ISBN 0816062188.
25.^ a b Anon. "Revised Management Scheme Information on the background and progress of
the Revised Management Scheme (RMS)". International Whaling Commission .
http://www.iwcoffice.org/conservation/rms.htm. Retrieved 14 March 2010.
26.^ Whaling on trial: Vindication!
27.^ "Sonar may cause Whale deaths". BBC News. 2003-10-08.
28.^ Piantadosi CA, Thalmann ED (2004-04-15). "Pathology: whales, sonar and decompression
sickness". Nature 428 (6894): 716–718. PMID 15085881.
29.^ Bird, Jonathon. "Sperm Wales:The deep rivers of the ocena". The Wonders of the Seas.
jonathon.bird.org. http://www.oceanicresearch.org/education/wonders/spermwhales.htm. Retrieved
14 February 2010.
30.^ a b Jones, Adair. "In search of . . . whales in literature". Wordpress.com. wordpress.
http://adairjones.wordpress.com/2009/09/29/in-search-of-whales-in-literature/. Retrieved 14 February
2010.
31.^ Anon. "Whales". Tinirau education resource.
http://collections.tepapa.govt.nz/exhibitions/whales/EducationResource.aspx?irn=198. Retrieved 14
February 2010.
32.^ a b c d Anon. "Whale Mythology from around the World". The Creative Continuum.
worldtrans.org. http://www.worldtrans.org/creators/whale/myths0.html. Retrieved 14 February 2010.
33.^ Qutb, Sayyid. "Jonah and the Whale". Arab news. Arab News. http://www.arabnews.com/?
page=5&section=0&article=121636&d=19&m=4&y=2009. Retrieved 14 February 2010.
Further reading
• Carwardine, M. (2000). Whales, Dolphins and Porpoises. Dorling Kindersley.
ISBN 0751327816 .
• Williams, Heathcote (1988). Whale Nation. New York: Harmony Books. ISBN 0517569329 .
External links
Wikimedia Commons has media related to: Whale
• WikiAnswers: questions and answers about whales

• Whale Evolution
• Greenpeace work defending whales
• Save the Whales, founded in 1977
• AquaNetwork Marine Mammal Project
• Whales in the Wild - slideshow by Life magazine
• Oldest whale fossil confirms amphibious origins
• Research on dolphins and whales from Science Daily
• Whale and Dolphin Conservation Society – latest news and information on whales and
dolphins
• The Oceania Project – Caring for whales and dolphins
• Whales Tohorā Exhibition Minisite from the Museum of New Zealand Te Papa Tongarewa
• Whales in Te Ara the Encyclopedia of New Zealand
• Orca and other whales video at Squid Force
• www.whales.org.za Whales information portal
• World Wide Fund for Nature (WWF) – information on whales, dolphins, and porpoises
• Whale Trackers – An online documentary series about whales, dolphins and porpoises
Extant Cetacea species
Kingdom Animalia · Phylum Chordata · Class Mammalia · Infraclass Eutheria · Superorder

Laurasiatheria · (unranked) Cetartiodactyla · (unranked) Whippomorpha
[hide] Suborder Mysticeti (Baleen whales)
Balaena Bowhead whale (B. mysticetus)
Balaenidae Southern right whale (E. australis) · North Atlantic

Eubalaena
right whale (E. glacialis) · North Pacific right whale (E.
(Right whales)
japonica)
Common minke whale (B. acutorostrata) ·

Antarctic minke whale (B. bonaerensis) · Sei whale (B.
Balaenopteridae Balaenoptera borealis) · Bryde's whale (B. brydei) · Pygmy Bryde's
(Rorquals) whale (B. edeni) · Blue whale (B. musculus) · B. omurai ·
Fin whale (B. physalus)
Megaptera Humpback whale (M. novaeangliae)

Eschrichtiidae Gray whale (E.
Eschrichtius
robustus)
Neobalaenidae Pygmy right whale (C.

Caperea
marginata)
[hide] Suborder Odontoceti (Toothed whales) (cont. below)
Delphinidae Commerson's dolphin (C. commersonii) ·

(Oceanic dolphins) Cephalorhynchus Chilean dolphin (C. eutropia) · Haviside's dolphin
(C. heavisidii) · Hector's dolphin (C. hectori)
Long-beaked common dolphin (D.

Delphinus capensis) · Short-beaked common dolphin (D.
delphis)
Feresa Pygmy killer whale (F. attenuata)
Globicephala Short-finned pilot whale (G.

(Pilot whales) macrorhynchus) · Long-finned pilot whale (G.
melas)
Grampus Risso's dolphin (G. griseus)
Lagenodelphis Fraser's dolphin (L. hosei)
Atlantic white-sided dolphin (L. acutus) ·

White-beaked dolphin (L. albirostris) · Peale's
Lagenorhynchus dolphin (L. australis) · Hourglass dolphin (L.
cruciger) · Pacific white-sided dolphin (L.
obliquidens) · Dusky dolphin (L. obscurus)
Lissodelphis Northern right whale dolphin (L. borealis) ·

(Right whale dolphins) Southern right whale dolphin (L. peronii)
Irrawaddy dolphin (O. brevirostris) ·

Orcaella
Australian snubfin dolphin (O. heinsohni)
Orcinus Killer whale (O. orca)
Peponocephala Melon-headed whale (P. electra)

Pseudorca False killer whale (P. crassidens)
Tucuxi (S. fluviatilis) · Costero (S.

Sotalia
guianensis)
Pacific humpback dolphin (S. chinensis) ·

Sousa Indian humpback dolphin (S. plumbea) · Atlantic
humpback dolphin (S. teuszii)
Pantropical spotted dolphin (S. attenuata) ·

Clymene dolphin (S. clymene) · Striped dolphin (S.
Stenella
coeruleoalba) · Atlantic spotted dolphin (S.
frontalis) · Spinner dolphin (S. longirostris)
Steno Rough-toothed dolphin (S. bredanensis)
Indo-Pacific bottlenose dolphin (T.

Tursiops aduncus) · Common bottlenose dolphin (T.
truncatus)
[hide] Suborder Odontoceti (Toothed whales) (cont. above)
Delphinapterus Beluga (D. leucas)

Monodontidae
Monodon Narwhal (M. monoceros)
Neophocaena Finless porpoise (N. phocaeniodes)
Phocoenidae Spectacled porpoise (P. dioptrica) · Harbor

(Porpoises) Phocoena porpoise (P. phocoena) · Vaquita (P. sinus) · Burmeister's
porpoise (P. spinipinnis)
Phocoenoides Dall's porpoise (P. dalli)
Physeteridae Sperm whale (P.

Physeter
macrocephalus)
Kogiidae Pygmy sperm whale (K. breviceps) · Dwarf sperm whale

Kogia
(K. simus)
Iniidae Amazon river dolphin (I.
Inia
geoffrensis)
Lipotidae Baiji (L.

Lipotes
vexillifer)
Platanistidae Ganges and Indus River dolphin (P.

Platanista
gangetica)
Pontoporiidae La Plata dolphin (P.

Pontoporia
blainvillei)
Ziphiidae Arnoux's beaked shale (B. arnuxii) · Baird's beaked

(Beaked whales) Berardius
whale (B. bairdii)
Northern bottlenose whale (H. ampullatus) ·

Hyperoodon
Southern bottlenose whale (H. planifrons)
Indopacetus Tropical bottlenose whale (I. pacificus)
Mesoplodon Sowerby's beaked whale (M. bidens) · Andrew's

beaked whale (M. bowdoini) · Hubbs' beaked whale (M.
carlhubbsi) · Blainville's beaked whale (M. densirostris) ·
Gervais' beaked whale (M. europaeus) · Ginkgo-toothed
beaked whale (M. ginkgodens) · Gray's beaked whale (M.
(Mesoplodont
grayi) · Hector's beaked whale (M. hectori) · Strap-toothed
whales)
whale (M. layardii) · True's beaked whale (M. mirus) ·
Perrin's beaked whale (M. perrini) · Pygmy beaked whale
(M. peruvianus) · Stejneger's beaked whale (M.
stejnegeri) · Spade-toothed whale (M. traversii)
Tasmacetus Shepherd's beaked whale (T. sheperdi)
Ziphius Cuvier's beaked whale (Z. cavirostris)
Retrieved from "http://en.wikipedia.org/wiki/Whale"
Categories: Cetaceans
W000
Parallel evolution

Parallel evolution is the development of a similar trait in related, but distinct, species descending from
the same ancestor, but from different clades. [1] [2]
Contents
[hide]
• 1 Parallel vs. convergent evolution
• 2 Parallel speciation
• 3 Examples
• 3.1 Parallel evolution between marsupials and
placentals
• 4 References
• 6 See also
[edit] Parallel vs. convergent evolution

Evolution at an amino acid position. In each case, the left-hand species changes from incorporating
alanine (A) at a specific position within a protein in a hypothetical common ancestor deduced from
comparison of sequences of several species, and now incorporates serine (S) in its present-day form. The
right-hand species may undergo divergent, parallel, or convergent evolution at this amino acid position
relative to that of the first species.
For a particular trait, proceeding in each of two lineages from a specified ancestor to a later
descendant, parallel and convergent evolutionary trends can be strictly defined and clearly distinguished
from one another.[2] When both descendants are similar in a particular respect, evolution is defined as
parallel if the ancestors considered were also similar, and convergent if they were not.
When the ancestral forms are unspecified or unknown, or the range of traits considered is not clearly
specified, the distinction between parallel and convergent evolution becomes more subjective. For instance,
the striking example of similar placental and marsupial forms is described by Richard Dawkins in The Blind
Watchmaker as a case of convergent evolution, because mammals on each continent had a long
evolutionary history prior to the extinction of the dinosaurs under which to accumulate relevant differences.
Stephen Jay Gould describes many of the same examples as parallel evolution starting from the common
ancestor of all marsupials and placentals. Many evolved similarities can be described in concept as parallel
evolution from a remote ancestor, with the exception of those where quite different structures are co-opted to
a similar function. For example, consider Mixotricha paradoxa, an eukaryotic microbe which has assembled a
system of rows of apparent cilia and basal bodies closely resembling that of ciliates but which are actually
smaller symbiont microorganisms, or the differently oriented tails of fish and whales. Conversely, any case in
which lineages do not evolve together at the same time in the same ecospace might be described as
convergent evolution at some point in time.
The definition of a trait is crucial in deciding whether a change is seen as divergent, or as parallel or
convergent. In the image above, note that since serine and threonine possess similar structures with an
alcohol side chain, the example marked "divergent" would be termed "parallel" if the amino acids were
grouped by similarity instead of being considered individually. As another example, if genes in two species
independently become restricted to the same region of the animals through regulation by a certain
transcription factor, this may be described as a case of parallel evolution - but examination of the actual DNA
sequence will probably show only divergent changes in individual basepair positions, since a new
transcription factor binding site can be added in a wide range of places within the gene with similar effect.
A similar situation occurs considering the homology of morphological structures. For example, many
insects possess two pairs of flying wings. In beetles, the first pair of wings is hardened into wing covers with
little role in flight, while in flies the second pair of wings is condensed into small halteres used for balance. If
the two pairs of wings are considered as interchangeable, homologous structures, this may be described as
a parallel reduction in the number of wings, but otherwise the two changes are each divergent changes in
one pair of wings.
Similar to convergent evolution, evolutionary relay describes how independent species acquire
similar characteristics through their evolution in similar ecosystems, but not at the same time (dorsal fins of
sharks and ichthyosaurs).
[edit] Parallel speciation

Defined as the repeated independent evolution of the same reproductive isolating mechanism
(Schluter and Nagel 1995). An example of this may occur when a species colonizes several new areas which
are isolated from, but environmentally similar to, each other. Similar selective pressures in these
environments result in parallel evolution among the traits that confer reproductive isolation.[3]
[edit] Examples
• Coloration that serves as a warning to predators and for mating displays have evolved in
many different species.
• In the plant kingdom, the most familiar examples of parallel evolution are the forms of leaves,
where very similar patterns have appeared again and again in separate genera and families.
• In butterflies, many close similarities are found in the patterns of wing colouration, both within
and between families.
• Old and New world porcupines shared a common ancestor, both evolved strikingly similar
quill structures; this is also an example of convergent evolution as similar structures evolved in
hedgehogs, echidnas and tenrecs.
• Contemporaneous evolution of the extinct browsing-horses and extinct paleotheres both of
which shared the same environmental space.
• Some extinct Archosaurs evolved an upright posture and likely were warm-blooded. These
two characteristics are also found in most mammals. Interestingly, modern crocodiles have a four
chambered heart and a crurotarsal, the latter being also a characteristic of therian mammals.
• The extinct pterosaurs and the birds both evolved wings as well as a distinct beak, but not
from a recent common ancestor.
• Internal fertilization has evolved independently in sharks, some amphibians and amniotes.
• The Patagium is a fleshy membrane that is found in gliding mammals such as: flying lemurs,
flying squirrels, sugar gliders and the extinct Volaticotherium. These mammals acquired the
patagium independently.
• Pyrotherians have evolved a body plan similar to proboscideans.
[edit] Parallel evolution between marsupials and placentals
One of the most spectacular examples of parallel evolution is provided by the two main branches of
the mammals, the placentals and marsupials, which have followed independent evolutionary pathways
following the break-up of land-masses such as Gondwanaland roughly 100 million years ago. In South
America, marsupials and placentals shared the ecosystem (prior to the Great American Interchange); in
Australia, marsupials prevailed; and in the Old World the placentals won out. However, in all these localities
mammals were small and filled only limited places in the ecosystem until the mass extinction of dinosaurs
sixty-five million years later. At this time, mammals on all three landmasses began to take on a much wider
variety of forms and roles. While some forms were unique to each environment, surprisingly similar animals
have often emerged in two or three of the separated continents. Examples of these include the litopterns and
horses, whose legs are difficult to distinguish; the European sabre-toothed cat (Machairodontinae) and the
South American marsupial sabre-tooth (Thylacosmilus); the Tasmanian wolf and the European wolf; likewise
marsupial and placental moles, flying squirrels, and (arguably) mice.
[edit] References
1. ^ Parallel evolution: Online Biology Glossary
2. ^ a b Zhang, J. and Kumar, S. 1997. Detection of convergent and parallel evolution at the
amino acid sequence level. Mol. Biol. Evol. 14, 527-36.
3. ^ http://www.talkorigins.org/faqs/faq-speciation.html
Notes
• Dawkins, R. 1986. The Blind Watchmaker. Norton & Company.
• Mayr. 1997. What is Biology. Harvard University Press
• Schluter, D., E. A. Clifford, M. Nemethy, and J. S. McKinnon. 2004. Parallel evolution and
inheritance of quantitative traits. American Naturalist 163: 809–822.

• Photographic comparison of marsupial and placental mammals
[edit] See also

• Convergent evolution
• Evolutionary relay
• Homology (biology)
• Mimicry
[hide]v · d · eEvolutionary ecology
Patterns of
evolution Convergent evolution · Parallel evolution · Divergent evolution
Signals Antipredator adaptation · Aposematism · Mimicry · Crypsis

(Countershading) · Unkenreflex
Retrieved from "http://en.wikipedia.org/wiki/Parallel_evolution"

W000
Animal
"Animalia" redirects here. For other uses, see Animalia (disambiguation).

For other uses, see Animal (disambiguation).
Animals
Temporal range: Ediacaran - Recent
PreЄ
g
Domain: Eukarya
(unranked) Opisthokonta
(unranked) Holozoa
(unranked) Filozoa
Animalia
Kingdom:
Linnaeus, 1758
Phyla
• Subkingdom Parazoa
• Porifera
• Placozoa
• Subkingdom Eumetazoa
• Radiata (unranked)
• Ctenophora
• Cnidaria
• Bilateria (unranked)
• Orthonectida
• Rhombozoa
• Acoelomorpha
• Chaetognatha
• Superphylum Deuterostomia
• Chordata
• Hemichordata
• Echinodermata
• Xenoturbellida
• Vetulicolia †
• Protostomia (unranked)
• Superphylum
Ecdysozoa
• Kinorhyncha
• Loricifera
• Priapulida
• Nematoda
• Nematomorpha
• Lobopodia
• Onychophora
• Tardigrada
• Arthropoda
• Superphylum Platyzoa
• Platyhelminthes
• Gastrotricha
• Rotifera
• Acanthocephala
• Gnathostomulid
a
• Micrognathozoa
• Cycliophora
• Superphylum
Lophotrochozoa
• Sipuncula
• Hyolitha †
• Nemertea
• Phoronida
• Bryozoa
• Entoprocta
• Brachiopoda
• Mollusca
• Annelida
• Echiura
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or
Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of
metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and
independently. All animals are also heterotrophs, meaning they must ingest other organisms for sustenance.
Most known animal phyla appeared in the fossil record as marine species during the Cambrian
explosion, about 542 million years ago.
Contents
[hide]
• 1 Etymology
• 2 Characteristics
• 2.1 Structure
• 2.2 Reproduction and development
• 2.3 Food and energy sourcing
• 3 Origin and fossil record
• 4 Groups of animals
• 4.1 Porifera, Radiata and basal Bilateria
• 4.2 Deuterostomes
• 4.3 Ecdysozoa
• 4.4 Platyzoa
• 4.5 Lophotrochozoa
• 5 Model organisms
• 6 History of classification
• 7 See also
• 8 References
• 8.1 Bibliography
Etymology
The word "animal" comes from the Latin word animalis, meaning "having breath".[1] In everyday
colloquial usage, the word usually refers to non-human animals.[2] Frequently, only closer relatives of
humans such as mammals and other vertebrates are meant in colloquial use.[3] The biological definition of
the word refers to all members of the kingdom Animalia, encompassing creatures as diverse as sponges,
jellyfish, insects and humans.[4]
Characteristics
Animals have several characteristics that set them apart from other living things. Animals are
eukaryotic and mostly multicellular,[5] which separates them from bacteria and most protists. They are
heterotrophic,[6] generally digesting food in an internal chamber, which separates them from plants and
algae.[7] They are also distinguished from plants, algae, and fungi by lacking rigid cell walls.[8] All animals
are motile,[9] if only at certain life stages. In most animals, embryos pass through a blastula stage,[10] which
is a characteristic exclusive to animals.
Structure
With a few exceptions, most notably the sponges (Phylum Porifera) and Placozoa, animals have
bodies differentiated into separate tissues. These include muscles, which are able to contract and control
locomotion, and nerve tissues, which send and process signals. Typically, there is also an internal digestive
chamber, with one or two openings.[11] Animals with this sort of organization are called metazoans, or
eumetazoans when the former is used for animals in general.[12]
All animals have eukaryotic cells, surrounded by a characteristic extracellular matrix composed of
collagen and elastic glycoproteins.[13] This may be calcified to form structures like shells , bones, and
spicules.[14] During development, it forms a relatively flexible framework[15] upon which cells can move
about and be reorganized, making complex structures possible. In contrast, other multicellular organisms,
like plants and fungi, have cells held in place by cell walls, and so develop by progressive growth.[11] Also,
unique to animal cells are the following intercellular junctions: tight junctions, gap junctions, and
desmosomes.
Reproduction and development
A newt lung cell stained with fluorescent dyes undergoing mitosis, specifically early anaphase
Nearly all animals undergo some form of sexual reproduction. They have a few specialized
reproductive cells, which undergo meiosis to produce smaller, motile spermatozoa or larger, non-motile ova.
These fuse to form zygotes, which develop into new individuals.
Many animals are also capable of asexual reproduction. This may take place through
parthenogenesis, where fertile eggs are produced without mating, or in some cases through fragmentation.
A zygote initially develops into a hollow sphere, called a blastula, which undergoes rearrangement
and differentiation. In sponges, blastula larvae swim to a new location and develop into a new sponge. In
most other groups, the blastula undergoes more complicated rearrangement. It first invaginates to form a
gastrula with a digestive chamber, and two separate germ layers — an external ectoderm and an internal
endoderm. In most cases, a mesoderm also develops between them. These germ layers then differentiate to
form tissues and organs.
Food and energy sourcing

Main article: Animal nutrition
All animals are heterotrophs, meaning that they feed directly or indirectly on other living things. They
are often further subdivided into groups such as carnivores, herbivores, omnivores, and parasites.
Predation is a biological interaction where a predator (a heterotroph that is hunting) feeds on its prey
(the organism that is attacked). Predators may or may not kill their prey prior to feeding on them, but the act
of predation always results in the death of the prey. The other main category of consumption is detritivory, the
consumption of dead organic matter. It can at times be difficult to separate the two feeding behaviours, for
example, where parasitic species prey on a host organism and then lay their eggs on it for their offspring to
feed on its decaying corpse. Selective pressures imposed on one another has led to an evolutionary arms
race between prey and predator, resulting in various antipredator adaptations.
Most animals feed indirectly from the energy of sunlight. Plants use this energy to convert sunlight
into simple sugars using a process known as photosynthesis. Starting with the molecules carbon dioxide
(CO2) and water (H2O), photosynthesis converts the energy of sunlight into chemical energy stored in the
bonds of glucose (C6H12O6) and releases oxygen (O2). These sugars are then used as the building blocks
which allow the plant to grow.[11] When animals eat these plants (or eat other animals which have eaten
plants), the sugars produced by the plant are used by the animal. They are either used directly to help the
animal grow, or broken down, releasing stored solar energy, and giving the animal the energy required for
motion. This process is known as glycolysis.
Animals living close to hydrothermal vents and cold seeps on the ocean floor are not dependent on
the energy of sunlight. Instead chemosynthetic archaea and bacteria form the base of the food chain.
Origin and fossil record

Further information: Urmetazoon
Dunkleosteus was a gigantic, 10-foot-long (3.0 m) prehistoric fish.[16]
Vernanimalcula guizhouena is a fossil believed by some to represent the earliest known member of
the Bilateria.
Animals are generally considered to have evolved from a flagellated eukaryote. Their closest known
living relatives are the choanoflagellates, collared flagellates that have a morphology similar to the
choanocytes of certain sponges. Molecular studies place animals in a supergroup called the opisthokonts,
which also include the choanoflagellates, fungi and a few small parasitic protists. The name comes from the
posterior location of the flagellum in motile cells, such as most animal spermatozoa, whereas other
eukaryotes tend to have anterior flagella.
The first fossils that might represent animals appear in the Trezona Formation at Trezona Bore, West
Central Flinders, South Australia.[17] These fossils are interpreted as being early sponges. They were found
in 665-million-year-old rock.[17]
The next oldest possible animal fossils are found towards the end of the Precambrian, around 610
million years ago, and are known as the Ediacaran or Vendian biota. These are difficult to relate to later
fossils, however. Some may represent precursors of modern phyla, but they may be separate groups, and it
is possible they are not really animals at all.
Aside from them, most known animal phyla make a more or less simultaneous appearance during
the Cambrian period, about 542 million years ago. It is still disputed whether this event, called the Cambrian
explosion, represents a rapid divergence between different groups or a change in conditions that made
fossilization possible.
Some paleontologists suggest that animals appeared much earlier than the Cambrian explosion,
possibly as early as 1 billion years ago. Trace fossils such as tracks and burrows found in the Tonian era
indicate the presence of triploblastic worms, like metazoans, roughly as large (about 5 mm wide) and
complex as earthworms.[18] During the beginning of the Tonian period around 1 billion years ago, there was
a decrease in Stromatolite diversity, which may indicate the appearance of grazing animals, since
Stromatolites diversity increased when grazing animals went extinct at the End Permian and End Ordovician
extinction events, and decreased shortly after the grazer populations recovered. However the discovery that
tracks very similar to these early trace fossils are produced today by the giant single-celled protist Gromia
sphaerica casts doubt on their interpretation as evidence of early animal evolution.[19][20]
Groups of animals
The relative number of species contributed to the total by each phylum of animals.
Porifera, Radiata and basal Bilateria
Orange elephant ear sponge, Agelas clathrodes, in foreground. Two corals in the background: a sea
fan, Iciligorgia schrammi, and a sea rod, Plexaurella nutans.
The sponges (Porifera) were long thought to have diverged from other animals early. They lack the
complex organization found in most other phyla. Their cells are differentiated, but in most cases not
organized into distinct tissues. Sponges typically feed by drawing in water through pores. Archaeocyatha,
which have fused skeletons, may represent sponges or a separate phylum. However, a phylogenomic study
in 2008 of 150 genes in 29 animals across 21 phyla[21] revealed that it is the Ctenophora or comb jellies
which are the basal lineage of animals, at least among those 21 phyla. The authors speculate that sponges—
or at least those lines of sponges they investigated—are not so primitive, but may instead be secondarily
simplified.
Among the other phyla, the Ctenophora and the Cnidaria, which includes sea anemones, corals, and
jellyfish, are radially symmetric and have digestive chambers with a single opening, which serves as both the
mouth and the anus. Both have distinct tissues, but they are not organized into organs. There are only two
main germ layers, the ectoderm and endoderm, with only scattered cells between them. As such, these
animals are sometimes called diploblastic. The tiny placozoans are similar, but they do not have a permanent
digestive chamber.
The remaining animals form a monophyletic group called the Bilateria. For the most part, they are
bilaterally symmetric, and often have a specialized head with feeding and sensory organs. The body is
triploblastic, i.e. all three germ layers are well-developed, and tissues form distinct organs. The digestive
chamber has two openings, a mouth and an anus, and there is also an internal body cavity called a coelom
or pseudocoelom. There are exceptions to each of these characteristics, however — for instance adult
echinoderms are radially symmetric, and certain parasitic worms have extremely simplified body structures.
Genetic studies have considerably changed our understanding of the relationships within the
Bilateria. Most appear to belong to two major lineages: the deuterostomes and the protostomes, the latter of
which includes the Ecdysozoa, Platyzoa, and Lophotrochozoa. In addition, there are a few small groups of
bilaterians with relatively similar structure that appear to have diverged before these major groups. These
include the Acoelomorpha, Rhombozoa, and Orthonectida. The Myxozoa, single-celled parasites that were
originally considered Protozoa, are now believed to have developed from the Medusozoa as well.
Deuterostomes
Superb Fairy-wren, Malurus cyaneus

Deuterostomes differ from the other Bilateria, called protostomes, in several ways. In both cases
there is a complete digestive tract. However, in protostomes, the initial opening (the archenteron) develops
into the mouth, and an anus forms separately. In deuterostomes this is reversed. In most protostomes, cells
simply fill in the interior of the gastrula to form the mesoderm, called schizocoelous development, but in
deuterostomes, it forms through invagination of the endoderm, called enterocoelic pouching. Deuterostomes
also have a dorsal, rather than a ventral, nerve chord and their embryos undergo different cleavage.
All this suggests the deuterostomes and protostomes are separate, monophyletic lineages. The main
phyla of deuterostomes are the Echinodermata and Chordata. The former are radially symmetric and
exclusively marine, such as starfish, sea urchins, and sea cucumbers. The latter are dominated by the
vertebrates, animals with backbones. These include fish, amphibians, reptiles, birds, and mammals.
In addition to these, the deuterostomes also include the Hemichordata, or acorn worms. Although
they are not especially prominent today, the important fossil graptolites may belong to this group.
The Chaetognatha or arrow worms may also be deuterostomes, but more recent studies suggest
protostome affinities.
Ecdysozoa
Yellow-winged darter, Sympetrum flaveolum
The Ecdysozoa are protostomes, named after the common trait of growth by moulting or ecdysis.
The largest animal phylum belongs here, the Arthropoda, including insects, spiders, crabs, and their kin. All
these organisms have a body divided into repeating segments, typically with paired appendages. Two
smaller phyla, the Onychophora and Tardigrada, are close relatives of the arthropods and share these traits.
The ecdysozoans also include the Nematoda or roundworms, perhaps the second largest animal
phylum. Roundworms are typically microscopic, and occur in nearly every environment where there is water.
A number are important parasites. Smaller phyla related to them are the Nematomorpha or horsehair worms,
and the Kinorhyncha, Priapulida, and Loricifera. These groups have a reduced coelom, called a
pseudocoelom.
The remaining two groups of protostomes are sometimes grouped together as the Spiralia, since in
both embryos develop with spiral cleavage.
Platyzoa
Pseudobiceros bedfordi, (Bedford's flatworm)

The Platyzoa include the phylum Platyhelminthes, the flatworms. These were originally considered
some of the most primitive Bilateria, but it now appears they developed from more complex ancestors.[22] A
number of parasites are included in this group, such as the flukes and tapeworms. Flatworms are
acoelomates, lacking a body cavity, as are their closest relatives, the microscopic Gastrotricha.[23]
The other platyzoan phyla are mostly microscopic and pseudocoelomate. The most prominent are
the Rotifera or rotifers, which are common in aqueous environments. They also include the Acanthocephala
or spiny-headed worms, the Gnathostomulida, Micrognathozoa, and possibly the Cycliophora.[24] These
groups share the presence of complex jaws, from which they are called the Gnathifera.
Lophotrochozoa
Roman snail, Helix pomatia

The Lophotrochozoa include two of the most successful animal phyla, the Mollusca and Annelida.
[25][26] The former, which is the second-largest animal phylum by number of described species, includes
animals such as snails, clams, and squids, and the latter comprises the segmented worms, such as
earthworms and leeches. These two groups have long been considered close relatives because of the
common presence of trochophore larvae, but the annelids were considered closer to the arthropods because
they are both segmented.[27] Now, this is generally considered convergent evolution, owing to many
morphological and genetic differences between the two phyla.[28]
The Lophotrochozoa also include the Nemertea or ribbon worms, the Sipuncula, and several phyla
that have a ring of ciliated tentacles around the mouth, called a lophophore.[29] These were traditionally
grouped together as the lophophorates.[30] but it now appears that the lophophorate group may be
paraphyletic,[31] with some closer to the nemerteans and some to the molluscs and annelids.[32][33] They
include the Brachiopoda or lamp shells, which are prominent in the fossil record, the Entoprocta, the
Phoronida, and possibly the Bryozoa or moss animals.[34]
Model organisms
Main articles: Model organism and Animal testing
Because of the great diversity found in animals, it is more economical for scientists to study a small
number of chosen species so that connections can be drawn from their work and conclusions extrapolated
about how animals function in general. Because they are easy to keep and breed, the fruit fly Drosophila
melanogaster and the nematode Caenorhabditis elegans have long been the most intensively studied
metazoan model organisms, and were among the first life-forms to be genetically sequenced. This was
facilitated by the severely reduced state of their genomes, but as many genes, introns, and linkages lost,
these ecdysozoans can teach us little about the origins of animals in general. The extent of this type of
evolution within the superphylum will be revealed by the crustacean, annelid, and molluscan genome
projects currently in progress. Analysis of the starlet sea anemone genome has emphasised the importance
of sponges, placozoans, and choanoflagellates, also being sequenced, in explaining the arrival of 1500
ancestral genes unique to the Eumetazoa.[35]
An analysis of the homoscleromorph sponge Oscarella carmela also suggests that the last common
ancestor of sponges and the eumetazoan animals was more complex than previously assumed.[36]
Other model organisms belonging to the animal kingdom include the mouse ( Mus musculus) and
zebrafish (Danio rerio).
Carolus Linnaeus, known as the father of modern taxonomy
History of classification
Aristotle divided the living world between animals and plants, and this was followed by Carolus
Linnaeus (Carl von Linné), in the first hierarchical classification. Since then biologists have begun
emphasizing evolutionary relationships, and so these groups have been restricted somewhat. For instance,
microscopic protozoa were originally considered animals because they move, but are now treated
separately.
In Linnaeus's original scheme, the animals were one of three kingdoms, divided into the classes of
Vermes, Insecta, Pisces, Amphibia, Reptila, Aves, and Mammalia. Since then the last five have all been
subsumed into a single phylum, the Chordata, whereas the various other forms have been separated out.
The above lists represent our current understanding of the group, though there is some variation from source
to source.
See also
Animals portal
Book:Animal
Wikispecies has information related to: Animalia
• Ethology
• Animal colouration
• Animal rights
• Fauna
• List of animal names
• List of animals by number of neurons
• Lists of animals
References
1. ^ Cresswell, Julia (2010). The Oxford Dictionary of Word Origins (2 ed.). New York: Oxford
University Press. ISBN 9780199547937. "‘having the breath of life’, from anima ‘air, breath, life’ ."
2. ^ Webster's. "Animal Definition". http://www.yourdictionary.com/animal. Retrieved September
17, 2009.
3. ^ "Animals". Merriam-Webster's. http://m-w.com/dictionary/animals. Retrieved 16 May 2010.
"2 a : one of the lower animals as distinguished from human beings b : mammal; broadly :
vertebrate"
4. ^ "Animal". The American Heritage Dictionary (Forth ed.). Houghton Mifflin Company. 2006.
5. ^ National Zoo. "Panda Classroom".
http://nationalzoo.si.edu/Animals/GiantPandas/PandasForKids/classification/classification.htm.
Retrieved September 30, 2007.
6. ^ Jennifer Bergman. "Heterotrophs".
http://www.windows.ucar.edu/tour/link=/earth/Life/heterotrophs.html&edu=high. Retrieved September
30, 2007.
7. ^ Douglas AE, Raven JA, AE (January 2003). "Genomes at the interface between bacteria
and organelles". Philosophical transactions of the Royal Society of London. Series B, Biological
sciences 358 (1429): 5–17; discussion 517–8. doi:10.1098/rstb.2002.1188. ISSN 0962-8436.
PMID 12594915.
8. ^ Davidson, Michael W.. "Animal Cell Structure".
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Walter (2002). Molecular Biology of the Cell (4 ed.). New York.
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applications. John Wiley and Sons. p. 212. ISBN 9780470061534.
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Claire C.; Erwin, Douglas H.; Poirier, Gerald R.; Yao, Nan et al. (17 August 2010). "Possible animal-
body fossils in pre-Marinoan limestones from South Australia". Nature Geoscience 3: 653.
doi:10.1038/ngeo934. http://www.nature.com/ngeo/journal/vaop/ncurrent/full/ngeo934.html.
18.^ Seilacher, A., Bose, P.K. and Pflüger, F., A (Oct 1998). "Animals More Than 1 Billion Years
Ago: Trace Fossil Evidence from India". Science 282 (5386): 80–83.
doi:10.1126/science.282.5386.80. ISSN 0036-8075. PMID 9756480.
19.^ Matz, MV; Frank, TM; Marshall, NJ; Widder, EA; Johnsen, S; Tamara M. Frank, N. Justin
Marshall, Edith A. Widder and Sonke Johnsen (2008-12-09). "Giant Deep-Sea Protist Produces
Bilaterian-like Traces". Current Biology (Elsevier Ltd) 18 (18): 1–6. doi:10.1016/j.cub.2008.10.028.
ISSN 0960-9822. PMID 19026540. http://www.biology.duke.edu/johnsenlab/pdfs/pubs/sea
%20grapes%202008.pdf. Retrieved 2008-12-05.
20.^ Reilly, Michael (2008-11-20). "Single-celled giant upends early evolution". MSNBC.
21.^ Dunn et al. 2008. "Broad phylogenomic sampling improves resolution of the animal tree of
life". Nature 06614.
22.^ Ruiz-Trillo, I., I; Ruiz-Trillo, Iñaki; Riutort, Marta; Littlewood, D. Timothy J.; Herniou,
Elisabeth A.; Baguñà, Jaume (March 1999). "Acoel Flatworms: Earliest Extant Bilaterian Metazoans,
Not Members of Platyhelminthes". Science 283 (5409): 1919–1923.
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23.^ Todaro, Antonio. "Gastrotricha: Overview". Gastrotricha: World Portal. University of
Modena & Reggio Emilia. http://www.gastrotricha.unimore.it/overview.htm. Retrieved 2008-01-26.
24.^ Kristensen, Reinhardt Møbjerg (July 2002). "An Introduction to Loricifera, Cycliophora, and
Micrognathozoa". Integrative and Comparative Biology (Oxford Journals) 42 (3): 641–651.
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25.^ "Biodiversity: Mollusca". The Scottish Association for Marine Science. Archived from the
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26.^ Russell, Bruce J. (Writer), Denning, David (Writer). (2000). Branches on the Tree of Life:
Annelids. [VHS]. BioMEDIA ASSOCIATES.
27.^ Eernisse, Douglas J., D. J.; Eernisse, Douglas J.; Albert, James S.; Anderson , Frank E. (1
September 1992). "Annelida and Arthropoda are not sister taxa: A phylogenetic analysis of spiralean
metazoan morphology". Systematic Biology 41 (3): 305–330. doi:10.2307/2992569. ISSN 10635157.
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28.^ Eernisse, Douglas J.; Kim, Chang Bae; Moon, Seung Yeo; Gelder, Stuart R.; Kim, Won
(September 1996). "Phylogenetic Relationships of Annelids, Molluscs, and Arthropods Evidenced
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29.^ Collins, Allen G. (1995). The Lophophore. University of California Museum of Paleontology.
http://www.ucmp.berkeley.edu/glossary/gloss7/lophophore.html.
30.^ Adoutte, A., A; Adoutte, André; Balavoine, Guillaume; Lartillot, Nicolas; Lespinet, Olivier;
Prud'homme, Benjamin; de Rosa, Renaud (April 25, 2000). "The new animal phylogeny: Reliability
and implications". Proceedings of the National Academy of Sciences 97 (9): 4453–4456.
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http://www.pnas.org/cgi/content/full/97/9/4453. Retrieved 2007-11-19.
31.^ Passamaneck, Yale J. (2003). "Molecular Phylogenetics of the Metazoan Clade
Lophotrochozoa" (PDF). pp. 124. http://handle.dtic.mil/100.2/ADA417356.
32.^ Sundberg, P; Turbeville, JM; Lindh, S; Sundberg, Per; Turbevilleb, J. M.; Lindha, Susanne
(September 2001). "Phylogenetic relationships among higher nemertean (Nemertea) taxa inferred
from 18S rDNA sequences". Molecular Phylogenetics and Evolution 20 (3): 327–334.
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33.^ Boore, JL; Boore, Jeffrey L.; Staton, Joseph L (February 2002). "The mitochondrial genome
of the Sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca"
(PDF). Molecular Biology and Evolution 19 (2): 127–137. ISSN 0022-2844. PMID 11801741.
http://mbe.oxfordjournals.org/cgi/reprint/19/2/127.pdf. Retrieved 2007-11-19.
34.^ Nielsen, Claus (April 2001). "Bryozoa (Ectoprocta: ‘Moss’ Animals)". Encyclopedia of Life
Sciences (John Wiley & Sons, Ltd). doi:10.1038/npg.els.0001613.
http://mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0001613/current/abstract.
35.^ N.H. Putnam, et al., NH (July 2007). "Sea anemone genome reveals ancestral eumetazoan
gene repertoire and genomic organization". Science 317 (5834): 86–94.
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36.^ Wang, X., X; Wang, Xiujuan; Lavrov Dennis V. (2006-10-27). "Mitochondrial Genome of the
homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in
the Common Ancestor of Sponges and Other Animals". Molecular Biology and Evolution (Oxford
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Bibliography
• Klaus Nielsen. Animal Evolution: Interrelationships of the Living Phyla (2nd edition). Oxford
University Press, 2001.
• Knut Schmidt-Nielsen. Animal Physiology: Adaptation and Environment. (5th edition).
Cambridge University Press, 1997.
External links
Find more about Animalia on Wikipedia's sister projects:
• Tree of Life Project

• Animal Diversity Web - University of Michigan's database of animals, showing taxonomic
classification, images, and other information.
• ARKive - multimedia database of worldwide endangered/protected species and common
species of UK.
• Scientific American Magazine (December 2005 Issue) - Getting a Leg Up on Land About the
evolution of four-limbed animals from fish.
[hide]v · d · eEukaryota
Domain : Archaea · Bacteria · Eukaryota
Archaeplastida, or Plantae Viridiplantae/Plantae sens

sensu lato Rhodophyta · Glaucocystophyceae
AH
Hacrobia, or non-SAR
Haptophyta · Cryptophyta
chromalveolata
AH/SAR Heterokont
Bikonta Ochrophyta · Bigyra
("S")
Halvaria
SAR Ciliates · Myzozoa (A
Alveolata
Dinoflagellata)
Rhizaria Cercozoa · Retaria (Foraminifera, Radiolaria)
Excavata Discoba (Euglenozoa, Percolozoa) · Metamonad · Malawimonas

Unikonta Apusomonadida (Apusomonas, Amastigomonas) · Ancyromonadida (Anc
Apusozoa
Hemimastigida (Hemimastix, Spironema, Stereonema)
Amoebozoa Lobosea · Conosa · Phalansterium · Breviata
Opisthokonta Mesomycetozoea Dermocystida · Ichthyop
Filasterea
Minis
Holozoa Choanoflagellatea
Filozoa
(Bila
Metazoa
Cten
or "Animalia"
Mes
(Plac
Holomycota Dikarya (Ascomycota, Basidio

Fungi Glomeromycota · Zygomycota · Blast
Chytridiomycota/Neocallimastigomyc
Nuclearia · Micronuclearia · R
Nucleariidae
Pinaciophora · Pompholyxophrys · Fo

Arthropoda

Gastrotricha
Gnat
Rotifera · Aca
Gnathostomu
Micrognathoz
Cycliophora
Troch
(Sipuncula, N
Mollusca, An
Lophotrochozoa
Lophophorata
Entoprocta, P
Brachiopoda
Ambulacraria
Xenoturbellida
Deuterostomia
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Category · Portal
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Catholic Church and evolution


Since the publication of Charles Darwin's On the Origin of Species in 1859, the attitude of the
Catholic Church on the theory of evolution has slowly been refined. For about 100 years, there was no
authoritative pronouncement on the subject. By 1950, Pope Pius XII agreed to the academic freedom to
study the scientific implications of evolution, so long as Catholic dogma is not violated.[1] Today[update], the
Church's unofficial position is an example of theistic evolution, stating that faith and scientific findings
regarding human evolution are not in conflict, though humans are regarded as a special creation, and that
the existence of God is required to explain both monogenism and the spiritual component of human origins.
No infallible declarations by the Pope or an Ecumenical Council have been made.
The Creation of Adam, from the Sistine Chapel ceiling, by Michelangelo, c. 1511
Contents
[hide]
• 1 Early reaction
• 2 Pope Pius IX
• 3 Popes Leo XIII and Pius X
• 4 Pope Pius XII
• 5 Pope John Paul II
• 6 Pope Benedict XVI and today
• 7 Catholic teaching and evolution
• 7.1 Polygenism
• 8 Catholic schools and evolution
• 9 Unofficial Catholic organizations
• 10 See also
• 11 Notes
• 12 References
[edit] Early reaction
In medieval art God was depicted in the Garden of Eden and other pre-Incarnation subjects as God
the Son, already with the appearance of Jesus, as here in The Garden of Earthly Delights by Hieronymus
Bosch.
Catholic concern about evolution has always been very largely concerned with the implications of
evolutionary theory for the origin of the human species; even by 1859, the Church did not insist on a literal
reading of the Book of Genesis, which had long been undermined by developments in geology and other
fields.[2] No high-level Church pronouncement has ever attacked head-on the theory of evolution as applied
to non-human species.[3] The early Church Fathers taught creationism—though there was debate being over
whether God created the world in six days, as Clement of Alexandria taught,[4] or in a single moment as held
by Augustine,[5] and a literal interpretation of Genesis was normally taken for granted in the Middle Ages and
later, until questioned by science. However modern literal Creationism has had little support among the
higher levels of the Church.
The Catholic Church delayed official pronouncements on Darwin's Origin of Species for many
decades. While many hostile comments were made by local clergy, Origin of Species was never placed on
the Index Librorum Prohibitorum;[6] in contrast, Henri Bergson's non-Darwinian Creative Evolution (1907),
was on the Index from 1948 until it was abolished in 1966.[7] However, a number of Catholic writers who
published works specifying how evolutionary theory and Catholic theology might be reconciled ran into
trouble of some sort with the Vatican authorities.[8]
The first notable statement after Darwin published his theory appeared in 1860 from a council of the
German bishops, who pronounced that:
Our first parents were formed immediately by God. Therefore we declare that the opinion of
those who do not fear to assert that this human being, man as regards his body, emerged finally from
the spontaneous continuous change of imperfect nature to the more perfect, is clearly opposed to
Sacred Scripture and to the Faith.[9]
No Vatican response was made to this, which implied agreement.[10] In the following decades, a
consistently and aggressively anti-evolution position was taken by the influential Jesuit periodical La Civiltà
Cattolica which, though unofficial, was generally believed to have accurate information about the views and
actions of the Vatican authorities.[11] The opening in 1998 of the Archive of the Congregation for the
Doctrine of the Faith (in the 19th century called the Holy Office and the Congregation of the Index) has
revealed that on many crucial points this belief was mistaken, and the journal's accounts of specific cases,
often the only ones made public, were not accurate. The original documents show the Vatican's attitude was
much less fixed than appeared to be the case at the time.[12]
In 1868, the Blessed John Henry Newman corresponded with a fellow priest regarding Darwin's
theory and made the following comments:
As to the Divine Design, is it not an instance of incomprehensibly and infinitely marvellous
Wisdom and Design to have given certain laws to matter millions of ages ago, which have surely
and precisely worked out, in the long course of those ages, those effects which He from the first
proposed. Mr. Darwin's theory need not then to be atheistical, be it true or not; it may simply be
suggesting a larger idea of Divine Prescience and Skill. Perhaps your friend has got a surer clue
to guide him than I have, who have never studied the question, and I do not [see] that 'the
accidental evolution of organic beings' is inconsistent with divine design — It is accidental to us,
not to God.[13]
In 1894 a letter was received by the Holy Office, asking for confirmation of the Church's position on a
theological book of generally Darwinist cast by a French Dominican theologian, L’évolution restreinte aux
espèces organiques, par le père Léroy dominicain . The records of the Holy Office document lengthy debates,
with a number of experts consulted, whose views varied considerably. In 1895 the Congregation decided
against the book, and Fr. Léroy was summoned to Rome, where it was explained that his views were
unacceptable, and he agreed to withdraw the book, which was placed on the Index. Again, the concerns of
the experts had concentrated entirely on human evolution.[14]
To reconcile general evolutionary theory with the origin of the human species, with a soul, the
concept of "special transformism" was developed, according to which the first humans had evolved by
Darwinist processes, up to the point where a soul was added by God to "pre-existent and living matter" (in
the words of Pius XII's Humani Generis) to form the first fully human individuals; this would normally be
considered to be at the point of conception.[15] Léroy's book endorsed this concept; what led to its rejection
by the Congregation appears to have been his view that the human species was able to evolve without divine
intervention to a fully human state, but lacking only a soul. The theologians felt that some immediate and
particular divine intervention was also required to form the physical nature of humans, before the addition of
a soul, even if this was worked on near-human hominids produced by evolutionary processes.[16]
The following year, 1896, John Augustine Zahm, a well-known American Holy Cross priest who had
been a professor of physics and chemistry at the Catholic University of Notre Dame, Indiana, and was then
Procurator General of his Order in Rome, published Evolution and Dogma, arguing that Church teaching, the
Bible, and evolution did not conflict.[17] By 1898 it had been placed on the Index and Zahm forced to recant
his views, though he remained sufficiently well thought of to return to the United States as Provincial superior
of his Order.[18] In the meantime his book (in an Italian translation with the imprimatur of Siena[19]) had had
a great impact on Geremia Bonomelli, the Bishop of Cremona in Italy, who added an appendix to a book of
his own, summarizing and recommending Zahn's views. Bonomelli too was pressured, and retracted his
views in a public letter, also in 1898.[20]
[edit] Pope Pius IX

The Origin of Species was published in 1859, during the papacy of Pope Pius IX, who defined
dogmatically papal infallibility during the First Vatican Council in 1869-70. The council has a section on "Faith
and Reason" that includes the following on science and faith:
"9. Hence all faithful Christians are forbidden to defend as the legitimate conclusions of
science those opinions which are known to be contrary to the doctrine of faith, particularly if they have
been condemned by the Church; and furthermore they are absolutely bound to hold them to be errors
which wear the deceptive appearance of truth." (Vatican Council I)
"10. Not only can faith and reason never be at odds with one another but they mutually support
each other, for on the one hand right reason established the foundations of the faith and, illuminated
by its light, develops the science of divine things; on the other hand, faith delivers reason from errors
and protects it and furnishes it with knowledge of many kinds." (Vatican Council I)
On God the Creator, the Vatican Council was very clear. The definitions preceding the "anathema"
(as a technical term of Catholic theology, let him be "cut off" or excommunicated, cf. Gal 1:6-9; Titus 3:10-11;
Matt 18:15-17) signify an infallible dogma of Catholic faith (De Fide):
1. On God the creator of all things
1. If anyone denies the one true God, creator and lord of things visible and invisible: let
him be anathema.
2. If anyone is so bold as to assert that there exists nothing besides matter: let him be
anathema.
3. If anyone says that the substance or essence of God and that of all things are one
and the same: let him be anathema.
4. If anyone says that finite things, both corporal and spiritual, or at any rate, spiritual,
emanated from the divine substance; or that the divine essence, by the manifestation and
evolution of itself becomes all things or, finally, that God is a universal or indefinite being
which by self determination establishes the totality of things distinct in genera, species and
individuals: let him be anathema.
5. If anyone does not confess that the world and all things which are contained in it,
both spiritual and material, were produced, according to their whole substance, out of nothing
by God; or holds that God did not create by his will free from all necessity, but as necessarily
as he necessarily loves himself; or denies that the world was created for the glory of God: let
him be anathema.
According to Catholic theologian Dr. Ludwig Ott in his 1952 treatise Fundamentals of Catholic
Dogma,[21] it is to be understood that these condemnations are of the errors of modern materialism (that
matter is all there is), pantheism (that God and the universe are identical), and ancient pagan and gnostic-
manichean dualism (where God is not responsible for the entire created world, since mere "matter" is evil not
good, see Ott, page 79).
The First Vatican Council also upholds the ability of reason to know God from his creation:
"1. The same Holy mother Church holds and teaches that God, the source and end of all
things, can be known with certainty from the consideration of created things, by the natural power of
human reason: ever since the creation of the world, his invisible nature has been clearly perceived in
the things that have been made." (Chapter 2, On Revelation; cf. Romans 1:19-20; and Wisdom
chapter 13)
[edit] Popes Leo XIII and Pius X

Providentissimus Deus, "On the Study of Holy Scripture", was an encyclical issued by Pope Leo XIII
on 18 November 1893 on the interpretation of Scripture. It was intended to address the issues arising from
both the "higher criticism" and new scientific theories, and their relation with Scripture. Nothing specific
concerning evolution was said, and initially both those in favour and against evolution found things to
encourage them in the text; however a more conservative interpretation came to be dominant, and the
influence of the conservative Jesuit Cardinal Camillo Mazzella detected. Leo stressed the unstable and
changing nature of scientific theory, and criticised the "thirst for novelty and the unrestrained freedom of
thought" of the age, but accepted that the apparent literal sense of the Bible might not always be correct. In
biblical interpretation, Catholic scholars should not "depart from the literal and obvious sense, except only
where reason makes it untenable or necessity requires". Leo stressed that both theologians and scientists
should confine themselves to their own disciplines as much as possible.[22]
An earlier encyclical of Leo's on marriage, Arcanum Divinae Sapientiae (1880) had described in
passing the Genesis account of the creation of Eve from Adam's side as "what is to all known, and cannot be
doubted by any ..."[23]
The Pontifical Biblical Commission issued a decree ratified by Pope Pius X on June 30, 1909 that
stated that the literal historical meaning of the first chapters of Genesis could not be doubted in regard to "the
creation of all things by God at the beginning of time; the special creation of man; the formation of the first
woman from the first man; the unity of the human race...". As in 1860, "special creation" was only referred to
in respect of the human species.[24]
[edit] Pope Pius XII

Pope Pius XII's encyclical of 1950, Humani Generis, was the first encyclical to specifically refer to
evolution, and took up a neutral position, again concentrating on human evolution:
"The Church does not forbid that...research and discussions, on the part of men experienced
in both fields, take place with regard to the doctrine of evolution, in as far as it inquires into the origin of
the human body as coming from pre-existent and living matter."[25]
Pope Pius XII's teaching can be summarized as follows:
• The question of the origin of man's body from pre-existing and living matter is a legitimate
matter of inquiry for natural science. Catholics are free to form their own opinions, but they should do
so cautiously; they should not confuse fact with conjecture, and they should respect the Church's
right to define matters touching on Revelation.
• Catholics must believe, however, that the human soul was created immediately by God.
Since the soul is a spiritual substance it is not brought into being through transformation of matter,
but directly by God, whence the special uniqueness of each person.
• All men have descended from an individual, Adam, who has transmitted original sin to all
mankind. Catholics may not, therefore, believe in "polygenism," the scientific hypothesis that
mankind descended from a group of original humans (that there were many Adams and Eves).
Some theologians believe Pius XII explicitly excludes belief in polygenism as licit. The relevant
sentence is this:
"Now it is in no way apparent how such an opinion (polygenism) can be reconciled with that
which the sources of revealed truth and the documents of the Teaching Authority of the Church
propose with regard to original sin, which proceeds from a sin actually committed by an individual
Adam and which, through generation, is passed on to all and is in everyone as his own." (Pius XII,
Humani Generis, 37 and footnote refers to Romans 5:12-19; Council of Trent, Session V, Canons 1-4)
[edit] Pope John Paul II
"...new findings lead us toward the recognition of evolution as more than a hypothesis."
— John Paul II, 1996[26]
In an October 22, 1996, address to the Pontifical Academy of Sciences, Pope John Paul II updated
the Church's position to accept evolution of the human body:
"In his encyclical Humani Generis (1950), my predecessor Pius XII has already affirmed that
there is no conflict between evolution and the doctrine of the faith regarding man and his vocation,
provided that we do not lose sight of certain fixed points....Today, more than a half-century after the
appearance of that encyclical, some new findings lead us toward the recognition of evolution as more
than a hypothesis. In fact it is remarkable that this theory has had progressively greater influence on
the spirit of researchers, following a series of discoveries in different scholarly disciplines. The
convergence in the results of these independent studies – which was neither planned nor sought –
constitutes in itself a significant argument in favor of the theory."[26]
In the same address, Pope John Paul II rejected any theory of evolution that provides a materialistic
explanation for the human soul:
"Theories of evolution which, because of the philosophies which inspire them, regard the spirit
either as emerging from the forces of living matter, or as a simple epiphenomenon of that matter, are
incompatible with the truth about man."
[edit] Pope Benedict XVI and today

Statements by Cardinal Schönborn, a close colleague of Benedict XVI, especially a piece in the New
York Times on July 7, 2005,[27] appeared to support Intelligent Design, giving rise to speculation about a
new direction in the Church's stance on the compatibility between evolution and Catholic dogma; many of
Schönborn's complaints about Darwinian evolution echoed pronouncements originiating from the Discovery
Institute, an interdenominational Christian think tank.[28][29][29] However, Cardinal Schönborn's book
Chance or Purpose (2007, originally in German) accepted with certain qualifications the "scientific theory of
evolution", but attacked "evolutionism as an ideology", which he said sought to displace religious teaching
over a wide range of issues.[30] Nonetheless, in the mid-1980s, Pope Benedict XVI, while serving as Prefect
of the Sacred Congregation of the Doctrine of the Faith, wrote a defense of the doctrine of creation against
Catholics who stressed the sufficiency of "selection and mutation."[31] Humans, he insisted, are "not the
products of chance and error," and "the universe is not the product of darkness and unreason;[31] it comes
from intelligence, freedom, and from the beauty that is identical with love."[31]
A five-day conference held in March 2009 by the Pontifical University in Rome, marking the 150th
anniversary of the publication of the Origin of Species, generally confirmed the lack of conflict between
evolutionary theory and Catholic theology, and the rejection of Intelligent Design by Catholic scholars.[32]
The Church has deferred to scientists on matters such as the age of the earth and the authenticity of
the fossil record. Papal pronouncements, along with commentaries by cardinals, have accepted the findings
of scientists on the gradual appearance of life. In fact, the International Theological Commission in a July
2004 statement endorsed by Cardinal Ratzinger, then president of the Commission and head of the
Congregation for the Doctrine of the Faith, now Pope Benedict XVI, includes this paragraph:
According to the widely accepted scientific account, the universe erupted 15 billion years ago in
an explosion called the 'Big Bang' and has been expanding and cooling ever since. Later there
gradually emerged the conditions necessary for the formation of atoms, still later the
condensation of galaxies and stars, and about 10 billion years later the formation of planets. In
our own solar system and on earth (formed about 4.5 billion years ago), the conditions have
been favorable to the emergence of life. While there is little consensus among scientists about
how the origin of this first microscopic life is to be explained, there is general agreement among
them that the first organism dwelt on this planet about 3.5 - 4 billion years ago. Since it has been
demonstrated that all living organisms on earth are genetically related, it is virtually certain that
all living organisms have descended from this first organism. Converging evidence from many
studies in the physical and biological sciences furnishes mounting support for some theory of
evolution to account for the development and diversification of life on earth, while controversy
continues over the pace and mechanisms of evolution.[33]
The Church's stance is that any such gradual appearance must have been guided in some way by
God, but the Church has thus far declined to define in what way that may be. Commentators tend to interpret
the Church's position in the way most favorable to their own arguments. The ITC statement includes these
paragraphs on evolution, the providence of God, and "intelligent design":
In freely willing to create and conserve the universe, God wills to activate and to sustain in act all
those secondary causes whose activity contributes to the unfolding of the natural order which he
intends to produce. Through the activity of natural causes, God causes to arise those conditions
required for the emergence and support of living organisms, and, furthermore, for their
reproduction and differentiation. Although there is scientific debate about the degree of
purposiveness or design operative and empirically observable in these developments, they have
de facto favored the emergence and flourishing of life. Catholic theologians can see in such
reasoning support for the affirmation entailed by faith in divine creation and divine providence. In
the providential design of creation, the triune God intended not only to make a place for human
beings in the universe but also, and ultimately, to make room for them in his own trinitarian life.
Furthermore, operating as real, though secondary causes, human beings contribute to the
reshaping and transformation of the universe.
A growing body of scientific critics of neo-Darwinism point to evidence of design (e.g., biological
structures that exhibit specified complexity) that, in their view, cannot be explained in terms of a
purely contingent process and that neo-Darwinians have ignored or misinterpreted. The nub of
this currently lively disagreement involves scientific observation and generalization concerning
whether the available data support inferences of design or chance, and cannot be settled by
theology. But it is important to note that, according to the Catholic understanding of divine
causality, true contingency in the created order is not incompatible with a purposeful divine
providence. Divine causality and created causality radically differ in kind and not only in degree.
Thus, even the outcome of a truly contingent natural process can nonetheless fall within God’s
providential plan for creation.[33]
In addition, while he was the Vatican's chief astronomer, Fr. George Coyne, issued a statement on
18 November 2005 saying that "Intelligent design isn't science even though it pretends to be. If you want to
teach it in schools, intelligent design should be taught when religion or cultural history is taught, not science."
Cardinal Paul Poupard added that "the faithful have the obligation to listen to that which secular modern
science has to offer, just as we ask that knowledge of the faith be taken in consideration as an expert voice in
humanity." He also warned of the permanent lesson we have learned from the Galileo affair, and that "we
also know the dangers of a religion that severs its links with reason and becomes prey to fundamentalism."
Fiorenzo Facchini, professor of evolutionary biology at the University of Bologna, called intelligent design
unscientific, and wrote in the January 16–17, 2006 edition L'Osservatore Romano: "But it is not correct from a
methodological point of view to stray from the field of science while pretending to do science....It only creates
confusion between the scientific plane and those that are philosophical or religious. Kenneth R. Miller is
another prominent Catholic scientist widely known for vehemently opposing creationism and intelligent
design. Nevertheless, some Catholic scientists, such as John C. Sanford and Michael Behe have strongly
opposed evolution and have supported the Intelligent design movement, the latter individual even
establishing the Center for Science and Culture of the Discovery Institute.[34]
In a commentary on Genesis authored as Cardinal Ratzinger titled In the Beginning... Benedict XVI
spoke of "the inner unity of creation and evolution and of faith and reason" and that these two realms of
knowledge are complementary, not contradictory:
We cannot say: creation or evolution, inasmuch as these two things respond to two different
realities. The story of the dust of the earth and the breath of God, which we just heard, does not
in fact explain how human persons come to be but rather what they are. It explains their inmost
origin and casts light on the project that they are. And, vice versa, the theory of evolution seeks
to understand and describe biological developments. But in so doing it cannot explain where the
'project' of human persons comes from, nor their inner origin, nor their particular nature. To that
extent we are faced here with two complementary -- rather than mutually exclusive -- realities.
– Cardinal Ratzinger, In the Beginning: A Catholic Understanding of the Story of Creation and
the Fall [Eerdmans, 1986, 1995], see especially pages 41-58)[page needed]
In a book released in 2008, his comments prior to becoming Pope were recorded as:
The clay became man at the moment in which a being for the first time was capable of forming,
however dimly, the thought of "God." The first Thou that – however stammeringly – was said by
human lips to God marks the moment in which the spirit arose in the world. Here the Rubicon of
anthropogenesis was crossed. For it is not the use of weapons or fire, not new methods of
cruelty or of useful activity, that constitute man, but rather his ability to be immediately in relation
to God. This holds fast to the doctrine of the special creation of man . . . herein . . . lies the
reason why the moment of anthropogenesis cannot possibly be determined by paleontology:
anthropogenesis is the rise of the spirit, which cannot be excavated with a shovel. The theory of
evolution does not invalidate the faith, nor does it corroborate it. But it does challenge the faith to
understand itself more profoundly and thus to help man to understand himself and to become
increasingly what he is: the being who is supposed to say Thou to God in eternity.
– Joseph Ratzinger[35]
On September 2–3, 2006 at Castel Gandolfo, Pope Benedict XVI conducted a seminar examining the
theory of evolution and its impact on Catholicism's teaching of Creation. The seminar is the latest edition of
the annual "Schülerkreis" or student circle, a meeting Benedict has held with his former Ph.D. students since
the 1970s.[36][37] The essays presented by his formers students, including natural scientists and
theologians, were published in 2007 under the title Creation and Evolution (in German, Schöpfung und
Evolution). In Pope Benedict's own contribution he states that "the question is not to either make a decision
for a creationism that fundamentally excludes science, or for an evolutionary theory that covers over its own
gaps and does not want to see the questions that reach beyond the methodological possibilities of natural
science," and that "I find it important to underline that the theory of evolution implies questions that must be
assigned to philosophy and which themselves lead beyond the realms of science."
In commenting on statements by his predecessor, he writes that "it is also true that the theory of
evolution is not a complete, scientifically proven theory." Though commenting that experiments in a
controlled environment were limited as "we cannot haul 10,000 generations into the laboratory," he does not
endorse creationism or intelligent design. He defends theistic evolution, the reconciliation between science
and religion already held by Catholics. In discussing evolution, he writes that "The process itself is rational
despite the mistakes and confusion as it goes through a narrow corridor choosing a few positive mutations
and using low probability....This....inevitably leads to a question that goes beyond science....where did this
rationality come from?" to which he answers that it comes from the "creative reason" of God.[38][39][40]
[edit] Catholic teaching and evolution

The Catechism of the Catholic Church (1994, revised 1997) on faith, evolution and science states:
159. Faith and science: "...methodical research in all branches of knowledge, provided it is
carried out in a truly scientific manner and does not override moral laws, can never conflict with
the faith, because the things of the world and the things of faith derive from the same God. The
humble and persevering investigator of the secrets of nature is being led, as it were, by the hand
of God in spite of himself, for it is God, the conserver of all things, who made them what they
are." (Vatican II GS 36:1) 283. The question about the origins of the world and of man has been
the object of many scientific studies which have splendidly enriched our knowledge of the age
and dimensions of the cosmos, the development of life-forms and the appearance of man.
These discoveries invite us to even greater admiration for the greatness of the Creator,
prompting us to give him thanks for all his works and for the understanding and wisdom he gives
to scholars and researchers.... 284. The great interest accorded to these studies is strongly
stimulated by a question of another order, which goes beyond the proper domain of the natural
sciences. It is not only a question of knowing when and how the universe arose physically, or
when man appeared, but rather of discovering the meaning of such an origin....
Paragraph 283 has been noted as making a positive comment regarding the theory of evolution, with
the clarification that "many scientific studies" which have enriched knowledge of "the development of life-
forms and the appearance of man" refers to mainstream science and not to "creation science".[41]
Concerning the doctrine on creation, Ludwig Ott in his Fundamentals of Catholic Dogma identifies
the following points as essential beliefs of the Catholic faith ("De Fide"):[42]
• All that exists outside God was, in its whole substance, produced out of nothing by God.
• God was moved by His Goodness to create the world.
• The world was created for the Glorification of God.
• The Three Divine Persons are one single, common Principle of the Creation.
• God created the world free from exterior compulsion and inner necessity.
• God has created a good world.
• The world had a beginning in time.
• God alone created the world.
• God keeps all created things in existence.
• God, through His Providence, protects and guides all that He has created.
[edit] Polygenism
Polygenism is the belief, religious or scientific, that the human race descended from two or more
ancestral types.[43] This is in contrast to monogenism, which teaches that the human race has descended
from a single pair of individuals.[44]
Few in the Catholic Church teach polygenism. This is because polygenism does not appear to be
reconcilable with the doctrine of Original Sin inherited by all from Adam.[45] Those who do teach it speculate
that evolution brought about not a single couple but many men, who constituted the primitive human
population. One of these, considered the leader of mankind, rebelled against God and that this sin passed on
to all men, even those alive who did not yet know sin.[46]
This theory is contradicted by the dogmas of the Catholic Church. As stated in Denzinger, The
Sources of Catholic Dogma, from the marriage of the first man and woman in the Bible, all men and women
take their origin and that men then were divided into tribes and nations across the world.[47] Dogma further
teaches that all men are descended from Adam, who was created from the Earth, and his wife, who came
from his rib – that these first two did not have human parents who proceeded them.[48]
[edit] Catholic schools and evolution

As in other countries, Catholic schools in the United States teach evolution as part of their science
curriculum. They teach the fact that evolution occurs and the modern evolutionary synthesis, which is the
scientific theory that explains why evolution occurs. This is the same evolution curriculum that secular
schools teach. Bishop DiLorenzo of Richmond, chair of the Committee on Science and Human Values in a
December 2004 letter sent to all U.S. bishops: "...Catholic schools should continue teaching evolution as a
scientific theory backed by convincing evidence. At the same time, Catholic parents whose children are in
public schools should ensure that their children are also receiving appropriate catechesis at home and in the
parish on God as Creator. Students should be able to leave their biology classes, and their courses in
religious instruction, with an integrated understanding of the means God chose to make us who we are."[49]
[edit] Unofficial Catholic organizations

See also: List of Catholic creationist organisations
There have been several organizations composed of Catholic laity and clergy which have advocated
positions both supporting evolution and opposed to evolution. For example:
• The Kolbe Center for the Study of Creation operates out of Mt. Jackson, Virginia and is a
Catholic lay apostolate promoting creationism.[50]
• The "Faith Movement" was founded by Catholic Fr. Edward Holloway in Surrey, England[51]
and "argues from Evolution as a fact, that the whole process would be impossible without the
existence of the Supreme Mind we call God."[52]
• The "Daylight Origins Society" was founded in 1971 by John G. Campbell (d.1983) as the
"Counter Evolution Group". Its goal is "to inform Catholics and others of the scientific evidence
supporting Special Creation as opposed to Evolution, and that the true discoveries of Science are in
conformity with Catholic doctrines." It publishes the "Daylight" newsletter.[53]
• The Center for Science and Culture of the Discovery Institute was founded, in part, by
Catholic biochemist Michael Behe, who is currently a senior fellow at the Center.[54][55]
There are many Catholic organizations who gain insight into the relation between Catholic faith and
evolution from the writings of Fr. Pierre Teilhard de Chardin.[citation needed] However, there have been
numerous condemnations of Teilhard by church officials and other Catholics.[56][57][58]
The website "catholic.net", successor to the "Catholic Information Center on the Internet", sometimes
features polemics against evolution.[59] Many "traditionalist" organizations are also opposed to evolution,
see e.g. the theological journal Living Tradition.[60]
[edit] See also

• Erich Wasmann
• St. George Jackson Mivart
• Relationship between religion and science
• Jainism and non-creationism
• Jewish views on evolution
• Hindu views on evolution
• Catholic Church and science
[edit] Notes
1. ^ Humani Generis, http://en.wikipedia.org/wiki/Humani_Generis#Evolutionism
2. ^ O'Leary, 7-15; Harrison, section "The Defence: Fr. Domenichelli"
3. ^ Harrison, especially Conclusion section 2
4. ^ Clement of Alexandria, Stromata Book VI, "For the creation of the world was concluded in
six days" http://www.newadvent.org/fathers/02106.htm
5. ^ Teske, Roland J. (1999). "Genesi ad litteram liber imperfectus, De". In Allan D. Fitzgerald
(ed.). Augustine Through the Ages: An Encyclopedia. Wm. B. Eerdmans Publishing. pp. 377–378.
ISBN 9780802838438.
6. ^ Rafael Martinez, professor of the philosophy of science at the Santa Croce Pontifical
University in Rome, in a speech reported on Catholic Ireland net Accessed May 26, 2009
7. ^ 1948 Index listing - for some reason the date of publication is given as 1914 not 1907
8. ^ The six leading examples are the subject of Artigas's book. Apart from Léroy, Zahm and
Bonomelli, discussed below, there were St. George Jackson Mivart, the English Bishop John Hedley,
and Raffaello Caverni. Each of these has a chapter in Artigas.
9. ^ Quoted in Harrison
10.^ Harrison
11.^ Artigas, 2,5,
12.^ Artigas, 2,5,7-9,220 etc.
13.^ John Henry Newman, Letter to J. Walker of Scarborough, May 22, 1868, The Letters and
Diaries of John Henry Newman, Oxford: Clarendon Press, 1973
14.^ Harrison analyses the records at length.
15.^ Harrison, Conclusion section 4
16.^ Harrison, especially Conclusion sections.
17.^ Evolution and dogma By John Augustine Zahm Online text
18.^ The Zahn affair is the subject of Artigas's Chapter 4, and of Appleby's essay
19.^ Artigas, 209
20.^ Artigas, 209-216
21.^ Grundriss der Katholischen Dogmatik (in German), Ludwig Ott, Verlag Herder, Freibury,
1952; First published in English as Fundamentals of Catholic Dogma, Ludwig Ott, translated by Dr.
Patrick Lynch and edited by James Canon Bastible, D.D., The Mercier Press, Limited, May, 1955.
22.^ O'Leary, 71
23.^ Arcanum Divinae Sapientiae, Encyclical, Vatican website. Quotation from s.5. Cited by in
Did women evolve from beasts, Harrison , Brian W. Living Tradition.
24.^ EVOLUTION: A CATHOLIC PERSPECTIVE, James B. Stenson, Catholic Position Papers,
Series A, Number 116, March, 1984, Japan Edition, Seido Foundation for the Advancement of
Education, 12-6 Funado-Cho, Ashiya-Shi Japan.
25.^ Pius XII, encyclical Humani Generis
26.^ a b John Paul II, Message to the Pontifical Academy of Sciences on Evolution
27.^ Cardinal Christoph Schönborn, "Finding Design in Nature," published in the New York
Times, July 7, 2005.
28.^ Matt Young, Taner Edis. Why Intelligent Design Fails: A Scientific Critique of the New
Creationism. Rutgers, The State University. http://books.google.com/books?
id=hYLKdtlVeQgC&pg=PR7&dq=archbishop+of+Vienna+intelligent+design&hl=en&ei=3VAUTZqTKo
uTnwekienDDg&sa=X&oi=book_result&ct=result&resnum=1&ved=0CCYQ6AEwAA#v=onepage&q=
archbishop%20of%20Vienna%20intelligent%20design&f=false. Retrieved 2010-12-02. "An influential
Roman Catholic cardinal, Cristoph Schonborn, the archbishop of Vienna, appeared to retreat from
John Paul II's support for evolution and wrote in the New York Times that descent with modification is
a fact, but evolution in the sense of "an unguided, unplanned process of random variation and natural
selection" is false. Many of Schonborn's complaints about Darwinian evolution echoed
pronouncements originiating from the Discovery Institute, the right-wing American think tank that
plays a central role in the ID movement (and whose public relations firm submitted Schonborn's
article to the Times)."
29.^ a b Parliamentary Assembly, Working Papers: 2007 Ordinary Session. Council of Europe
Publishing. http://books.google.com/books?
id=imUrkSP_5sUC&pg=PA66&dq=archbishop+of+Vienna+intelligent+design&hl=en&ei=3VAUTZqT
KouTnwekienDDg&sa=X&oi=book_result&ct=result&resnum=8&ved=0CEkQ6AEwBw#v=onepage&
q=archbishop%20of%20Vienna%20intelligent%20design&f=false. Retrieved 2010-12-02. "Christoph
Schonborn, the Archbishop of Vienna, published an article in the New York Times stating that the
declarations made by Pope John Paul II could not be interpreted as recognising evolution. At the
same time, he repeated arguments put forward by the supporters of the intelligent design ideas."
30.^ Review by John F. McCarthy, Living Tradition. Quotes p. 150 of the English edition.
31.^ a b c Ronald L. Numbers. The creationists: from scientific creationism to intelligent design .
Random House. http://books.google.com/books?
id=GQ3TI5njXfIC&pg=PA395&dq=archbishop+of+Vienna+intelligent+design&hl=en&ei=3VAUTZqTK
ouTnwekienDDg&sa=X&oi=book_result&ct=result&resnum=3&ved=0CDEQ6AEwAg#v=onepage&q
=archbishop%20of%20Vienna%20intelligent%20design&f=false. Retrieved 2010-12-02. "Miffed by
Krauss's comments, officers at the Discovery Institute arranged for the cardinal archbishop of
Vienna, Cristoph Sconborn (b. 1945), to write an op-ed peice for the Times dismissing the late pope's
statement as "rather vague and unimportant" and denying the truth of "evolution in the neo-Darwinian
sense-an unguided, unplanned process of random variation and natural selection." The cardinal, it
seems, had received the backing of the new pope, Benedict XVI, the former Joseph Ratzinger (b.
1927), who in the mid-1980s, while serving as prefect of the Sacred Congregation of the Doctrine of
the Faith, successor to the notorious Inquisition, had written a defense of the doctrine of creation
agasint Catholics who stressed the sufficiency of "selection and mutation." Humans, Benedict XVI
insisted, are "not the products of chance and error," and "the universe is not the product of darkness
and unreason. It comes from intelligence, freedom, and from the beauty that is identical with love."
Recent discoveries in microbiology and biochemistry, he was happy to say, had revealed
"reasonable design.""
32.^ Richard Owen report, London Times Online, accessed May 26, 2009
33.^ a b Communion and Stewardship: Human Persons Created in the Image of God , plenary
sessions held in Rome 2000-2002, published July 2004
34.^ Roger Stanyard, Paul Braterman, Roy Thearle et al.. "Michael Behe in Britain, 2010 Part 1".
British Centre for Science Education.
http://www.bcseweb.org.uk/index.php/Main/MichaelBeheInBritain. Retrieved 2010-12-02. "Michael
Behe is not an evangelical Calvinist but a conservative, possibly ultra-conservative, Roman Catholic
who accepts the old age of the earth and common descent (in the latter case Dembski doesn't). Behe
has nine children who have all been home-schooled. The limited evidence we have suggests that
Behe is a ultra-Catholic who does not question the Roman Catholic Church."
35.^ Creation and Evolution: A Conference With Pope Benedict XVI in Castel Gandolfo , S.D.S.
Stephan Horn (ed), pp. 15-16
36.^ Pope to Dissect Evolution With Former Students, Stacy Meichtry, Beliefnet
37.^ Benedict's Schulerkreis, John L. Allen Jr, National Catholic Reporter Blog, Sep 8, 2006
38.^ Pope says science too narrow to explain creation, Tom Heneghan, San Diego Union-
Tribune, April 11, 2007
39.^ Evolution not completely provable: Pope, Sydney Morning Herald, April 11, 2007
40.^ Pope praises science but stresses evolution not proven, USA Today, 4/12/2007
41.^ Akin, Jimmy (January 2004). "Evolution and the Magisterium". This Rock.
http://www.catholic.com/thisrock/2004/0401bt.asp. Retrieved 2007-08-14.
42.^ Fundamentals of Catholic Dogma (originally published in 1952 in German), Ludwig Ott,
these specific De Fide statements found in Ott on "The Divine Act of Creation," pages 79-91. The
various Councils (Lateran IV, Vatican I, Florence, and others), the traditional statements of the
Saints, Doctors, Fathers, and Scriptures are cited by Ott to document the Catholic dogma that God is
ultimately the Creator of all things however he chose to do the creating (Genesis 1; Colossians
1:15ff; Hebrews 3; Psalm 19).
43.^ http://dictionary.reference.com/browse/polygenism
44.^ http://dictionary.reference.com/browse/monogenism
45.^ J. Neuner, J. Jupuis, The Christian Faith [1996], page 169
46.^ Roberto Masi, L’Osservatore Romano, 17 April 1969
47.^ Enchiridion Symbolorum, Thirtieth Edition, 1954, paragraph 2280
48.^ Enchiridion Symbolorum, Thirtieth Edition, 1954, paragraph 228A
49.^ Catholic schools steer clear of anti-evolution bias, Jeff Severns Guntzel, National Catholic
Reporter, March 25, 2005
50.^ Kolbe Center for the Study of Creation: Defending Genesis from a Traditional Catholic
Perspective official website.
51.^ Catholicism: a New Synthesis, Edward Holloway, 1969.
52.^ Theistic Evolution and the Mystery of FAITH (cont'd), Anthony Nevard, Theotokos Catholic
Books website; Creation/Evolution Section.
53.^ Daylight Origins Society: Creation Science for Catholics official homepage.
54.^ William A. Dembski. Darwin's nemesis: Phillip Johnson and the intelligent design
movement. InterVarsity Press. http://books.google.com/books?
id=SU7VZD6ts20C&pg=PA349&dq=Michael+Behe+Center+for+Science+and+Culture&hl=en&ei=h2
YUTZPREsWynwfy56jXDg&sa=X&oi=book_result&ct=result&resnum=1&ved=0CCIQ6AEwADgU#v=
onepage&q=Michael%20Behe%20Center%20for%20Science%20and%20Culture&f=false. Retrieved
2010-12-02. "Michael J. Behe is progessor biological sciences at Lehigh University in
Pennsylvania...He is senior fellow with Discovery Institute's Center for Science and Culture."
55.^ Andrew J. Petto, Laurie R. Godfrey. Scientists confront intelligent design and creationism.
W. W. Norton & Company. http://books.google.com/books?
id=SCDB7hhLpwMC&pg=PA117&dq=Michael+Behe+Center+for+Science+and+Culture&hl=en&ei=
GWYUTfedM4SonAeSwLzADg&sa=X&oi=book_result&ct=result&resnum=9&ved=0CE8Q6AEwCA#
v=onepage&q=Michael%20Behe%20Center%20for%20Science%20and%20Culture&f=false.
Retrieved 2010-12-02. "Senior fellows at the CSC include mathematician David Berlinski, theological
and molecular biologist Jonathan Wells, biophysicist Michael Behe, mathematcian William Dembski,
philosopher Paul Nelson, and others."
56.^ Warning Considering the Writings of Father Teilhard de Chardin , Sacred Congregation of
the Holy Office, June 30, 1962.
57.^ Communiqué of the Press Office of the Holy See, English edition of L'Osservatore
Romano, July 20, 1981.
58.^ Letter about Teilhard de Chardin, Etienne Gilson writing to Cardinal De Lubac, in Teilhard
de Chardin: False Prophet, Dietrich von Hildebrand, Chicago: Franciscan Herald Press, 1968.
59.^ Theistic evolution: A tragic misunderstanding and grave error – Christians should realize
that evolution is not part of genuine natural science, but is an excuse invented by men to reject God. ,
Clement A. Butel, Catholic.net website
60.^ Living Tradition[specify]
[edit] References
• Appleby, R. Scott. Between Americanism and Modernism; John Zahm and Theistic
Evolution, in Critical Issues in American Religious History: A Reader, Ed. by Robert R. Mathisen, 2nd
revised edn., Baylor University Press, 2006, ISBN 1-932792-39-2, 9781932792393. Google books
• Artigas, Mariano; Glick, Thomas F., Martínez, Rafael A.; Negotiating Darwin: the Vatican
confronts evolution, 1877-1902, JHU Press, 2006, ISBN 0-8018-8389-X, 9780801883897, Google
books
• Harrison, Brian W., Early Vatican Responses to Evolutionist Theology, Living Tradition,
Organ of the Roman Theological Forum, May 2001.
• O'Leary, John. Roman Catholicism and modern science: a history, Continuum International
Publishing Group, 2006, ISBN 0-8264-1868-6, 9780826418685 Google books

• Bennett, Gaymon, Hess, Peter M. J. and others, The Evolution of Evil, Vandenhoeck &
Ruprecht, 2008, ISBN 3-525-56979-3, 9783525569795, Google books
• Johnston, George (1998). Did Darwin Get It Right?. Huntington: Our Sunday Visitor.
ISBN 0879739452. (google books)
• Kung, Hans, The beginning of all things: science and religion, trans. John Bowden, Wm. B.
Eerdmans Publishing, 2007, ISBN 0-8028-0763-1, 9780802807632. Google books
• Olson, Richard, Science and religion, 1450-1900: from Copernicus to Darwin, Greenwood
Publishing Group, 2004, ISBN 0-313-32694-0, 9780313326943. Google books
• Vatican Council I (1869-70), the full documents.
• 1913 Catholic Encyclopedia: Catholics and Evolution and Evolution, History and Scientific
Foundation of
• Pope Pius XII, Humani Generis 1950 encyclical
• Roberto Masi, "The Credo of Paul VI: Theology of Original Sin and the Scientific Theory of
Evolution" (L'Osservatore Romano, 17 April 1969).
• Pope John Paul II, general audience of 10 July 1985. "Proofs for God's Existence are Many
and Convergent."
• Cardinal Ratzinger's Commentary on Genesis Excerpts from In the Beginning: A Catholic
Understanding of the Story of Creation and the Fall.
• International Theological Commission (2004). "Communion and Stewardship: Human
Persons Created in the Image of God."
• Cardinal Paul Poupard, "Vatican Cardinal: Listen to What Modern Science has to Offer,"
November 3, 2005.
• Mark Brumley, "Evolution and the Pope, of Ignatius Insight
• John L. Allen Teaching of Benedict XVI on Evolution before becoming Pope.
• Benedict XVI's inaugural address.
• Pontifical Academy of Sciences
Retrieved from "http://en.wikipedia.org/wiki/Catholic_Church_and_evolution"
Categories: Roman Catholicism and science | Evolution and religion

W000
Kansas evolution hearings


Intelligent design
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v·d·e
The Kansas Evolution Hearings were a series of hearings held in Topeka, Kansas, United States
May 5 to May 12, 2005 by the Kansas State Board of Education and its State Board Science Hearing
Committee to change how evolution and the origin of life would be taught in the state's public high school
science classes. The hearings were arranged by the conservative Christian Board of Education with the
intent of introducing intelligent design into science classes via the Teach the Controversy method.[1][2]
The hearings raised the issues of creation and evolution in public education and were attended by all
the major participants in the intelligent design movement but were ultimately boycotted by the scientific
community over concern of lending credibility to the claim, made by proponents of intelligent design, that
evolution is purportedly the subject of wide dispute within the scientific and science education communities.
The Discovery Institute, hub of the intelligent design movement, played a central role in starting the
hearings by promoting its Critical Analysis of Evolution lesson plan[3] which the Kansas State Board of
Education eventually adopted over objections of the State Board Science Hearing Committee, and
campaigning on behalf of conservative Republican candidates for the Board.[4]
Local science advocacy group Kansas Citizens for Science organized a boycott of the hearings by
mainstream scientists, who accused it of being a kangaroo court and argued that their participation would
lend an undeserved air of legitimacy to the hearings.[5] Board member Kathy Martin declared at the
beginning of the hearings "Evolution has been proven false. ID (Intelligent Design) is science-based and
strong in facts." At their conclusion she proclaimed that evolution is "an unproven, often disproven" theory.
"ID has theological implications. ID is not strictly Christian, but it is theistic," asserted Martin.[6] The
scientific community rejects teaching intelligent design as science; a leading example being the United
States National Academy of Sciences, which issued a policy statement saying "Creationism, intelligent
design, and other claims of supernatural intervention in the origin of life or of species are not science
because they are not testable by the methods of science."[7]
2005.[8]
Contents
[hide]
• 1 Background
• 2 New science standards
• 2.1 Opposition to new standards
• 2.2 Support for new standards
• 2.3 Decision
• 2.4 Criticism
• 3 List of participants
• 4 Result
• 5 References
[edit] Background
The hearings were one of a number of Discovery Institute intelligent design campaigns that sought to
establish new science education standards consistent with conservative Christian beliefs, both in the state
and nationwide, and reverse what they saw as a domination in science education by the scientific theory of
evolution, which they viewed as atheistic, in direct conflict to their religious beliefs.
Kansas Board of Education elections in 2004 gave religious conservatives a 6-4 majority. In 2005,
prompted by the Kansas Intelligent Design Network[9] and the Discovery Institute, the board sought new high
school science standards. The revisions did not entirely eliminate evolution from instruction, but presented it
as a theory greatly challenged and disputed, in line with the Discovery Institute's Teach the Controversy
campaign. The new standards presented intelligent design as an alternative to evolution through the
Institute's Critical Analysis of Evolution. Board member Connie Morris sent a taxpayer-funded newsletter to
constituents calling evolution an "age-old fairy tale" that was defended with "anti-God contempt and
arrogance." Describing herself as a Christian who believes in a literal interpretation of Genesis, Morris wrote
that evolution was "biologically, genetically, mathematically, chemically, metaphysically and etc. wildly and
utterly impossible."[10]
The Intelligent Design Network originally proposed over 20 pages of revisions to the science
standards. Their proposals were rejected by the science standards committee (made up of Kansas scientists
and educators) appointed by the Board of Education, and were also rejected by 12 independent scientists
who reviewed the proposed revisions.[11]
Each side was invited to provide witnesses to testify before the board for intelligent design or
evolution, with the taxpayers of Kansas covering the travel expenses.[12] The scientific community refused to
participate en masse. The pro-intelligent design group, the Intelligent Design Network, invited 22 witnesses.
Among these were a number of non-scientists, and a number of scientists with no professional experience in
biology.
[edit] New science standards

On November 8, 2005 the Kansas Board of Education approved the following changes to its science
standards:[13]
1. Add to the mission statement a goal that science education should seek to help students
make "informed" decisions.
2. Provide a definition of science that is not strictly limited to natural explanations.[14][15]
3. Allow intelligent design to be presented as an alternative explanation to evolution as
presented in mainstream biology textbooks, without endorsing it.
4. State that evolution is a theory and not a fact.
5. Require informing students of purported scientific controversies regarding evolution.
[edit] Opposition to new standards

In addition to the over 70 scientific societies, institutions and other scientific professional groups that
have issued statements supporting evolution education and opposing intelligent design, the Kansas Board of
Education was presented a letter from 38 Nobel laureates, the Elie Wiesel Foundation for Humanity Nobel
Laureates Initiative, calling upon the Board of Education to reject intelligent design and support the teaching
of evolution. It stated:
"Logically derived from confirmable evidence, evolution is understood to be the result of an
unguided, unplanned process of random variation and natural selection. As the foundation of
modern biology, its indispensable role has been further strengthened by the capacity to study
DNA. In contrast, intelligent design is fundamentally unscientific; it cannot be tested as scientific
theory because its central conclusion is based on belief in the intervention of a supernatural
agent."[16]
The Discovery Institute has consistently insisted that its Critical Analysis of Evolution lesson plan is
not another attempt to open the door of public high school science classrooms for intelligent design, and
hence supernatural explanations. Discovery Institute spokesman Casey Luskin in February 2006 coined the
term "false fear syndrome" of those who said it was, and said:
"This is simply another instance of Darwinists attempting to oppose critical analysis of evolution
by pretending that it is equivalent to teaching intelligent design. This is a political tactic based
upon misinformation, misrepresentation, emotions, and false fears."[17]
In response, Nick Matzke says that it has proved that Critical Analysis of Evolution is a means of
teaching all the intelligent design arguments without using the intelligent design label.[18]
The Kansas science standards as proposed by the Discovery Institute and adopted by the state were
said to be "ID in disguise" by an assistant of a Discovery Institute Fellow, confirming the criticisms of
opponents to the standards. In discussing Discovery Institute radio commercials supporting their campaign
airing in Kansas on the blog of William A. Dembski, Dembski's research assistant and co-moderator of the
site, Joel Borofsky, said:
"My hope is that ID will be taught properly in Kansas. Having been born and raised there I would
love to claim to be from the first state to teach ID. There is a lot of movement among science
high school teachers to never teach ID, even if it becomes a law because "we don't know how to
teach philosophy." It would be nice to see them learn. I worked in a school and grew tired of
hearing them speak of how it's wrong to point out the weaknesses in Darwin's theory because,
"even if it is weak, it's still the best theory out there." (Shades of Dawkins anyone?)"[19]
To the statement that the Kansas science standards had nothing to do with intelligent design but
were only about teaching evolution in a "balanced" way, Borofsky responded:
"It really is ID in disguise. The entire purpose behind all of this is to shift it into schools...at least
that is the hope/fear among some science teachers in the area. The problem is, if you are not
going to be dogmatic in Darwinism that means you inevitably have to point out a fault or at least
an alternative to Darwinism. So far, the only plausible theory is ID. If one is to challenge Darwin,
then one must use ID. To challenge Darwin is to challenge natural selection/spontaneous first
cause...which is what the Kansas board is attempting to do. When you do that, you have to
invoke the idea of ID."[19]
In response to the reception to his comments,[20][21] Dembski's research assistant issued a

clarification, stating that he was only voicing his personal opinion, not that of others in the movement, and
that he is Dembski's "assistant on theological work, not necessarily the ID movement."[22]
The Discovery Institute continues to deny allegations that its true agenda is religious, and downplays
the religious source of much of its funding. In an interview of Stephen C. Meyer when ABC News asked
about the Discovery Institute's many evangelical Christian donors the institute's public relations
representative stopped the interview saying "I don't think we want to go down that path."[23]
Both the National Academy of Sciences and the National Science Teachers Association spoke out
against the new science standards; in addition to separate statements from each opposing the standards, the
two groups issued a joint statement that the new Kansas standards are improved, but as currently written,
they overemphasize controversy in the theory of evolution and distort the definition of science. The National
Academy of Sciences and National Science Teachers Association offered to work with the board to resolve
these issues so the state standards could use text from the National Research Council's National Science
Education Standards and National Science Teachers Association's Pathways to Science Standards, though
they ultimately declined to grant use of the text due to Kansas State Board of Education members insisting
on language "emphasizing controversy in the theory of evolution" and "distorting the definition of
science."[24]
The position of the scientific community is that there is no controversy to teach, that evolution is
widely accepted within the scientific community as a valid, well-supported theory and that such
disagreements that do exist are about the details of evolution's mechanisms, not the validity of evolution
itself.
For example the National Association of Biology Teachers in a statement endorsing evolution as
noncontroversial quoted Theodosius Dobzhansky "Nothing in biology makes sense except in the light of
evolution." and went on to state that the quote "accurately reflects the central, unifying role of evolution in
biology. The theory of evolution provides a framework that explains both the history of life and the ongoing
adaptation of organisms to environmental challenges and changes." They emphasized that "Scientists have
firmly established evolution as an important natural process" and that "The selection of topics covered in a
biology curriculum should accurately reflect the principles of biological science. Teaching biology in an
effective and scientifically honest manner requires that evolution be taught in a standards-based instructional
framework with effective classroom discussions and laboratory experiences."[25]
[edit] Support for new standards

The hub of the intelligent design movement, the Discovery Institute and its Center for Science and
Culture, played a central role in bringing about the Kansas evolution hearings, first by supporting ID
proponents in their bids for seats on the board, and later in aggressively lobbying for a "Teach the
Controversy" solution.[26] Teach the Controversy is a controversial political-action campaign originating from
the Discovery Institute that seeks to advance an education policy for US public schools that introduces
intelligent design to public school science curricula and seeks to redefine science [4] to allow for supernatural
explanations by eliminating "methodological naturalism" from science and replacing it with "theistic realism".
[27] Teach the Controversy proponents portray evolution as a "theory in crisis."
As well as proposing its own draft science standards to the Kansas State Board of Education[28] and
Critical Analysis of Evolution high school lesson plan,[29] the Discovery Institute participated in presenting a
letter to the Kansas State Board of Education from Institute associate, Dr. Philip S. Skell.[30] A notable
intelligent design proponent, Dr. Skell's letter to the board touts the alleged benefits of the Teach the
Controversy approach, as well his credentials as a member of the National Academy of Sciences, despite the
fact the National Academy of Sciences issued a policy statement against the Teach the Controversy solution
and intelligent design as a concept.
Two intelligent design proponents, John H. Calvert, a lawyer and a Managing Director of Intelligent
Design Network, Inc., and William S. Harris, Ph.D., co-author with Calvert of Intelligent Design: The Scientific
Alternative to Evolution (National Catholic Bioethics Quarterly, Autumn 2003) were instrumental in pushing
for the successful adoption of the new standards, including submitting a Suggested Findings of Fact and
Conclusions of Law[31] and numerous other documents.[32] Both are active participants in the intelligent
design movement.[33]
Discovery Institute fellows used the media coverage of the hearings to take their message to the
public. The Institute's vice president and program director, Stephen C. Meyer, appeared on the Fox News
show The Big Story with John Gibson, where he debated Eugenie Scott, executive director of the National
Center for Science Education. There Meyer sought to convey the Institute's message that debate over
evolution is not a ploy to get religious ideas into public schools, that evolution is a theory in crisis, and that
students were currently being taught in error there was no scientific controversy over evolution.[34]
The proposed changes were not supported by most of the 26 members of the panel that reviews
state science curriculum.
[edit] Decision
On November 8, 2005, the Board of Education voted to instruct science students along the lines of
the Discovery Institute, that evolution could not rule out a supernatural or theistic source, that evolution itself
was not fact but only a theory and one in crisis, and that ID must be considered a viable alternative to
evolution.
[edit] Criticism
A concern has been raised that this article's Criticism section may be compromising
the article's neutral point of view of the subject. Possible resolutions may be to integrate the
material in the section into the article as a whole, or to rewrite the contents of the section.
Please see the discussion on the talk page. (August 2010)

may be challenged and removed. (August 2010)
The hearings drew criticism from leading scientists and organizations, some comparing the hearings
to the sensationalism of the Scopes "Monkey Trial". Many scientists and scientific groups, despite being
invited to participate by the organizers, chose not to, and it has been referred to as the "Kansas kangaroo
court". Some organized active boycotts, others ignored it on the basis that any attention paid to it by the
scientific community could have been used adversely.
The board has been accused of misuse of the political process for holding the hearings in the first
place. Estimates place the cost of the hearings at $10,000, all funded by taxes. The board was also criticized
for possible unfairness towards Pedro Irigonegaray, the Topeka lawyer who argued in favor of evolution.
Supporters cite that Calvert was given more time to argue his side.
Concerns have also been raised that such a public attack on accepted theory could hamper the
abilities of Kansas students to excel in science, as well as endanger their later prospects regarding
universities and the job market.
Kansas has had experience with the debate before. In 1999 they voted to remove any mention of
macroevolution, the age of the Earth, and the origin of the Universe from science curriculum. In 2001 the
position was reversed as the membership of the board was changed due to the previous year's elections. But
the board elections in 2004 have given conservatives a majority of the ten seats, causing the curriculum to
again be evaluated.
[edit] List of participants

The following is a list of those who testified in the Kansas evolution hearings (in order), most of whom
are affiliated with the Discovery Institute and all of whom are intelligent design advocates or other forms of
creationists, or advocates of some other form of anti-evolution.
April 19, 2005 (Prehearings Statements)
1. Pedro L. Irigonegaray (for mainstream science)
May 5, 2005
1. William S. Harris - Biochemist, Professor of Medicine, University of Missouri at Kansas City,
Director of the Lipoprotein Research Laboratory, St. Luke’s Hospital, Kansas City, Missouri, signer of
the Discovery Institute's A Scientific Dissent from Darwinism,[35] and co-author, with John Calvert, of
Intelligent Design: The Scientific Alternative to Evolution .[36][37][38]
2. Charles Thaxton - Editor of the book Of Pandas and People, Fellow of the Discovery
Institute's Center for Science and Culture,[39] signer of the Discovery Institute's A Scientific Dissent
from Darwinism.[35]
3. Jonathan Wells - author of Icons of Evolution and Fellow of the Discovery Institute's Center
for Science and Culture,[39] signer of the Discovery Institute's A Scientific Dissent from Darwinism.
[35]
4. Bruce Simat - Associate Professor of Biology at Northwestern College in St. Paul, Minnesota,
[40] signer of the Discovery Institute's A Scientific Dissent from Darwinism. [35][41]
5. Giuseppe Sermonti - Chief Editor of Rivista di Biologia/Biology Forum and author of Why Is a
Fly Not a Horse? which is published by the Discovery Institute.[42]
6. Ralph Seelke - PhD Professor of Microbiology, University of Wisconsin - Superior, self-
described Christian apologetist,[40] signer of the Discovery Institute's A Scientific Dissent from
Darwinism.[35]
May 6, 2005
1. Edward Peltzer - Oceanographer, Associate Editor, Marine Chemistry, Senior Research
Specialist Monterey Bay Aquarium Research Institute, signer of the Discovery Institute's A Scientific
Dissent from Darwinism.[35]
2. Russell Carlson - Professor of Biochemistry and Molecular Biology University of Georgia,
signer of the Discovery Institute's A Scientific Dissent from Darwinism. [35] Member of DI research
fellow William Dembski's The International Society for Complexity, Information, and Design (ISCID)
[43][44]
3. John C. Sanford - Cornell University Associate Professor of Horticultural Sciences, inventor
of the "gene gun," intelligent design advocate.[45][46][47]
4. Robert DiSilvestro - Biochemist, Professor of Nutrition, Ohio State University,[48] signer of
the Discovery Institute's A Scientific Dissent from Darwinism.[35][49][50]
5. Bryan Leonard - High school biology teacher, involved in a doctoral thesis controversy in
which he was supported by the Discovery Institute.[48][51][52][53]
6. Dan Ely - Professor of Biology, University of Akron in Ohio,[40] self-described intelligent
design teacher[54] who assisted in drafting the adopted lesson plan.[55]
7. Roger DeHart - High school biology teacher, Oaks Christian High School in Westlake Village,
California, who claims teaching intelligent design cost him two jobs. Author of a companion study
guide Icons of Evolution- A Study Guide to Jonathan Wells' Icons of Evolution.[56][40][55]
8. Jill Gonzalez-Bravo - eighth grade Kansas science teacher, who endorsed the Discovery
Institute-promulgated science standards in her testimony and in an interview conducted by the
Discovery Institute.[57] Additionally, Gonzalez-Bravo appeared in a commercial favoring the teaching
of intelligent design.[58]
9. John Millam - Software developer, signer of the Discovery Institute's A Scientific Dissent
from Darwinism, denier of common dissent, advocate of intelligent design.[35][59]
May 7, 2005
1. Nancy Bryson - Former Division Head of the Dept of Science and Mathematics at Mississippi
University for Women who claims to have lost her position over a presentation Critical Thinking on
Evolution that presented alternatives to Darwinian evolution which a senior professor of biology
derided the speech as "religion masquerading as science."[60][61] Bryson is often cited by the
Discovery Institute as one who was "demonized and blacklisted" by "Darwinian fundamentalists."[62]
2. James Barham - Scholar, author, intelligent design advocate specializing in evolutionary
epistemology, the philosophy of mind, and the foundations of biology, known for "Why I am not a
Darwinist" in Debating Darwin, From Darwin to DNA[63] and quoted in Dembski's Uncommon
Dissent...Intellectuals Who Find Darwinism Unconvincing.[64][65]
3. Stephen C. Meyer - Program Director of the Discovery Institute's Center for Science and
Culture, Discovery Institute co-founder, signer of the Discovery Institute's A Scientific Dissent from
Darwinism.[35]
4. Angus Menuge - philosopher of science, Dept. of Philosophy Concordia University
Wisconsin, who participated in Discovery Institute sponsored symposia leading up to the 2006
election for seats opening in the state Board of Education.[66][67] Menuge also describes himself as
someone whose interests "now are in promoting Christian teaching and scholarship...".[68][69]
5. Warren Nord - Professor of Philosophy of Religion and Education, University of North
Carolina, Chapel Hill,[40] and Kitzmiller v. Dover Area School District defense witness who withdrew
before testifying along with other Discovery Institute associates William Dembski, John Campbell,
and Stephen C. Meyer.[70]
6. Mustafa Akyol - Columnist in the Turkish daily newspaper Referans, and freelance writer in
the U.S., vocal advocate of intelligent design.[71][72]
7. Michael Behe - Biochemist at Lehigh University and prominent intelligent design proponent,
Center for Science and Culture Fellow,[39] and signer of the Discovery Institute's A Scientific Dissent
from Darwinism,[35] presented irreducible complexity with the claim that it was supported by a paper
he had co-authored with David Snoke.[73]
8. John Calvert - Lawyer who has worked closely with the Discovery Institute in finding
constitutionally allowable ways to bring intelligent design and failing there, Teach the Controversy,
into public schools. Managing Director of Intelligent Design network, inc., an organization that seeks
intelligent design taught in public education.
May 12, 2005 (Closing Statements)
1. Pedro L. Irigonegaray (for mainstream science)
2. John Calvert (for intelligent design)
[edit] Result
The Kansas Board of Education voted 6–4 August 9, 2005 to include greater criticism of evolution in
its school science standards, but it decided to send the standards to an outside academic for review before
taking a final vote. The standards received final approval on November 8, 2005. The new standards were
approved by 6 to 4, reflecting the makeup of religious conservatives on the board.[74] In July 2006 the Board
of Standards issued a "rationale statement" which claimed that the current science curriculum standards do
not include intelligent design.[75] Members of the scientific community critical of the standards contended
that the board's statement was misleading in that they contained a "significant editorializing that supports the
Discovery Institute and the Intelligent Design network’s campaign position that Intelligent Design is not
included in the standards", the standards did "say that students should learn about ID, and that ID content
ought to be in the standards", and that the standards presented the controversy over intelligent design as a
scientific one, denying the mainstream scientific view.[75][76]
Kansas joined Ohio in adopting the Discovery Institute's Critical Analysis of Evolution public school
science standards during that period. While other states were backing away from teaching alternatives to
evolution, the Oklahoma House passed a bill Thursday, March 2, 2006 that contained Discovery Institute
language encouraging schools to expose students to alternative views about the origin of life. Popular
reaction included the creation of the intelligent design parody Flying Spaghetti Monsterism. Its founder
insisted it should be offered as a "third" theory on origins, suggesting possible legal action if it was not
included and intelligent design was.
On August 1, 2006, 4 of the 6 conservative Republicans who approved the Critical Analysis of
Evolution classroom standards lost their seats in a primary election. The moderate Republican and liberal
Democrats gaining seats, largely supported by Governor Kathleen Sebelius, vowed to overturn the 2005
school science standards and adopt those recommended by a State Board Science Hearing Committee that
were rejected by the previous board.[77]
One of the members who lost her seat, Connie Morris, a conservative from St. Francis in the
northwest corner of the state, pointed to the "liberal media" for her loss, noting that "liberal opportunists" do
not mind "slandering people and harming their families and their reputation and their business and their
communities and their state ... It's a shame, and I feel bad for them when they face God on Judgment Day."
Although four born-again Christians remained on the Board, she believed that the new board would waste no
time adopting new science standards, expecting that in the following January, when the new members are
sworn in, the Board would rescind existing standards and adopt new ones that "let government schools teach
children that we are no more than chaotic, random mutants."[78]
2005. The definition of science was once again returned to "the search for natural explanations for what is
observed in the universe."[8]
[edit] References
1. ^ Transcripts, Kansas Evolution Hearings Page 6. Via Talk Origins Archive.
2. ^ A Real Monkey Trial Peter Dizikes. Salon, May 13, 2005.
3. ^ CSC - Key Resources for Parents and School Board Members
4. ^ 6News Lawrence: Some question group's move with elections nearing
5. ^ Wichita Eagle, "Scientists Right to Boycott Evolution Hearings," March 30, 2005; "Evolution
Hearings Rejected by Scientists," April 12, 2005.
6. ^ Reason Magazine - Unintelligent Design
7. ^ [1].
8. ^ a b "Evolution of Kansas science standards continues as Darwin's theories regain
prominence". International Herald-Tribune. 2007-02-13.
http://www.iht.com/articles/ap/2007/02/13/america/NA-GEN-US-Kansas-Evolution-History.php.
9. ^ [2] intelligentdesignetwork.org, also known as IDnet
10.^ David Klepper, "Kansas School Board's Hearings on Evolution End in Acrimony," Knight
Ridder Newspapers, May 12, 2005.
11.^ http://www.ksde.org/outcomes/sciencestdreview.html
12.^ The Panda's Thumb: Kansas Evolution Hearings
13.^ 2005 The Kansas state science standards Kansas State Dept. of Education
14.^ We also emphasize that the Science Curriculum Standards do not include Intelligent
Design, the scientific disagreement with the claim of many evolutionary biologists that the apparent
design of living systems is an illusion. While the testimony presented at the science hearings
included many advocates of Intelligent Design, these standards neither mandate nor prohibit
teaching about this scientific disagreement.[3]
15.^ The new definition adopted: "Science is a systematic method of continuing investigation
that uses observations, hypothesis testing, measurement, experimentation, logical argument and
theory building, to lead to more adequate explanations of natural phenomena."
16.^ Elie Wiesel Foundation for Humanity Nobel Laureates Initiative (PDF file)
17.^ False Fear Epidemic over Critical Analysis of Evolution Spreads to Wisconsin Casey
Luskin. Discovery Institute, February 2006.
18.^ No one here but us Critical Analysis-ists... Nick Matzke. The Panda's Thumb, July 11, 2006
19.^ a b Radio Commercials Air in Kansas Supporting Standupforscience.com’s Approach to
Teaching Evolution Joel Borofsky. Uncommondescent.com, July 29, 2006
20.^ Revealing slip of the keyboard. PZ Myers. Pharyngula, July 31, 2006.
21.^ Which Creationist is Lying? Jeffrey Shallit. Recursivity, August 1, 2006.
22.^ Am I really that important? Joel Borofsky. UncommonDescent, August 3, 2006.
23.^ Small Group Wields Major Influence in Intelligent Design Debate ABC News, November 9,
2005
24.^ "Kansas Denied Use of National Science Education Standards". The National Academies.
2005-10-27. http://www.nationalacademies.org/morenews/20051027.htm.
25.^ Bisconti, Michael J. (2006-09-27). "NABT's Statement on Teaching Evolution". Internet
Archive Wayback Machine. National Association of Biology Teachers. Archived from the original on
2006-09-27.
http://web.archive.org/web/20060927160040/http://www.nabt.org/sub/position_statements/evolution.
asp. Retrieved 2008-03-20.
26.^ http://www.discovery.org/scripts/viewDB/index.php?command=view&program=CSC%20-
%20Views%20and%20News&id=2570
27.^ http://www.arn.org/docs/johnson/ratzsch.htm
28.^ discovery.org
29.^ discovery.org
30.^ discovery.org
31.^ kansasscience2005.com
32.^ intelligentdesignnetwork.org
33.^ intelligentdesignnetwork.org
34.^ "Evolution Vs. God in the Classroom - The Big Story w/ Gibson and Nauert". FOX News.
2005-05-06. http://www.foxnews.com/story/0,2933,155943,00.html. Retrieved 2010-02-17.
35.^ a b c d e f g h i j k A Scientific Dissent from Darwinism Discovery Institute.
36.^ Publications Intelligent Design Network.
37.^ Kansas hearing transcripts
38.^ Kansas hearing transcripts Q. Do you accept the general principle of common descent, that
all life is biologically related to the beginning of life? Yes or no. A. No. Q. Do you accept that human
beings are related by common descent to prehominid ancestors? Yes or no. A. No
39.^ a b c List of Discovery Institute's Center for Science and Culture Fellows
40.^ a b c d e Witnesses to who testified at Hearings Conducted by the Science Committee of the
Kansas State Board of Education KansasScience2005.com
41.^ Kansas hearing transcripts Q. Sir, the first question I'd like to ask you is, do you accept the
evolutionary theory of common descent of humans from prehominids? A. From the data that I've
been following it's probably not true.
42.^ Why is a Fly Not a Horse? Discovery Institute, Center for Science and Culture.
43.^ ISCID
45.^ ID at Cornell, John Sanford and Allen MacNeill Dembski. Uncommondescent.com, April 14,
2006
46.^ Intelligent Design: Professors discuss Teaching the Controversial Subject Xiaowei Cathy
Tang. Cornell Daily Sun, November 15, 2005
48.^ a b Professors Defend Ohio Grad Student Under Attack by Darwinists Discovery Institute
News.
50.^ Evolution News, see January 10, 2006 update
51.^ Not So Intelligently Designed Ph.D. Panel Inside Higher Ed, June 10, 2005.
52.^ Kansas hearing transcripts Q. The record will reflect your answer. Do you-- do you accept
the general principle of common descent, that all of life was biologically related to the beginning of
life? Yes or no? A. No.
53.^ http://www.pandasthumb.org/archives/2006/08/the_politically_ohio.html
54.^ Biologist Dan Ely testifies in Support of Ohio's Critical Analysis of Evolution Lesson Plan
Discovery Institute's Center for Science and Culture.
55.^ a b Kansas hearing transcripts
56.^ Icons of Evolution--A Study Guide Discovery Institute's Center for Science and Culture.
57.^ A Kansas Teacher Stands Up For Science Intelligent Design The Future.
58.^ Radio Commercials Air in Kansas Supporting Standupforscience.com's Approach to
Teaching Evolution
59.^ Kansas hearing transcripts Q. Do you accept that human beings are related by common
descent to prehominid ancestors? Yes or no? A. No. Q. What is the alternative explanation for how
the human species came into existence if you do not accept common descent? A. Design.
60.^ Kansas Evolution Hearings Transcripts of an Intelligently-Designed "Kangaroo Court"
TalkOrigins.com
61.^ MUW educator returned to post ClarionLedger.com.
62.^ Join The Free Speech on Evolution Campaign Scientists, teachers, and students are under
attack for questioning evolution - Help us Help Them Discovery Institute's Center for Science and
Culture.
63.^ Debating Darwin, From Darwin to DNA Edited by William A. Dembski. Cambridge
University Press.
64.^ A review of Uncommon Dissent Bruce Thornton. CaliforniaRepublic.org
66.^ Statewide Symposiums Will Deliver the Truth About Kansas Science Standards And
Teaching of Evolution Discovery Institute.
68.^ Menuge's page at Concordia University Wisconsin
69.^ Menuge's Argument for Design
70.^ Kansas hearing transcripts"But when you teach only Neo-Darwinism, the inevitable
conclusion to draw is that doesn't explain everything. Design theory does not require God-- or a
Christian God--"
71.^ Under God or Under Darwin? Mustafa Akyol. National Review.
73.^ "Kansas Evolution Hearings: Michael Behe and John Calvert".
http://www.talkorigins.org/faqs/kansas/kangaroo10.html. Retrieved 2008-03-10.
74.^ usatoday.com
75.^ a b kcfs.org
76.^ pandasthumb.org
77.^ msnbc.msn.com
78.^ Brown, Jim (2006-08-11). "Official Cries Foul as Liberals Take Over Kansas Education
Board". Agape Press (Internet Archive Wayback Machine). Archived from the original on 2006-10-06.
http://web.archive.org/web/20061006223857/http://headlines.agapepress.org/archive/8/112006d.asp
. Retrieved 2008-05-04.
• National Science Education Standards; National Academy Press; 1996 (Fifth Printing
February 1998); ISBN 0309053269.
• Benchmarks for Scientific Literacy, American Association for the Advancement of Science
(AAAS); 1993; ISBN 9780195089868.

Kansas portal
Science portal
Education portal
• Summary of Key Changes to Kansas Science Standards adopted by the Kansas State Board
of Education (PDF)
• Review of the Kansas Science Education Standards by the National Academy of Sciences
(PDF file)
• Joint Statement from the National Academy of Sciences and the National Science Teachers
Association (PDF file)
• Transcripts of Kansas Evolution Hearings
• "Echoes of Scopes Trial Heard in Intelligent Design Hearing" from the Boston Globe
• "Evolution Hearings Open in Kansas" from CNN
• Creationism: God's gift to the ignorant , Richard Dawkins, The Times, May 21, 2005
Retrieved from "http://en.wikipedia.org/wiki/Kansas_evolution_hearings"
Categories: Education in Kansas | Politics of Kansas | Intelligent design movement | Intelligent

design controversies | Discovery Institute campaigns
W000
Group selection

The neutrality of this article is disputed. Please see the discussion on the talk page.
Please do not remove this message until the dispute is resolved. (January 2011)
In evolutionary biology, group selection refers to the idea that alleles can become fixed or spread in a
population because of the benefits they bestow on groups, regardless of the alleles' effect on the fitness of
individuals within that group.
Group selection was used as a popular explanation for adaptations, especially by V. C. Wynne-
Edwards.[1][2] For several decades, however, critiques, particularly by George C. Williams,[3]John Maynard
Smith[4] and C.M. Perrins (1964), cast serious doubt on group selection as a major mechanism of evolution,
and though some scientists have pursued the idea over the last few decades, only recently have group
selection models seen a minor resurgence[5][6] (albeit not as a fundamental mechanism but as a
phenomenon emergent from standard selection[6]).
Contents
[hide]
• 1 Overview
• 2 The haystack model and trait groups
• 3 Multilevel selection theory
• 4 Group selection indicated by gene-culture coevolution
• 5 Group selection due to differing ESSs
• 6 See also
• 7 References
[edit] Overview
Specific syndromes of selective factors can create situations where groups are selected because
they display group properties that are selected-for. Some mosquito-transmitted rabbit viruses, for instance,
are only transmitted to uninfected rabbits from infected rabbits that are still alive. This creates a selective
pressure on every group of viruses already infecting a rabbit not to become too virulent and kill their host
rabbit before enough mosquitoes have bitten it. In natural systems such viruses display much lower virulence
levels than do mutants of the same viruses that in laboratory culture readily out-compete non-virulent variants
(or than do tick-transmitted viruses—ticks, unlike mosquitoes, bite dead rabbits).
However, theoretical models of the 1960s seemed to imply that the effect of group selection was
negligible. Alleles are likely to be held on a population-wide level, leaving nothing for group selection to select
for. Additionally, generation time is much longer for groups than it is for individuals. Assuming conflicting
selection pressures, individual selection will occur much faster, swamping any changes potentially favored by
group selection. The Price equation can partition variance caused by natural selection at the individual level
and the group level, and individual level selection generally causes greater effects.
Experimental results starting in the late 1970s demonstrated that group selection was far more
effective than the then-current theoretical models had predicted.[7] A review of this experimental work has
shown that the early group selection models were flawed because they assumed that genes acted
independently, whereas in the experimental work it was apparent that gene interaction, and more importantly,
genetically based interactions among individuals, were an important source of the response to group
selection (e.g.[8]). As a result many are beginning to recognize that group selection, or more appropriately
multilevel selection, is potentially an important force in evolution.
More recently, Yaneer Bar-Yam has claimed that the gene-centered view (and thus Ronald Fisher's
treatment of evolution) relies upon a mathematical approximation that is not generally valid. Bar-Yam argues
that the approximation is a dynamic form of the Mean Field approximation frequently used in physics and
whose limitations are recognized there. In biology, the approximation breaks down when there are spatial
populations resulting in inhomogeneous genetic types (called symmetry breaking in physics). Such symmetry
breaking may also correspond to speciation.
Spatial populations of predators and prey have also been shown to show restraint of reproduction at
equilibrium, both individually[9] and through social communication,[10] as originally proposed by Wynne-
Edwards. While these spatial populations do not have well-defined groups for group selection, the local
spatial interactions of organisms in transient groups are sufficient to lead to a kind of multi-level selection.
There is however as yet no evidence that these processes operate in the situations where Wynne-Edwards
posited them; Rauch et al.'s analysis,[9] for example, is of a host-parasite situation, which was recognised as
one where group selection was possible even by E. O. Wilson (1975), in a treatise broadly hostile to the
whole idea of group selection.[11] Specifically, the parasites do not individually moderate their transmission;
rather, more transmissible variants "continually arise and grow rapidly for many generations but eventually go
extinct before dominating the system."
[edit] The haystack model and trait groups

may be challenged and removed. (January 2009)
Maynard Smith can be credited with what has become known as the "haystack model" of group
selection. As a non-mathematical introduction to the idea, imagine a group of animals that spend most of
their time living and breeding in haystacks but that occasionally all come out of their haystacks
simultaneously, mix together and then separate into equal groups, which once again go off to inhabit
separate haystacks. We can then imagine a trait that benefits each haystack group, perhaps leading to
behaviorally altruistic acts that cost an individual some fitness but enhance the fitness of its group even more,
and a selfish trait that, for the purposes of this discussion, we can call the absence of the altruistic trait.
Each of these two traits works on a different level of selection. Within the individual haystacks the
selfish organisms benefit in terms of evolutionary fitness. This is because the selfish organisms benefit from
the actions of the altruistic organisms but do not pay any of the evolutionary costs for being altruistic
(sacrificing some good for that of others). Thus, in each generation the number of altruists in the group would
shrink compared to the number of selfish organisms. As a result one might first think that a group beneficial
trait, especially an altruistic one, would be doomed to eventually die out. But we must remember the strange
nature of these hypothetical organisms. Every so often, at the same time, all the members of all the
haystacks form one large group, randomly assort into equal groups, and then move back into the haystacks.
Because of this an altruistic behavior can take hold by the following reasoning. While the number of selfish
organisms in each haystack increases in percentage every generation, the total population of haystacks that
contain altruists produce more offspring over all than those that do not. This means that populations with
altruists are going to be over-represented when all the haystacks are abandoned to form a larger group. So
long as the number of generations spent in each haystack is not so long as to dramatically reduce the
number of altruists, and so long as the group benefit of the altruistic trait is significant enough, the number of
altruists in all the haystack populations can rise.
However, though Maynard Smith gave a mathematical model by which group selection might work,
he was skeptical that it would happen in nature often enough to be worth considering. His reasoning was that
the specific conditions for group selection to take hold, namely the repeated isolation, mixture, and reisolation
of organisms would be so rare and unlikely to occur in nature that it was almost certainly not a significant
evolutionary force.
In their 1998 book Unto Others, and in various articles before this, Sober and David Sloan Wilson
challenge this view. While one of their challenges takes the form of naming organisms, such as the so called
"brain worm" (Dicrocoelium dendriticum), which has a life cycle much like that of the haystack organisms
above, they present a more significant argument, based on the notion of trait groups.
Trait groups can occur within larger groups through the interaction of particular genetic traits, and
need not interact for a generation to promote survival value. Sober and Wilson see kin selection, which is
often considered an alternative to group selection, as a special case of a trait groups. To see how a trait
group could be beneficial, let's imagine an altruist trait, such as cooperation with another organism even in
such cases were it only benefits 40% as much as the organism it helps, and a selfish trait such as
cooperating with another organism only when it will benefit more than the organism it helps. The first trait is
considered altruistic in Sober and Wilson’s sense because the within-group fitness of the altruistic organism
drops every time it cooperates compared with the other member of the group. Now imagine five organisms,
one of which is altruistic in regards to this trait, and the rest of which are selfish. Assume that each case of
cooperation increases the chance of survival and reproduction by 10 units, which is divided among the
interacting pair (group of two). Now assume that member of the population groups/interacts with each other
member of the population one time. After all the interactions have taken place, the selfish organisms have
each acquired 6 units. This is because they all refuse to cooperation with other selfish members (since it is
impossible for both members to benefit more than the other), but each takes advantage of the altruist benefits
over that individual in a ratio of 60% to 40%. The altruist on the other hand has interacted with 4 selfish
organisms and thus has earned 16 units (four for each encounter) and thus has a greater survival advantage
than the selfish members of the population. The altruist ends up winning the survival "war" even though it
came out behind in every survival "battle".
Because individuals can form hundreds or even thousands of trait groups within its life span, the trait
group selection model does not have to rely on the unlikely situation of an entire population isolating into
groups, merging, and then isolating into groups again. Likewise the rate at which trait groups can form and
dissolve can be many times faster than the rate at which individuals reproduce, providing cumulative as
opposed to all-or-nothing benefits. It is important to note that this argument has not settled the issue of group
selection however. There is still heavy debate as to whether or not such formations count as “real” groups in
the traditional biological sense of groups affected by group selection.
[edit] Multilevel selection theory

See also: Unit of selection
In recent years, the limitations of earlier models have been addressed, and newer models suggest
that selection may sometimes act above the gene level. Recently David Sloan Wilson and Elliot Sober have
argued that the case against group selection has been overstated. They focus their argument on whether
groups can have functional organization in the same way individuals do and, consequently, whether groups
can also be "vehicles" for selection. For example, groups that cooperate better may have out-reproduced
those that did not. Resurrected in this way, Wilson & Sober's new group selection is usually called multilevel
selection theory.[12]
David Sloan Wilson, the developer of Multilevel Selection Theory (MLS) compares the many layers of
competition and evolution to the “Russian Matryoska Dolls” within one another.[13] The lowest level is the
genes, next come the cells, and then the organism level and finally the groups. The different levels function
cohesively to maximize fitness, or reproductive success. After establishing these levels, MLS goes further by
saying that selection for the group level, which is competition between groups, must outweigh the individual
level, which is individuals competing within a group, for a group-beneficiating trait to spread.[14] MLS theory
focuses on the phenotype this way because it looks at the levels that selection directly acts upon.[13]
MLS theory is not leaning towards individual or group selection but can be used to evaluate the
balance between group selection and individual selection on a case-by-case scenario.[14] Some
experiments done imply that group selection can prevail, such as the experiment conducted by William Muir
of Purdue University comparing egg productivity in hens. In the experiment, he demonstrates the existence of
group selection by showing that in individual selection, a hyper-aggressive strain had been produced that led
to many fatal attacks only after six generations.[15] Group selection has been most often postulated in
humans and, notably, social insects that make cooperation a driving force of their adaptations over time.[16]
For humans, a highly pro-social, cognitive thinking species, social norms can be seen as a means of
reducing the individual level variation and competition and shift selection in humans to the group level.
Wilson ties the MLS theory regarding humans to another upcoming theory known as gene-culture evolution
by acknowledging that culture seems to characterize a group-level mechanism for human groups to adapt to
environmental changes.[14] The ways to test MLS is through social psychological experimentation and
multilevel modeling equations.
Although Richard Dawkins and fellow advocates of the gene-centered view of evolution remain
unconvinced,[17][18][19] Wilson & Sober's work has been part of a broad revival of interest in multilevel
selection as an explanation for evolutionary phenomena. Indeed, in a 2005 article,[20] E. O. Wilson argued
that kin selection could no longer be thought of as underlying the evolution of extreme sociality, for two
reasons. First, some authors have shown that the argument that haplodiploid inheritance, characteristic of
the Hymenoptera, creates a strong selection pressure towards nonreproductive castes is mathematically
flawed.[21] Second, eusociality no longer seems to be confined to the hymenopterans; increasing numbers of
highly social taxa have been found in the years since Wilson's foundational text on sociobiology was
published in 1975,[11] including a variety of insect species, as well as a rodent species (the naked mole rat).
Wilson suggests the equation for Hamilton's rule:[22]
rb > c
(where b represents the benefit to the recipient of altruism, c the cost to the altruist, and r their
degree of relatedness) should be replaced by the more general equation
(rbk + be) > c
in which bk is the benefit to kin (b in the original equation) and b e is the benefit accruing to the group
as a whole. He then argues that, in the present state of the evidence in relation to social insects, it appears
that be>>rbk, so that altruism needs to be explained in terms of selection at the colony level rather than at the
kin level. However, it is well understood in social evolution theory that kin selection and group selection are
not distinct processes, and that the effects of multi-level selection are already fully accounted for in
Hamilton's original rule, rb>c.[23]
[edit] Group selection indicated by gene-culture coevolution

Gene-culture coevolution is a modern hypothesis (applicable mostly to humans) that combines
evolutionary biology and modern sociobiology to indicate group selection.[24] It treats culture as a separate
evolutionary system that acts in parallel to the usual genetic evolution to transform human traits. It is believed
that this approach of combining genetic influence with cultural influence over several generations is not
present in the other hypotheses such as reciprocal altruism and kin selection, making gene-culture evolution
one of the strongest realistic hypotheses for group selection. Fehr provides evidence of group selection
taking place in humans presently with experimentation through logic games such as prisoner’s dilemma, the
type of thinking that humans have developed many generations ago.[25]
Gene-culture coevolution, or cumulative cultural evolution, allows humans to culturally evolve highly
distinct adaptations to the local pressures and environments much quicker than with genetic evolution alone.
Robert Boyd and Peter J. Richerson, two strong proponents of cultural evolution, postulate that the act of
social learning, or learning in a group as done in group selection, allows human populations to accrue
information over many generations.[26] This leads to the cultural evolution of highly adaptive behaviors and
technology alongside genetic evolution. Specifically, they believe that the ability to collaborate with each
other evolved during the Middle Pleistocene, a million years ago, in response to a rapidly-changing climate.
[26]
Herbert Gintis approaches cultural evolution of group selection in a much more statistical approach to
prove that societies that promote pro-social norms, as in group selection, have higher survival rates than
societies that do not.[27] He does so by developing a multilevel gene-culture coevolutionary model that
explains the process whereby altruistic social norms will hinder socially harmful and fitness reducing norms
and consequently will be internalized. In his equations, he differentiates between a genetic group selection
model that is sensitive to group size and migration rates versus his own model that is much less affected by
these constraints and therefore more accurate.[28]
[edit] Group selection due to differing ESSs

The problem with group selection is that for a whole group to get a single trait, it must spread through
the whole group first by regular evolution. But, as J. L. Mackie suggested, when there are many different
groups, each with a different Evolutionarily Stable Strategy (ESS), there is selection between the different
ESSs, since some are worse than others.[29] For example, a group where altruism arose would outcompete
a group where every creature acted in its own interest.
[edit] See also
• Eva Jablonka
• Group Selection, a 1971 book, by G. C. Williams, arguing against group selection
[edit] References
• Sober, Elliott and Wilson, David Sloan (1998). Unto Others: The Evolution and Psychology of
Unselfish Behavior. Harvard University Press.
1. ^ Wynne-Edwards, V.C. (1962). Animal Dispersion in Relation to Social Behaviour .
Edinburgh: Oliver & Boyd.
2. ^ Wynne-Edwards, V. C. (1986) Evolution Through Group Selection, Blackwell. ISBN 0-632-
01541-1
3. ^ Williams, G.C. (1972) Adaptation and Natural Selection: A Critique of Some Current
Evolutionary Thought. Princeton University Press.ISBN 0-691-02357-3
4. ^ Maynard Smith, J. (1964). "Group selection and kin selection". Nature 201: 1145–1147.
doi:10.1038/2011145a0.
5. ^ Koeslag, J.H. (1997). Sex, the prisoner's dilemma game, and the evolutionary inevitability
of cooperation. J. theor. Biol. 189, 53--61
6. ^ a b Koeslag, J.H. (2003). Evolution of cooperation: cooperation defeats defection in the
cornfield model. J. theor. Biol. 224, 399-410
7. ^ Wade, M. J. (1977). "An experimental study of group selection". Evolution 31 (1): 134–153.
8. ^ Goodnight, C. J. and L. Stevens. 1997. Experimental studies of group selection: What do
they tell us about group selection in nature. American Naturalist 150:S59–S79.
9. ^ a b Rauch, E. M., Sayama, H., & Bar-Yam, Y. (2003). Dynamics and genealogy of strains in
spatially extended host-pathogen models. Journal of Theoretical Biology, 221, 655–664 [1].
10.^ Werfel, J., & Bar-Yam, Y. (2004). The evolution of reproductive restraint through social
communication. Proceedings of the National Academy Of Sciences Of The United States Of
America, 101, 11019–11020.
11.^ a b Wilson, E.O. 1975. Sociobiology: The New Synthesis Belknap Press, ISBN 0-674-
81621-8.
12.^ link Wilson, D.S. & Sober, E. 1994. Reintroducing group selection to the human behavioral
sciences. Behavioral and Brain Sciences 17 (4): 585–654.
13.^ a b Wilson, D. S., & Wilson, E. O. (2008). Evolution "for the good of the group". [Article].
American Scientist, 96(5), 380-389.
14.^ a b c O'Gorman, R., Wilson, D. S., & Sheldon, K. M. (2008). For the good of the group?
Exploring group-level evolutionary adaptations using multilevel selection theory. [Article]. Group
Dynamics-Theory Research and Practice, 12(1), 17-26. doi: 10.1037/1089-2699.12.1.17
15.^ Muir, W. M. (2009). Genetic selection and behaviour. [Meeting Abstract]. Canadian Journal
of Animal Science, 89(1), 182-182.
16.^ Boyd, R., & Richerson, P. J. (2009). Culture and the evolution of human cooperation.
17.^ See the chapter God's utility function in Dawkins, Richard (1995). River Out of Eden. New
York: Basic Books. ISBN 0-465-06990-8.
18.^ link Dawkins, R. (1994). Burying the Vehicle. Commentary on Wilson & Sober: Group
Selection. Behavioural and Brain Sciences. 17 (4): 616–617.
19.^ link Dennett, D.C. (1994). E Pluribus Unum? Commentary on Wilson & Sober: Group
Selection. Behavioural and Brain Sciences. 17 (4): 617–618.
20.^ Wilson, E. O. (2005). Kin Selection as the Key to Altruism: its Rise and Fall. "Social
Research" 72 (1): 159–166.
21.^ Trivers, R. (1976) Science 191(4224), 250-263
22.^ Hamilton, W.D. (1964). "The evolution of social behavior". Journal of Theoretical Biology 1:
295–311.
23.^ linkWest, S.A., Griffin, A.S. & Gardner, A. (2007) Social semantics: altruism, cooperation,
mutualism, strong reciprocity and group selection Journal of Evolutionary Biology 20:415-432.
24.^ Mesoudi, A., & Danielson, P.(2008). Ethics, evolution and culture. [Review]. Theory in
Biosciences, 127(3), 229-240. doi: 10.1007/s12064-008-0027-y
25.^ Fehr, E., & Fischbacher, U. (2003). The nature of human altruism. [Review]. Nature,
425(6960), 785-791. doi: 10.1038/nature02043
26.^ a b Boyd, R., & Richerson, P. J. (2009). Culture and the evolution of human cooperation.
27.^ Gintis, H. (2003). "The hitchhiker's guide to altruism: Gene-culture coevolution, and the
internalization of norms". Journal of Theoretical Biology 220 (4): 407–418. doi:10.1006/jtbi.2003.3104.
PMID 12623279.
28.^ Gintis, H. (2003). The hitchhiker's guide to altruism: Gene-culture coevolution, and the
internalization of norms. Journal of Theoretical Biology, 220(4), 407-418. doi: 10.1006/jtbi.2003.3104
29.^ The selfish Gene (Richard Dawkins)

• Bergstrom, T.C. (2002). Evolution of Social Behavior: Individual and Group Selection,
Journal of Economic Perspectives, 16, 67-88. Full text
• Bijma, P.; Muir, W.M.; Van Arendonk, J.A.M. (2007). "Multilevel Selection 1: Quantitative
Genetics of Inheritance and Response to Selection". Genetics 175 (1): 277–288.
doi:10.1534/genetics.106.062711. PMID 17110494.
• Bijma, P.; Muir, W.M.; Ellen, E. D.; Wolf, Jason B.; Van Arendonk, J.A.M. (2007). "Multilevel
Selection 2: Estimating the Genetic Parameters Determining Inheritance and Response to
Selection". Genetics 175 (1): 289–299. doi:10.1534/genetics.106.062729. PMID 17110493.
• Boyd, R. & Richerson, P.J. (2002). Group Beneficial Norms Spread Rapidly in a Structured
Population. Journal of Theoretical Biology, 215, 287–296. Full text
• West, S.A.; Griffin, A.S.; Gardner, A. (2008). "Social semantics: how useful has group
selection been?". Journal of Evolutionary Biology 21: 374–385.
http://www3.interscience.wiley.com/cgi-bin/fulltext/119412422/PDFSTART.
• Soltis, J., Boyd, R. & Richerson, P.J.(1995). Can Group-functional Behaviors Evolve by
Cultural Group Selection? An Empirical Test. Current Anthropology, 63, 473–494. Full text
• Wilson, D. S. (1987). "Altruism in Mendelian populations derived from sibling groups: The
haystack model revisited". Evolution 41 (5): 1059–1070. http://www.jstor.org/pss/2409191.
• Wilson, D.S. (2006). Human groups as adaptive units: toward a permanent consensus. In P.
Carruthers, S. Laurence & S. Stich (Eds.), The Innate Mind: Culture and Cognition. Oxford: Oxford
University Press. Full text

• The Controversy of the Group Selection Theory - a review from the "Science Creative
Quarterly" (a blog)
• Link to publications by D.S. Wilson
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W000
Endosymbiont

An endosymbiont is any organism that lives within the body or cells of another organism, i.e. forming
an endosymbiosis (Greek: ἔνδον endon "within", σύν syn "together" and βίωσις biosis "living"). Examples are
nitrogen-fixing bacteria (called rhizobia) which live in root nodules on legume roots, single-celled algae inside
reef-building corals, and bacterial endosymbionts that provide essential nutrients to about 10%–15% of
insects. Many instances of endosymbiosis are obligate- that is, either the endosymbiont or the host cannot
survive without the other, such as the gutless marine worms of the genus Riftia, which get nutrition from their
endosymbiotic bacteria. The most common examples of obligate endosymbiosis are mitochondria and
chloroplasts. Some human parasites, e.g. : Wucherichia bancrofti and Mansonella perstans thrive in their
hosts because of an obligate endosymbiosis with Wolbachi spp.. They can both be eliminated from their host
by treatments that target this bacterium. However, not all endosymbioses are obligate. Also, some
endosymbioses can be harmful to either of the organisms involved.
It is generally agreed that certain organelles of the eukaryotic cell, especially mitochondria and
plastids such as chloroplasts, originated as bacterial endosymbionts. This theory is called the endosymbiotic
theory, and was first articulated by the Russian botanist Konstantin Mereschkowski in 1905.[1]
Contents
[hide]
• 1 Endosymbiosis theory and mitochondria and chloroplasts
• 2 Bacterial endosymbionts in marine invertebrates
• 3 Symbiodinium dinoflagellate endosymbionts in marine
metazoa and protists[4]
• 4 Endosymbionts in protists
• 5 Bacterial endosymbionts in insects
• 6 Viral endosymbionts and endogenous retrovirus
• 7 See also
• 8 Notes
• 9 References and external links
• 9.1 Obligate bacterial endosymbiosis in marine
oligochaetes
• 9.2 Bacterial endosymbionts in echinoderms
• 9.3 Obligate bacterial endosymbionts in insects
[edit] Endosymbiosis theory and mitochondria and chloroplasts

Main article: Endosymbiotic theory
The endosymbiosis theory attempts to explain the origins of organelles such as mitochondria and
chloroplasts in eukaryotic cells. The theory proposes that chloroplasts and mitochondria evolved from certain
types of bacteria that prokaryotic cells engulfed through endophagocytosis. These cells and the bacteria
trapped inside them entered a symbiotic relationship, a close association between different types of
organisms over an extended time. However, more specifically, the relationship was endosymbiotic, meaning
that one of the organisms (the bacteria) lived within the other (the prokaryotic cells).
According to endosymbiosis theory, an anaerobic cell probably ingested an aerobic bacterium but
failed to digest it. The aerobic bacterium flourished within the cell because the cell's cytoplasm was abundant
in half-digested food molecules. The bacterium digested these molecules with oxygen and gained great
amounts of energy. Because the bacterium had so much energy, it probably leaked some of it as Adenosine
triphosphate into the cell's cytoplasm. This benefited the anaerobic cell because it enabled it to digest food
aerobically. Eventually, the aerobic bacterium could no longer live independently from the cell, and it
therefore became a mitochondrion. The origin of the chloroplast is very similar to that of the mitochondrion. A
cell must have captured a photosynthetic cyanobacterium and failed to digest it. The cyanobacterium thrived
in the cell and eventually evolved into the first chloroplast. Other eukaryotic organelles may have also
evolved through endosymbiosis; it has been proposed that cilia, flagella, centrioles, and microtubules may
have originated from a symbiosis between a Spirochaete bacterium and an early eukaryotic cell, but this is
not widely accepted among biologists.
There are several examples of evidence that support endosymbiosis theory.[2] Mitochondria and
chloroplasts contain their own small supply of DNA, which may be remnants of the genome the organelles
had when they were independent aerobic bacteria. The single most convincing evidence of the descent of
organelles from bacteria is the position of mitochondria and plastid DNA sequences in phylogenetic trees of
bacteria. Mitochondria have sequences that clearly indicate origin from a group of bacteria called the alpha-
Proteobacteria. Plastids have DNA sequences that indicate origin from the cyanobacteria (blue-green algae).
In addition, there are organisms alive today, called living intermediates, that are in a similar endosymbiotic
condition to the prokaryotic cells and the aerobic bacteria. Living intermediates show that the evolution
proposed by the endosymbiont theory is possible. For example, the giant amoeba Pelomyxa lacks
mitochondria but has aerobic bacteria that carry out a similar role. A variety of corals, clams, snails, and one
species of Paramecium permanently host algae in their cells. Many of the insect endosymbionts have been
shown to have ancient associations with their hosts, involving strictly vertical inheritance. In addition, these
insect symbionts have similar patterns of genome evolution to those found in true organelles: genome
reduction, rapid rates of gene evolution, and bias in nucleotide base composition favoring adenine and
thymine, at the expense of guanine and cytosine.
Further evidence of endosymbiosis are the prokaryotic ribosomes found within chloroplasts and
mitochondria as well as the double-membrane enclosing them. It used to be widely assumed that the inner
membrane is the original membrane of the once independent prokaryote, while the outer one is the food
vacuole (phagosomal membrane) it was enclosed in initially. However, this view neglects the fact that i) both
modern cyanobacteria and alpha-proteobacteria are Gram negative bacteria, which are surrounded by
double membranes; ii) the outer membranes of the endosymbiotic organelles (chloroplasts and mitochondria)
are very similar to those of these bacteria in their lipid and protein compositions.[3] Accumulating biochemical
data strongly suggest that the double membrane enclosing chloroplasts and mitochondria derived from those
of the ancestral bacteria, and the phagosomal membrane disappeared during organelle evolution. Triple or
quadruple membranes are found among certain algae, probably resulting from repeated endosymbiosis
(although little else was retained of the engulfed cell).
These modern organisms with endosymbiotic relationships with aerobic bacteria have verified the
endosymbiotic theory, which explains the origin of mitochondria and chloroplasts from bacteria. Researchers
in molecular and evolutionary biology no longer question this theory, although some of the details, such as
the mechanisms for loss of genes from organelles to host nuclear genomes, are still being worked out.
[edit] Bacterial endosymbionts in marine invertebrates
Extracellular endosymbionts are also represented in all four extant classes of Echinodermata
(Crinoidea, Ophiuroidea, Echinoidea, and Holothuroidea). Little is known of the nature of the association
(mode of infection, transmission, metabolic requirements, etc.) but phylogenetic analysis indicates that these
symbionts belong to the alpha group of the class Proteobacteria, relating them to Rhizobium and
Thiobacillus. Other studies indicate that these subcuticular bacteria may be both abundant within their hosts
and widely distributed among the Echinoderms in general.
Some marine oligochaeta (e.g. Olavius or Inanidrillus) have obligate extracellular endosymbionts that
fill the entire body of their host. These marine worms are nutritionally dependent on their symbiotic
chemoautotrophic bacteria lacking any digestive or excretory system (no gut, mouth or nephridia).
[edit] Symbiodinium dinoflagellate endosymbionts in marine metazoa

and protists[4]
Dinoflagellate endosymbionts of the genus Symbiodinium, commonly known as zooxanthellae, are
found in corals, mollusks (esp. giant clams, the Tridacna), sponges, and foraminifera. These endosymbionts
drive the amazing formation of coral reefs by capturing sunlight and providing their hosts with energy for
carbonate deposition.
Previously thought to be a single species, molecular phylogenetic evidence over the past couple
decades has shown there to be great diversity in Symbiodinium. In some cases there is specificity between
host and Symbiodinium clade. More often, however, there is an ecological distribution of Symbiodinium, the
symbionts switching between hosts with apparent ease. When reefs become environmentally stressed, this
distribution of symbionts is related to the observed pattern of coral bleaching and recovery. Thus the
distribution of Symbiodinium on coral reefs and its role in coral bleaching presents one of the most complex
and interesting current problems in reef ecology.
[edit] Endosymbionts in protists

Mixotricha paradoxa is a protozoan that lacks mitochondria, however, spherical bacteria live inside
the cell and serve the function of the mitochondria. Mixotricha also has three other species of symbionts that
live on the surface of the cell.
Paramecium bursaria, a species of ciliate, has a mutualistic symbiotic relationship with green alga
called Zoochlorella. The algae live inside the cell, in the cytoplasm.
[edit] Bacterial endosymbionts in insects

Scientists classify insect endosymbionts in two broad categories, 'Primary' and 'Secondary'. Primary
endosymbionts (sometimes referred to as P-endosymbionts) have been associated with their insect hosts for
many millions of years (from 10 to several hundred million years in some cases), they form obligate
associations (see below), and display cospeciation with their insect hosts. Secondary endosymbionts exhibit
a more recently developed association, are sometimes horizontally transferred between hosts, live in the
hemolymph of the insects (not specialized bacteriocytes, see below), and are not obligate.
Among primary endosymbionts of insects, the best studied are the pea aphid (Acyrthosiphon pisum)
and its endosymbiont Buchnera sp. APS,[5] the tsetse fly Glossina morsitans morsitans and its endosymbiont
Wigglesworthia glossinidia brevipalpis and the endosymbiotic protists in lower termites. As with
endosymbiosis in other insects, the symbiosis is obligate in that neither the bacteria nor the insect is viable
without the other. Scientists have been unable to cultivate the bacteria in lab conditions outside of the insect.
With special nutritionally-enhanced diets, the insects can survive, but are unhealthy, and at best survive only
a few generations.
In some insect groups, these endosymbionts live in specialized insect cells called bacteriocytes (also
called mycetocytes), and are maternally-transmitted, i.e. the mother transmits her endosymbionts to her
offspring. In some cases, the bacteria are transmitted in the egg, as in Buchnera; in others like
Wigglesworthia, they are transmitted via milk to the developing insect embryo. In termites, the
endosymbionts reside within the hindguts and are transmitted through trophallaxis among colony members.
The primary endosymbionts are thought to help the host either by providing nutrients that the host
cannot obtain itself, or by metabolizing insect waste products into safer forms. For example, the putative
primary role of Buchnera is to synthesize essential amino acids that the aphid cannot acquire from its natural
diet of plant sap. Similarly, the primary role of Wigglesworthia is probably to synthesize vitamins that the
tsetse fly does not get from the blood that it eats. In lower termites, the endosymbiotic protists play a major
role in the digestion of lignocellulosic materials which constitutes a bulk of the termites' diet.
Bacteria benefit from the reduced exposure to predators and competition from other bacterial
species, the ample supply of nutrients and relative environmental stability inside the host.
Genome sequencing reveals that obligate bacterial endosymbionts of insects have among the
smallest of known bacterial genomes and have lost many genes that are commonly found in closely related
bacteria. Several theories have been put forth to explain the loss of genes. Presumably some of these genes
are not needed in the environment of the host insect cell. A complementary theory suggests that the
relatively small numbers of bacteria inside each insect decrease the efficiency of natural selection in 'purging'
deleterious mutations and small mutations from the population, resulting in a loss of genes over many
millions of years. Research in which a parallel phylogeny of bacteria and insects was inferred supports the
belief that the primary endosymbionts are transferred only vertically (i.e. from the mother), and not
horizontally (i.e. by escaping the host and entering a new host).
Attacking obligate bacterial endosymbionts may present a way to control their insect hosts, many of
which are pests or carriers of human disease. For example aphids are crop pests and the tsetse fly carries
the organism Trypanosoma brucei that causes African sleeping sickness. Other motivations for their study is
to understand symbiosis, and to understand how bacteria with severely depleted genomes are able to
survive, thus improving our knowledge of genetics and molecular biology.
Less is known about secondary endosymbionts. The pea aphid (Acyrthosiphon pisum) is known to
contain at least three secondary endosymbionts, Hamiltonella defensa, Regiella insecticola, and Serratia
symbiotica. H. defensa aids in defending the insect from parasitoids. Sodalis glossinidius is a secondary
endosymbiont tsetse flies that lives inter- and intracellularly in various host tissues, including the midgut and
hemolymph. Phylogenetic studies have not indicated a correlation between evolution of Sodalis and tsetse.
[6] Unlike tsetse's P-symbiont Wigglesworthia, though, Sodalis has been cultured in vitro.[7]
[edit] Viral endosymbionts and endogenous retrovirus

Main article: Endogenous retrovirus
During pregnancy in viviparous mammals, endogenous retrovirii (ERVs) are activated and produced
in high quantities during the implantation of the embryo. On one hand they act as immunodepressors, and
protect the embryo from the immune system of the mother and on the other hand viral fusion proteins cause
the formation of the placental syncytium in order to limit the exchange of migratory cells between the
developing embryo and the body of the mother, where an epithelium won't do because certain blood cells are
specialized to be able to insert themselves between adjacent epithelial cells. The ERV is a virus similar to
HIV (the virus causing AIDS in humans). The immunodepressive action was the initial normal behavior of the
virus, similar to HIV. The fusion proteins was a way to spread the infection to other cells by simply merging
them with the infected one (similar to HIV). It is believed that the ancestors of modern vivipary mammals
evolved after an accidental infection of an ancestor with this virus, that permitted the fetus to survive the
immune system of the mother.[8]
The human genome project found several thousand ERVs, which are organized into 24 families.[9]
[edit] See also

• Protobiont
• Endophyte
[edit] Notes
1. ^ Mereschkowsky C (1905). "Über Natur und Ursprung der Chromatophoren im
Pflanzenreiche". Biol Centralbl 25: 593–604.
2. ^ Tree of Life Eukaryotes
3. ^ Inoue, K (2007). "The chloroplast outer envelope membrane: the edge of light and
excitement". Journal of Integrative Plant Biology 49: 1100–1111. doi:10.1111/j.1672-
9072.2007.00543.x.
4. ^ Baker AC (November 2003). "FLEXIBILITY AND SPECIFICITY IN CORAL-ALGAL
SYMBIOSIS: Diversity, Ecology, and Biogeography of Symbiodinium". Annual Review of Ecology,
Evolution, and Systematics 34: 661–89. doi:10.1146/annurev.ecolsys.34.011802.132417.
http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.ecolsys.34.011802.132417.
5. ^ Douglas, A E (1998). "Nutritional interactions in insect-microbial symbioses: Aphids and
their symbiotic bacteria Buchnera". Annual Review of Entomology 43: 17–38.
doi:10.1146/annurev.ento.43.1.17. ISSN 00664170. PMID 15012383.
6. ^ Aksoy, S., Pourhosseini, A. & Chow, A. 1995. Mycetome endosymbionts of tsetse flies
constitute a distinct lineage related to Enterobacteriaceae. Insect Mol Biol. 4, 15-22.
7. ^ Welburn, S.C., Maudlin, I. & Ellis, D.S. 1987. In vitro cultivation of rickettsia-like-organisms
from Glossina spp. Ann. Trop. Med. Parasitol. 81, 331-335.
8. ^ The Viruses That Make Us: A Role For Endogenous Retrovirus In The Evolution Of
Placental Species (by Luis P. Villarreal)
9. ^ Villarreal LP (October 2001). "Persisting Viruses Could Play Role in Driving Host
Evolution". ASM News (American Society for Microbiology).
http://newsarchive.asm.org/oct01/feature1.asp.
[edit] References and external links

• SmartyMap List Comparing Mitochondria and Chloroplasts
[edit] Obligate bacterial endosymbiosis in marine oligochaetes

• Dubilier N, Mülders C, Ferdelman T, et al (May 2001). "Endosymbiotic sulphate-reducing and
sulphide-oxidizing bacteria in an oligochaete worm". Nature 411 (6835): 298–302.
doi:10.1038/35077067. PMID 11357130.
[edit] Bacterial endosymbionts in echinoderms
• Burnett WJ, McKenzie JD (1 May 1997). "Subcuticular bacteria from the brittle star Ophiactis
balli (Echinodermata: Ophiuroidea) represent a new lineage of extracellular marine symbionts in the
alpha subdivision of the class Proteobacteria". Appl. Environ. Microbiol. 63 (5): 1721–4.
PMID 9143108. PMC 168468. http://aem.asm.org/cgi/pmidlookup?view=long&pmid=9143108.
[edit] Obligate bacterial endosymbionts in insects

• Wernegreen JJ (2004). "Primer – Endosymbiosis: Lessons in Conflict Resolution". PLoS Biol
2 (3): e68. doi:10.1371/journal.pbio.0020068. PMID 15024418. PMC 368163.
http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020068.
• A general review of bacterial endosymbionts in insects. P. Baumann, N. A. Moran and L.
Baumann, Bacteriocyte-associated endosymbionts of insects in M. Dworkin, ed., The prokaryotes,
Springer, New York, 2000. http://link.springer.de/link/service/books/10125/
• Wernegreen JJ (November 2002). "Genome evolution in bacterial endosymbionts of insects".
Nat. Rev. Genet. 3 (11): 850–61. doi:10.1038/nrg931. PMID 12415315.
• Douglas AE (January 1998). "Nutritional interactions in insect-microbial symbioses: Aphids
and Their Symbiotic Bacteria Buchnera". Annual Reviews of Entomology 43: 17–37.
doi:10.1146/annurev.ento.43.1.17. PMID 15012383.
http://arjournals.annualreviews.org/doi/full/10.1146/annurev.ento.43.1.17.
• Aksoy S, Maudlin I, Dale C, Robinson AS, O'Neill SL (January 2001). "Prospects for control
of African trypanosomiasis by tsetse vector manipulation". Trends Parasitol. 17 (1): 29–35.
doi:10.1016/S1471-4922(00)01850-X. PMID 11137738.
http://linkinghub.elsevier.com/retrieve/pii/S1471-4922(00)01850-X.
• Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (September 2000). "Genome
sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS". Nature 407 (6800):
81–6. doi:10.1038/35024074. PMID 10993077.
• Moran NA (April 1996). "Accelerated evolution and Muller's rachet in endosymbiotic
bacteria". Proc. Natl. Acad. Sci. U.S.A. 93 (7): 2873–8. doi:10.1073/pnas.93.7.2873. PMID 8610134.
Retrieved from "http://en.wikipedia.org/wiki/Endosymbiont"
Categories: Symbiosis | Microbial population biology | Microbiology | Environmental microbiology

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Multilineal evolution

This article does not cite any references or sources.
Multilineal evolution is a 20th century social theory about the evolution of societies and cultures. It is
composed of many competing theories by various sociologists and anthropologists. This theory has replaced
the older 19th century set of theories of unilineal evolution.
When critique of classical social evolutionism became widely accepted, modern anthropological and
sociological approaches have changed to reflect their responses to the critique of their predecessor. Modern
theories are careful to avoid unsourced, ethnocentric speculation, comparisons, or value judgements; more
or less regarding individual societies as existing within their own historical contexts. These conditions
provided the context for new theories such as cultural relativism and multilineal evolution.
By the 1940s cultural anthropologists such as Leslie White and Julian Steward sought to revive an
evolutionary model on a more scientific basis, and succeeded in establishing an approach known as the
neoevolutionism. White rejected the opposition between "primitive" and "modern" societies but did argue that
societies could be distinguished based on the amount of energy they harnessed, and that increased energy
allowed for greater social differentiation. Steward on the other hand rejected the 19th century notion of
progress, and instead called attention to the Darwinian notion of "adaptation,", arguing that all societies had
to adapt to their environment in some way.
The anthropologists Marshall Sahlins and Elman Service wrote a book, Evolution and Culture, in
which they attempted to synthesize White's and Steward's approaches. Other anthropologists, building on or
responding to work by White and Steward, developed theories of cultural ecology and ecological
anthropology. The most prominent examples are Peter Vayda and Roy Rappaport. By the late 1950s,
students of Steward such as Eric Wolf and Sidney Mintz turned away from cultural ecology to Marxism,
World Systems Theory, Dependency theory and Marvin Harris's Cultural materialism.
Today most anthropologists continue to reject 19th century notions of progress and the three original
assumptions of unilineal evolution. Following Steward, they take seriously the relationship between a culture
and its environment in attempts to explain different aspects of a culture. But most modern cultural
anthropologists have adopted a general systems approach, examining cultures as emergent systems and
argue that one must consider the whole social environment, which includes political and economic relations
among cultures. There are still others who continue to reject the entirety of the evolutionary thinking and look
instead at historical contingencies, contacts with other cultures, and the operation of cultural symbol systems.
As a result, the simplistic notion of 'cultural evolution' has grown less useful and given way to an entire series
of more nuanced approaches to the relationship of culture and environment. In the area of development
studies, authors such as Amartya Sen have developed an understanding of 'development' and 'human
flourishing' that also question more simplistic notions of progress, while retaining much of their original
inspiration.
[edit] See also

• Neoevolutionism
• Sociobiology
• Theory of modernisation
• Theory of post-industrial society
Retrieved from "http://en.wikipedia.org/wiki/Multilineal_evolution"
Categories: Sociological theories | Theories of history | Sociocultural evolution

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Experimental evolution

In evolutionary and experimental biology, the field of experimental evolution is concerned with testing
hypotheses and theories of evolution by use of controlled experiments. Evolution may be observed in the
laboratory as populations adapt to new environmental conditions and/or change by such stochastic
processes as random genetic drift. With modern molecular tools, it is possible to pinpoint the mutations that
selection acts upon, what brought about the adaptations, and to find out how exactly these mutations work.
Because of the large number of generations required for adaptation to occur, evolution experiments are
typically carried out with microorganisms such as bacteria, yeast or viruses.[1][2] However, laboratory studies
with rodents have shown that notable adaptations can occur within as few as 10-20 generations (see below)
and experiments with wild guppies have observed adaptations within comparable numbers of generations.[3]
Contents
[hide]
• 1 Evolution experiments throughout human history
• 2 Early experimental evolution
• 3 Modern experimental evolution
• 4 Lenski's long-term evolution experiment with Escherichia
coli
• 5 Garland's long-term experiment with laboratory house
mice
• 6 Other examples
• 7 See also
• 8 References
[edit] Evolution experiments throughout human history
This Chihuahua mix and Great Dane show the wide range of dog breed sizes created using artificial
selection.
Unwittingly, humans have carried out evolution experiments for as long as they have been
domesticating plants and animals. Selective breeding of plants and animals has led to varieties that differ
dramatically from their original wild-type ancestors. Examples are the cabbage varieties, maize, or the large
number of different dog breeds. The power of human breeding to create varieties with extreme differences
from a single species was already recognized by Charles Darwin. In fact, he started out his book The Origin
of Species with a chapter on variation in domestic animals. In this chapter, Darwin discussed in particular the
pigeon. He wrote:
Altogether at least a score of pigeons might be chosen, which if shown to an ornithologist, and
he were told that they were wild birds, would certainly, I think, be ranked by him as well-defined
species. Moreover, I do not believe that any ornithologist would place the English carrier, the
short-faced tumbler, the runt, the barb, pouter, and fantail in the same genus; more especially as
in each of these breeds several truly-inherited sub-breeds, or species as he might have called
them, could be shown him. (...) I am fully convinced that the common opinion of naturalists is
correct, namely, that all have descended from the rock-pigeon ( Columba livia), including under
this term several geographical races or sub-species, which differ from each other in the most
trifling respects.
– Charles Darwin, The Origin of Species

[edit] Early experimental evolution
Drawing of the incubator used by Dallinger in his evolution experiments
One of the first to carry out a controlled evolution experiment was William Dallinger. In the late 19th
century, he cultivated small unicellular organisms in a custom-built incubator over a time period of seven
years (1880-1886). Dallinger slowly increased the temperature of the incubator from an initial 60 °F up to 158
°F. The early cultures had shown clear signs of distress at a temperature of 73 °F, and were certainly not
capable of surviving at 158 °F. The organisms Dallinger had in his incubator at the end of the experiment, on
the other hand, were perfectly fine at 158 °F. However, these organisms would no longer grow at the initial 60
°F. Dallinger concluded that he had found evidence for Darwinian adaptation in his incubator, and that the
organisms had adapted to live in a high-temperature environment. Unfortunately, Dallinger's incubator was
accidentally destroyed in 1886, and Dallinger could not continue this line of research.
[edit] Modern experimental evolution

From the 1880s to 1980, experimental evolution was intermittently practiced by a variety of
evolutionary biologists, including the highly influential Theodosius Dobzhansky. Like other experimental
research in evolutionary biology during this period, much of this work lacked extensive replication and was
carried out only for relatively short periods of evolutionary time.
But by 1980, a variety of evolutionary biologists realized that the key to successful experimentation
lay in extensive parallel replication of evolving lineages as well as a larger number of generations of
selection. One of the first of a new wave of experiments using this strategy was the laboratory "evolutionary
radiation" of Drosophila melanogaster populations that Michael R. Rose started in February, 1980.[4] This
system started with ten populations, five cultured at later ages, and five cultured at early ages. Since then
more than 200 different populations have been created in this laboratory radiation, with selection targeting
multiple characters. Some of these highly differentiated populations have also been selected "backward" or
"in reverse," by returning experimental populations to their ancestral culture regime. Hundreds of people
have worked with these populations over the better part of three decades. Much of this work is summarized
in the papers collected in the book Methuselah Flies, listed below.
[edit] Lenski's long-term evolution experiment with Escherichia coli

On February 15, 1988, Richard Lenski started a long-term evolution experiment with the bacterium
E. coli. The experiment continues to this day, and is by now probably the largest controlled evolution
experiment ever undertaken. Since the inception of the experiment, the bacteria have grown for more than
50,000 generations. Lenski and colleagues regularly publish updates on the status of the experiments. [5]
[edit] Garland's long-term experiment with laboratory house mice

In 1993, Theodore Garland, Jr. and colleagues started a long-term experiment that involves selective
breeding for high voluntary activity levels on running wheels.[6] This experiment also continues to this day (>
50 generations). Mice from the four replicate "High Runner" lines evolved to run 3 times as many running-
wheel revolutions per day as compared with the four unselected control mice groups, mainly by running
faster than the control mice rather than running for more minutes/day.
The HR mice exhibit an elevated maximal aerobic capacity when tested on a motorized treadmill and
a variety of other traits that appear to be adaptations that facilitate high levels of sustained endurance
running (e.g., larger hearts, more symmetrical hindlimb bones). They also exhibit alterations in motivation
and the reward system of the brain. Pharmacological studies point to alterations in dopamine function and
the endocannabinoid system.[7] The High Runner lines have been proposed as a model to study human
attention-deficit hyperactivity disorder (ADHD), and administration of Ritalin reduces their wheel running
approximately to the levels of Control mice. Click here for a mouse wheel running video.
[edit] Other examples
Stickleback fish have both marine and freshwater species, the freshwater species evolving since the
last ice age. Fresh water species can survive colder temperatures. Scientists tested to see if they could
reproduce this evolution of cold-tolerance by keeping marine sticklebacks in cold freshwater. It took the
marine sticklebacks only three generations to evolve to match the 2.5 degree celsius improvement in cold-
tolerance found in wild freshwater sticklebacks. [1]
[edit] See also

• Domestication
• Evolutionary physiology
• Genetics
• Quantitative genetics
• Selective breeding
• Tame Silver Fox
[edit] References
1. ^ Buckling A, Craig Maclean R, Brockhurst MA, Colegrave N (February 2009). "The Beagle in
a bottle". Nature 457 (7231): 824–9. doi:10.1038/nature07892. PMID 19212400.
2. ^ Elena SF, Lenski RE (June 2003). "Evolution experiments with microorganisms: the
dynamics and genetic bases of adaptation". Nat. Rev. Genet. 4 (6): 457–69. doi:10.1038/nrg1088.
PMID 12776215.
3. ^ Reznick, D. N.; F. H. Shaw, F. H. Rodd, and R. G. Shaw (1997). "Evaluation of the rate of
evolution in natural populations of guppies (Poecilia reticulata)". Science 275 (5308): 1934–1937.
doi:10.1126/science.275.5308.1934. PMID 9072971.
4. ^ Rose, M. R. (1984). "Artificial selection on a fitness component in Drosophila
melanogaster". Evolution 38 (3): 516–526. doi:10.2307/2408701. http://jstor.org/stable/2408701.
5. ^ E. coli Long-term Experimental Evolution Project Site, Lenski, R. E.
6. ^ Artificial Selection for Increased Wheel-Running Behavior in House Mice, John G. Swallow,
Patrick A. Carter, and Theodore Garland, Jr, Behavior Genetics, Vol. 28, No. 3, 1998
7. ^ Keeney, B. K.; D. A. Raichlen, T. H. Meek, R. S. Wijeratne, K. M. Middleton, G. L.
Gerdeman, and T. Garland, Jr. (2008). "Differential response to a selective cannabinoid receptor
antagonist (SR141716: rimonabant) in female mice from lines selectively bred for high voluntary
wheel-running behavior". Behavioural Pharmacology 19 (8): 812–820.
doi:10.1097/FBP.0b013e32831c3b6b. PMID 19020416.
http://www.biology.ucr.edu/people/faculty/Garland/Keeney_et_al_2008_rimonabant.pdf.

• Bennett, A. F. (2003). "Experimental evolution and the Krogh Principle: generating biological
novelty for functional and genetic analyses". Physiological and Biochemical Zoology 76 (1): 1–11.
doi:10.1086/374275. PMID 12695982.
http://www.biology.ucr.edu/people/faculty/Garland/Bennett2003.pdf.
• Dallinger, W. H. 1887. The president's address. J. Roy. Microscop. Soc., 185-199.
• Elena, S. F., and R. E. Lenski. 2003. Evolution experiments with microorganisms: the
dynamics and genetic bases of adaptation. Nature Reviews Genetics 4: 457-469.
• Garland, T., Jr. 2003. Selection experiments: an under-utilized tool in biomechanics and
organismal biology. Pages 23-56 in V. L. Bels, J.-P. Gasc, A. Casinos, eds. Vertebrate biomechanics
and evolution. BIOS Scientific Publishers, Oxford, UK. PDF
• Garland, T., Jr., and M. R. Rose, eds. 2009. Experimental evolution: concepts, methods, and
applications of selection experiments. University of California Press, Berkeley, California. PDF of
Table of Contents
• Gibbs, A. G. 1999. Laboratory selection for the comparative physiologist. Journal of
Experimental Biology 202: 2709-2718.
• Lenski, R. E. 2004. Phenotypic and genomic evolution during a 20,000-generation
experiment with the bacterium Escherichia coli. Plant Breeding Reviews 24: 225-265.
• Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C. Tadler. 1991. Long-term experimental
evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. American
Naturalist 138: 1315-1341.
• McKenzie, J. A., and P. Batterham. 1994. The genetic, molecular and phenotypic
consequences of selection for insecticide resistance. Trends in Ecology and Evolution 9: 166-169.
• Reznick, D. N., M. J. Bryant, D. Roff, C. K. Ghalambor, and D. E. Ghalambor. 2004. Effect of
extrinsic mortality on the evolution of senescence in guppies. Nature 431: 1095-1099.
• Rose, M. R., H. B. Passananti, and M. Matos, eds. 2004. Methuselah flies: A case study in
the evolution of aging. World Scientific Publishing, Singapore.
• Swallow, J. G., and T. Garland, Jr. 2005. Selection experiments as a tool in evolutionary and
comparative physiology: insights into complex traits — An introduction to the symposium. Integrative
and Comparative Biology 45: 387-390. PDF
• E. coli Long-term Experimental Evolution Project Site , Lenski lab, Michigan State University
• A movie illustrating the dramatic differences in wheel-running behavior.
• Experimental Evolution Publications by Ted Garland: Artificial Selection for High Voluntary
Wheel-Running Behavior in House Mice — a detailed list of publications.
• Experimental Evolution — a list of laboratories that study experimental evolution.
• Network for Experimental Research on Evolution , University of California.
• New Scientist article on domestication by selection
Retrieved from "http://en.wikipedia.org/wiki/Experimental_evolution"
Categories: Evolutionary biology | Science experiments

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Intelligent design
Concepts
Fine-tuned universe
Theistic realism
Neo-creationism
Intelligent design
movement
Timeline
Discovery Institute
Wedge strategy
Politics
Kitzmiller v. Dover
Campaigns
Reactions
Creationism

v·d·e
Teach the Controversy is the name of a Discovery Institute campaign to promote intelligent design, a
variant of traditional creationism, while attempting to discredit evolution in United States public high school
science courses.[1][2][3][4][5][6] The central claim the Discovery Institute makes with 'Teach the Controversy'
is that fairness and equal time requires educating students with a 'critical analysis of evolution'[7] where "the
full range of scientific views",[8] evolution's "unresolved issues", and the "scientific weaknesses of
evolutionary theory"[9] will be presented and evaluated alongside intelligent design concepts like irreducible
complexity[10] presented as a scientific argument against evolution through oblique references to books by
design proponents listed in the bibliography of the Institute-proposed "Critical Analysis of Evolution" lesson
plans.[11] The intelligent design movement and the Teach the Controversy campaign are directed and
supported largely by the Discovery Institute, a conservative Christian[12][13] think tank based in Seattle,
Washington, USA. The overall goal of the movement is to "defeat [the] materialist world view" represented by
the theory of evolution and replace it with "a science consonant with Christian and theistic convictions."[14]
The scientific community and science education organizations have replied that there is no scientific
controversy regarding the validity of evolution and that the controversy exists solely in terms of religion and
politics.[15][16][17] A federal court, along with the majority of scientific organizations, including the American
Association for the Advancement of Science, say the Institute has manufactured the controversy they want to
teach by promoting a false perception that evolution is "a theory in crisis" due to it being the subject of
purported wide controversy and debate within the scientific community.[15][16][18][19] McGill University
Professor Brian Alters, an expert in the creation-evolution controversy, is quoted in an article published by
the NIH as stating that "99.9 percent of scientists accept evolution"[20] whereas intelligent design has been
rejected by the overwhelming majority of the scientific community.[21][22]
With the December 2005 ruling in Kitzmiller v. Dover Area School District, wherein Judge John E.
Jones III concluded that intelligent design is not science and "cannot uncouple itself from its creationist, and
thus religious, antecedents".[23] The Dover ruling also characterized "teaching the controversy" as part of a
religious ploy.[24] Intelligent design proponents were left with the Teach the Controversy strategy as the most
likely method left to realize the goals stated in the wedge document. Thus, the Teach the Controversy
strategy has become the primary thrust of the Discovery Institute in promoting its aims. Just as intelligent
design is a stalking horse for the campaign against what its proponents claim is a materialist foundation in
science that precludes God, Teach the Controversy has become a stalking horse for intelligent design.
Contents
[hide]
• 1 Origin of phrase
• 2 Overview
• 3 Shift in strategy
• 4 Repercussions
• 5 Political action
• 5.1 Political battles involving the Discovery Institute
• 6 Criticisms
• 6.1 The Discovery Institute
• 6.2 University course
• 7 See also
• 8 References
• 9.1 Audio and video
[edit] Origin of phrase

The term "teach the controversy" originated with Gerald Graff, a professor of English and education
at the University of Illinois at Chicago,[25] as an admonition to teach that established knowledge is not simply
given as a settled matter, but that it is created in a crucible of debate and controversy. To the chagrin of
Graff, who describes himself as a liberal secularist,[25] the idea was later appropriated by Phillip E. Johnson,
Discovery Institute program advisor and father of the ID movement. Discussing the 1999-2000 Kansas State
Board of Education controversy over the teaching of intelligent design in public school classrooms, Johnson
wrote "What educators in Kansas and elsewhere should be doing is to 'teach the controversy'." In his book
Johnson proposed casting the conflicting points of view and agendas as a scholarly controversy. Johnson's
usage differs somewhat from Graff's original concept. While Graff advocated that a comprehensive
understanding of what are considered to be "established" concepts must include teaching the debates and
conflicts by which they were established, Johnson appropriated the phrase to cast doubt upon the very
concept of established knowledge.[26]
The phrase was picked up by other Discovery Institute affiliates Stephen C. Meyer, David K. DeWolf,
and Mark E. DeForrest in their 1999 article, Teaching the Controversy: Darwinism, Design and the Public
School Science Curriculum[27] published by the Foundation for Thought and Ethics. The Foundation for
Thought and Ethics also publishes the controversial pro-intelligent design biology textbook Of Pandas and
People, suggested as an alternative to mainstream science and biology textbooks in the Critical Analysis of
Evolution lesson plans proposed by Teach the Controversy proponents.
[edit] Overview
The campaign was devised by Stephen C. Meyer and Discovery Institute founder and President
Bruce Chapman as a compromise strategy in March 2002. They had come to the realisation that the dispute
over intelligent design's (lack of) scientific standing was complicating their efforts to have evolution
challenged in the science classroom. This strategy was designed to move the focus onto an approach that
stresses open debate and evolution's purported weakness, but does not require students to study intelligent
design. The intention was to create doubt over evolution and avoid the question of whether the intelligent
designer was God, while giving the institute time to strengthen their purported theory of intelligent design.[28]
Another advantage of this strategy was to allay teacher fears of legal action.[29]
The Discovery Institute's strategy has been for the institute itself or groups acting on its behalf to
lobby state and local boards of education, and local, state and federal policymakers to enact policies and/or
laws, often in the form of textbook disclaimers and the language of state science standards, that undermine
or remove evolutionary theory from the public school science classroom by portraying it as "controversial"
and "in crisis;" a portrayal that stands in contrast to the overwhelming consensus of the scientific community
that there is no controversy, that evolution is one of the best supported theories in all of science, and that
whatever controversy does exist is political and religious, not scientific.[17][30] The Teach the Controversy
strategy has benefitted from 'stacking' municipal, county and state school boards with intelligent design
proponents[31] as alluded to in the Discovery Institute's Wedge Strategy.
As the primary organizer and promoter of the Teach the Controversy campaign, the Discovery
Institute has played a central role in nearly all intelligent design cases, often working behind the scenes to
orchestrate, underwrite and support local campaigns and intelligent design groups such as the Intelligent
Design Network.[32] It has provided support ranging from material assistance to federal, state and regionally
elected representatives in the drafting of bills to the provision of support and advice to individual parents
confronting their school boards. DI's goal is to move from battles over standards to curriculum writing and
textbook adoption while undermining the central positions of evolution in biology and methodological
naturalism in science. In order to make their proposals more palatable, the Institute and its supporters claim
to advocate presenting evidence both for and against evolution, thus encouraging students to evaluate the
evidence.
Though Teach the Controversy is presented by its proponents as encouraging academic freedom, it,
along with the Santorum Amendment, is viewed by many academics as a threat to academic freedom[33]
and is rejected by the National Science Teachers Association,[34] and the American Association for the
Advancement of Science.[16] The American Society for Clinical Investigation's Journal of Clinical
Investigation describes the Teach the Controversy strategy and campaign as a "hoax" and that "the
controversy is manufactured."[35]
Along with the objection that there is no scientific controversy to teach, another common objection is
that the Teach the Controversy campaign and intelligent design arise out of a Christian fundamentalist and
evangelistic movement that calls for broad social, academic and political changes.[36] Intelligent design
proponents argue their concepts and motives should be given independent consideration. Those critical of
intelligent design see the two as intertwined and inseparable, citing the foundational documents of the
movement such as the Wedge Document and statements made by intelligent design proponents to their
constituents. The judge in the Kitzmiller v. Dover Area School District trial considered testimony and
evidence from both sides on the question of the motives of intelligent design proponents when he ruled that
"ID cannot uncouple itself from its creationist, and thus religious, antecedents"[37] and "that ID is an
interesting theological argument, but that it is not science."[38]
In the debate surrounding the linking of the motives of intelligent design proponents to their
arguments, following the Kansas evolution hearings the chairman of the Kansas school board, Dr. Steve
Abrams, cited in The New York Times as saying that though he's a creationist who believes that God created
the universe 6,500 years ago, he is able to keep the two separate:
In my personal faith, yes, I am a creationist, ... But that doesn't have anything to do with science.
I can separate them. ... my personal views of Scripture have no room in the science classroom.
[39]
Afterward, Lawrence Krauss, a Case Western Reserve University physicist and astronomer, in a
New York Times essay said:
A key concern should not be whether Dr. Abrams's religious views have a place in the
classroom, but rather how someone whose religious views require a denial of essentially all
modern scientific knowledge can be chairman of a state school board. ... As we work to improve
the abysmal state of science education in our public schools, we will continue to do battle with
those who feel that knowledge is a threat to religious faith ... we should remember that the battle
is not against faith, but against ignorance.[40]
[edit] Shift in strategy

The roots of the intelligent design movement's strategy are found in the past attempts of creationists
to force religious views into public school science classes. The most recent of these was creation science,
which sought to provide a scientific veneer for the biblical account of Genesis. The characteristics of the
intelligent design movement are a direct response to the tactical and legal failings of earlier creationist
movements. Design proponent's strategies represent a natural evolution of the "creation science" movement,
proceeding still further in the direction of claiming the mantle of science while denying their religious
intentions in argument.
For example, the judge in the 2005 Kitzmiller v. Dover Area School District trial noted in his ruling
that evidence presented comparing the drafts of the intelligent design textbook Of Pandas and People before
and after the 1987 Edwards v. Aguillard ruling showed that the definition given in the book for creation
science in pre Edwards drafts is identical to the definition of intelligent design in post Edwards drafts;
cognates of the word creation - creationism and creationist, which appeared approximately 150 times were
deliberately and systematically replaced with the phrase 'intelligent design'; and the changes occurred shortly
after the Supreme Court ruled in Edwards that creation science is religious and cannot be taught in public
school science classes.[41]
A rudimentary form of the teach the controversy strategy had emerged first among creation scientists
following the Supreme Court's Edwards v. Aguillard decision. The Institute for Creation Research (ICR)
prepared an evaluation of what the movement should try next, suggesting "school boards and teachers
should be strongly encouraged at least to stress the scientific evidences and arguments against evolution in
their classes . . . even if they don't wish to recognize these as evidences and arguments for creationism."
Glenn Branch of the National Center for Science Education says this comment shows that the teach the
controversy strategy was "pioneered in the wake of Edwards v. Aguillard."[42]
Prior to the September 2005 start of the Kitzmiller v. Dover Area School District trial, the "Dover trial,"
prominent intelligent design proponents gradually shifted to a "Teach the Controversy" strategy. They had
realised that mandates requiring the teaching of intelligent design were unlikely to survive challenges based
on the Establishment Clause of the First Amendment, and that an unfavorable ruling had the effect of legally
ruling intelligent design a form of religious creationism.
Thus, the Discovery Institute repositioned itself. It publicly abandoned advocating for any policies or
laws that required the teaching of intelligent design in favor of a Teach the Controversy strategy.[43] Institute
Fellows reasoned that once the "fact" that a controversy indeed exists had been established in the public's
mind, then the reintroduction of intelligent design into public school criteria would be much less controversial
later.[44]
The best illustration of this shift in strategy is comparing the Discovery Institute's 1999 guidebook
Intelligent Design in Public School Science Curricula which concludes "school boards have the authority to
permit, and even encourage, teaching about design theory as an alternative to Darwinian evolution"[45] to
2006 statements by Phillip E. Johnson, that his intent was never to use public school education as the forum
for his ideas and that he hoped to ignite and perpetuate a debate in universities and among the higher
echelon of scientific thinkers.[46]
With the December 2005 ruling in Kitzmiller v. Dover Area School District, wherein Judge John E.
Jones III concluded that intelligent design is not science, intelligent design proponents were left with the
Teach the Controversy strategy as the most likely method left to realize the goals stated in the wedge
document. Thus, the Teach the Controversy strategy has become the primary thrust of the Discovery Institute
in promoting its aims. Just as intelligent design is a stalking horse for the campaign against what its
proponents claim is a materialist foundation in science that precludes God, Teach the Controversy has
become a stalking horse for intelligent design. But the Dover ruling also characterized "teaching the
controversy" as part of a religious ploy.[24]
By May 2006 the Discovery Institute, in a carefully calculated move,[2] sought to broaden the
faltering "teach the controversy" strategy to include examples of other supposed legitimate scientific
controversies. In Ohio and Michigan where school boards are again reviewing science curricula standards
the Discovery Institute and its allies proposed lesson plans that included global warming, cloning and stem
cell research as further examples of controversies that are akin to the alleged scientific controversy over
evolution. All four topics are widely accepted by the majority of the scientific community as legitimate
science, and all four are areas where US political conservatives have been known to be critical of the
scientific consensus. Members of the scientific community have responded to this tactic by pointing out that
like evolution whatever controversy may exist over cloning and stem cell research has been largely social
and political, while dissident viewpoints over global warming are often viewed as pseudoscience.[47][48]
Richard B. Hoppe, holder of a Ph.D. in Experimental Psychology from the University of Minnesota, described
the tactic in the following way:
Like the attacks on evolution, the attack on climate science is driven by the sectarian conviction
that 'materialistic' science is untrustworthy and must be replaced. As with intelligent design
creationism, science-deniers' so-called evidence takes the form of claims for the insufficiency of
current scientific explanations rather than concrete, testable alternative hypotheses. As in the
evolution debate, religious extremists use the clever strategy of denigrating the scientific
consensus on causality (global warming is human-caused via pollution) by pretending it
contrasts sharply with an alternative scientific theory that, properly-understood, is really just a
more nuanced view that's not really in opposition (current global warming is part of the earth’s
natural cycle but is being exacerbated by pollution). This exaggerates the intensity of normal
scientific debate in order to suggest there's something wrong with climate science, and then
uses this manufactured controversy to cloak the anti-science view and smuggle it into
classrooms — sectarian religious evangelism masquerading as science.[47]
With the Dover ruling describing "teach the controversy" as part of the same religious ploy as
presenting intelligent design as an alternative to evolution, intelligent design proponents have moved to a
fallback position, emphasizing contrived flaws in evolution and over-emphasizing remaining questions in the
theory what they call the Critical Analysis of Evolution .[49] The Critical Analysis of Evolution strategy is
viewed by Nick Matzke and other intelligent design critics as a means of teaching all the intelligent design
arguments without using the intelligent design label.[50] Critical Analysis of Evolution continues the themes
of the teach the controversy strategy, emphasizing what they say are the "criticisms" of evolutionary theory
and "arguments against evolution," which continues to be portrayed as "a theory in crisis." Early drafts of the
critical analysis of evolution lesson plan referred to the lesson as the "great evolution debate"; one of the
early drafts of the lesson plan had one section titled "Conducting the Macroevolution Debate". In a
subsequent draft, it was changed to "Conducting the Critical Analysis Activity". The wording for the two
sections is nearly identical, with just "debate" changed to "critical analysis activity" wherever it appeared, in
the manner of how intelligent design proponents simply replaced "creation" with "intelligent design" in Of
Pandas and People to repackage a creation science textbook into an intelligent design textbook.
[edit] Repercussions
The campaigns of intelligent design proponents seeking curricular challenges have been disruptive,
divisive and expensive for the affected communities. In pursuing the goal of establishing intelligent design at
the expense of evolution in public school science classes, intelligent design groups have threatened and
isolated high school science teachers, school board members and parents who opposed their efforts.[51][52]
[53][54][55][56] The campaigns run by intelligent design groups place teachers in the difficult position of
arguing against their employers while the legal challenges to local school districts are costly, diverting
funding away from education and into court battles. For example, as a result of Dover trial, the Dover Area
School District was forced to pay $1,000,011 in legal fees and damages for pursuing a policy of teaching the
controversy.[57]
Four days after the six-week Dover trial concluded, all eight of the Dover school board members who
were up for reelection were voted out of office. Televangelist Pat Robertson in turn told the citizens of Dover,
"If there is a disaster in your area, don't turn to God. You just rejected him from your city." Robertson said if
they have future problems in Dover, "I recommend they call on Charles Darwin. Maybe he can help
them."[58]
Critics, like Wesley R. Elsberry, say the Discovery Institute has cynically manufactured much of the
political and religious controversy to further its agenda, pointing to statements of prominent proponents like
Johnson:
Whether educational authorities allow the schools to teach about the controversy or not, public
recognition that there is something seriously wrong with Darwinian orthodoxy is going to keep
on growing. While the educators stonewall, our job is to continue building the community of
people who understand the difference between a science that tests its theories against the
evidence, and a pseudoscience that protects its key doctrines by imposing philosophical rules
and erecting legal barriers to freedom of thought.[59]
To the absence of actual scientific controversy over the validity of evolutionary theory, Johnson said:
If the science educators continue to pretend that there is no controversy to teach, perhaps the
television networks and the newspapers will take over the responsibility of informing the public.
[60]
And to the resistance of science educators over portraying evolution as controversial or disputed,
Johnson said:
If the public school educators will not "teach the controversy," our informal network can do the
job for them. In time, the educators will be running to catch up.[61]
Elsberry and others allege that statements like Johnson's are proof that the alleged scientific
controversy intelligent design proponents seek to have taught is a product of the institute's members and
staff. In the Dover trial's ruling the judge wrote that intelligent design proponents had misrepresented the
scientific status of evolution.[62]
According to published reports, the nonprofit Discovery Institute received grants and gifts totaling
$4.1 million for 2003 from 22 foundations. Of these, two-thirds had primarily religious missions.[63] The
institute spends more than $1 million a year for research, polls, lobbying and media pieces that support
intelligent design and their Teach the Controversy campaign[64] and is employing the same Washington,
D.C. public relations firm that promoted the Contract with America.[65]
[edit] Political action

The Discovery Institute aggressively promotes its Teach the Controversy campaign and intelligent
design to the public, education officials and public policymakers. Its efforts are largely aimed at conservative
Christian policymakers, where it is cast as a counterbalance to the liberal influences of "atheistic scientists"
and "Dogmatic Darwinists." As a measure of their success in this effort, on 1 August 2005, during a round-
table interview with reporters from five Texas newspapers, President Bush said that he believes schools
should discuss intelligent design alongside evolution when teaching students about the origin of life. Bush, a
conservative Christian, declined to go into detail on his personal views of the origin of life, but advocated the
Teach the Controversy approach - "I think that part of education is to expose people to different schools of
thought... you're asking me whether or not people ought to be exposed to different ideas, the answer is yes."
Christian conservatives, a substantial part of Bush's voting base, have been central in promoting the Teach
the Controversy campaign.
In some state battles, the ties of Teach the Controversy and intelligent design proponents to the
Discovery Institute's political and social activities have been made public resulting in their efforts being
temporarily thwarted. The Discovery Institute takes the view that all publicity is good and that no defeat is
real. The Institute has shown a willingness to back off, even to not advocate for the inclusion of ID, to ensure
that all science teachers are required to portray evolution as a "theory in crisis." The Institute's strategy is to
move, relentlessly, from standards battles, to curriculum writing, to textbook adoption, and back again doing
whatever it takes to undermine the central position of evolution in biology. Critics of this strategy and the
movement contend that the intelligent design controversy diverts much time, effort and tax money away from
the actual education of children.
[edit] Political battles involving the Discovery Institute
Main article: Intelligent design in politics
• 2000 Congressional briefing: In 2000, the leading ID proponents operating through the
Discovery Institute held a congressional briefing in Washington, D.C., to promote ID to lawmakers.
Sen. Rick Santorum was and continues to be one of ID's most vocal supporters. One result of this
briefing was that Sen. Santorum inserted pro-ID language into the No Child Left Behind bill calling for
students to be taught why evolution "generates so much continuing controversy," an assertion
heavily promoted by the Discovery Institute.
• 2001 Santorum Amendment: As a result of the 2000 Congressional briefing, the Discovery
Institute drafted and lobbied for the Santorum Amendment to the No Child Left Behind education act.
The amendment encouraged the "teach the controversy" approach to evolution education. The
amendment was passed by the U.S. Senate, but was left out of the final version of the Act, and
remains only in highly modified form in the conference report, where it does not carry the weight of
law. The conference report language is commonly touted by the Discovery Institute as model
language for bills and curricula. The Discovery Institute lobbies states, counties, and municipalities,
and offers them legal analysis and Institute-developed curricula and text books they proclaim meet
constitutional criteria established by the courts in previous creationism/evolution First Amendment
cases.
• 2002-2006 Ohio Board of Education: The Discovery Institute proposed a model lesson plan
that featured intelligent design prominently in its curricula. It was adopted in part in October 2002,
with the Board's advising that the science standards do "not mandate the teaching or testing of
intelligent design." This was touted by the Discovery Institute as a significant victory. By February
2006 the Ohio Board of Education voted 11-4 to delete the science standard and correlating lesson
plan adopted in 2002. [6] The board also rejected a competing plan from the institute to request a
legal opinion from the state attorney general on the constitutionality of the science standards.
Intelligent design proponents pledged to force another vote on the issue.
• 2005 Kansas evolution hearings: A series of hearings instigated by the institute held in
Topeka, Kansas May 2005 by the Kansas State Board of Education to review changes how the origin
of life would be taught in the state's public high school science classes. The hearings were boycotted
by the scientific community, and views expressed represented largely those of intelligent design
advocates. The result of the hearings was the adoption of new science standards by the Republican-
dominated board in defiance of the State Board Science Hearing Committee that relied upon the
institute's Critical Analysis of Evolution lesson plan and adopted the institute's Teach the Controversy
approach. In August 2006 conservative Republicans lost their majority on the board in a primary
election. The moderate Republican and Democrats gaining seats vowed to overturn the 2005 school
science standards and adopt those recommended by a State Board Science Hearing Committee that
were rejected by the previous board.
• 2005 Kitzmiller v. Dover Area School District: Eleven parents of students in the school district
of Dover, Pennsylvania, sued the Dover Area School District over a statement that the school board
required to be read aloud in ninth-grade science classes when evolution was taught endorsing
intelligent design as an alternative to evolution. The plaintiffs successfully argued that intelligent
design is a form of creationism, and that the school board policy thus violated the Establishment
Clause of the First Amendment. In December, 2005 United States federal court judge John E. Jones
III ruled that intelligent design is not science and is essentially religious in nature.
[edit] Criticisms
The theory of evolution is accepted by the vast majority of biologists and by the scientific community
in general, in such overwhelming numbers that the theory of evolution is viewed as having scientific
consensus. Over 70 scientific societies, institutions, and other professional groups representing tens of
thousands individual scientists have issued policy statements supporting evolution education and opposing
intelligent design.[66][67] Scientific controversies are minor and concern the details of the mechanisms of
evolution, not the validity of the over-arching theory of evolution. In the absence of an actual professional
controversy between groups of experts on evolution, critics say intelligent design proponents have merely
renamed the conflict that already existed between biologists and creationists, and that the controversy to
which intelligent design proponents refer is political in nature and thus, by definition, outside of the realm of
science and scientific educational curricula. Critics contend that intelligent design proponents ignore this
point by continuing to make the claim of a "scientific controversy."
For example, the National Association of Biology Teachers, in a statement endorsing evolution as
noncontroversial, quoted Theodosius Dobzhansky: "Nothing in biology makes sense except in the light of
evolution" and went on to state that the quote "accurately reflects the central, unifying role of evolution in
biology. The theory of evolution provides a framework that explains both the history of life and the ongoing
adaptation of organisms to environmental challenges and changes." They emphasized that "Scientists have
firmly established evolution as an important natural process" and that "The selection of topics covered in a
biology curriculum should accurately reflect the principles of biological science. Teaching biology in an
effective and scientifically honest manner requires that evolution be taught in a standards-based instructional
framework with effective classroom discussions and laboratory experiences."[68]
Prominent evolutionary biologists such as Richard Dawkins and Jerry Coyne have proposed various
'controversies' that are worth teaching, instead of intelligent design.[69] Dawkins compares teaching
intelligent design in schools to teaching flat earthism: perfectly fine in a history class but not in science. "If
you give the idea that there are two schools of thought within science, one that says the earth is round and
one that says the earth is flat, you are misleading children."[70]
Tufts University Professor of Philosophy Daniel C. Dennett, author of Darwin's Dangerous Idea,
describes how they generate a sense of controversy: "The proponents of intelligent design use an ingenious
ploy that works something like this: First you misuse or misdescribe some scientist's work. Then you get an
angry rebuttal. Then, instead of dealing forthrightly with the charges leveled, you cite the rebuttal as evidence
that there is a 'controversy' to teach."[44] Such a controversy is then self-fulfilling and self-sustaining, though
completely without any legitimate basis in the academic world.
Critics of the Teach the Controversy movement and strategy can also be found outside of the
scientific community. Barry W. Lynn, executive director of Americans United for Separation of Church and
State, described the approach of the movement's proponents as "a disarming subterfuge designed to
undermine solid evidence that all living things share a common ancestry." "The movement is a veneer over a
certain theological message. Every one of these groups is now actively engaged in trying to undercut sound
science education by criticizing evolution," said Lynn. "It is all based on their religious ideology. Even the
people who don't specifically mention religion are hard-pressed with a straight face to say who the intelligent
designer is if it's not God."[71] Bill Maher said of Teach the Controversy "You don't have to teach both sides
of a debate if one side is a load of crap."[72]
[edit] The Discovery Institute

According to critics of the Discovery Institute's efforts through the Teach the Controversy campaign
and the intelligent design movement, the Wedge strategy betrays the Institute's political rather than scientific
and educational purpose. The Discovery Institute and its Center for Science and Culture (CSC) has an
overarching conservative Christian social and political agenda that seeks to redefine both law and science
and how they are conducted, with the stated goal of a religious "renewal" of American culture.
Critics also allege that the Discovery Institute has a long-standing record of misrepresenting
research, law and its own policy and agenda and that of others:
• In announcing the Teach the Controversy strategy in 2002, the Discovery Institute’s Stephen
C. Meyer[73] presented an annotated bibliography of 44 peer-reviewed scientific articles that were
said to raise significant challenges to key tenets of what was referred to as "Darwinian evolution."[74]
In response to this claim the National Center for Science Education, an organization that works in
collaboration with National Academy of Sciences, the National Association of Biology Teachers, and
the National Science Teachers Association that support the teaching of evolution in public schools,
[75] contacted the authors of the papers listed and twenty-six scientists, representing thirty-four of the
papers, responded. None of the authors considered his or her research to provide evidence against
evolution.[76]
• The Discovery Institute, following the policies outlined by Phillip E. Johnson, obfuscates its
agenda. Opposed to the public statements to the contrary made by the Discovery Institute, Johnson
has admitted that the goal of intelligent design movement is to cast creationism as a scientific
concept:
• Our strategy has been to change the subject a bit so that we can get the issue of
intelligent design, which really means the reality of God, before the academic world and
into the schools.[77]
• This isn't really, and never has been a debate about science. It's about religion and
philosophy.[78]
• If we understand our own times, we will know that we should affirm the reality of God by
challenging the domination of materialism and naturalism in the world of the mind. With
the assistance of many friends I have developed a strategy for doing this....We call our
strategy the 'wedge.'[79]
• So the question is: "How to win?" That’s when I began to develop what you now see full-
fledged in the "wedge" strategy: "Stick with the most important thing" —the mechanism
and the building up of information. Get the Bible and the Book of Genesis out of the
debate because you do not want to raise the so-called Bible-science dichotomy. Phrase
the argument in such a way that you can get it heard in the secular academy and in a
way that tends to unify the religious dissenters. That means concentrating on, "Do you
need a Creator to do the creating, or can nature do it on its own?" and refusing to get
sidetracked onto other issues, which people are always trying to do.[80]
– Phillip E. Johnson
• Rob Boston of the Americans United for Separation of Church and State described
Johnson's vision of the Wedge as: "The objective [of the Wedge Strategy] is to convince people that
Darwinism is inherently atheistic, thus shifting the debate from creationism vs. evolution to the
existence of God vs. the non-existence of God. From there people are introduced to 'the truth' of the
Bible and then 'the question of sin' and finally 'introduced to Jesus.'"[81]
• Instead of producing original scientific data to support ID’s claims, the Discovery Institute has
promoted ID politically to the public, education officials and public policymakers through its Teach the
Controversy campaign.
Johnson's statements validate the criticisms leveled by those who allege that the Discovery Institute
and its allied organizations are merely stripping the obvious religious content from their anti-evolution
assertions as a means of avoiding the legal restriction on establishment. They argue that ID is simply an
attempt to put a patina of secularity on top of what is a fundamentally religious belief and agenda.
Given the history of the Discovery Institute as an organization committed to opposing any scientific
theory inconsistent with "the theistic understanding that nature and human beings are created by God",[82]
many scientists regard the movement purely as a ploy to insert creationism into the science curriculum rather
than as a serious attempt to discuss scientific evidence. In the words of Eugenie Scott of the National Center
for Education:
Teach the controversy' is a deliberately ambiguous phrase. It means 'pretend to students that
scientists are arguing over whether evolution took place.' This is not happening. I mean you go
to the scientific journals, you go to universities... and you ask the professors, is there an
argument going on about whether living things had common ancestors? They'll look at you
blankly. This is not a controversy.[83]
Though Teach the Controversy proponents cite the current public policy statements of the Discovery
Institute as belying the criticisms that their strategy is a creationist ploy and decry critics as biased in failing to
recognize that the intelligent design movement's Teach the Controversy strategy as really just a question of
science with no religion involved, is itself belied by Discovery Institute's former published policy statements,
[84] its "Wedge Document", and statements made to its constituency by its leadership, and in particular
Phillip E. Johnson.
Writes Johnson in the foreword to Creation, Evolution, & Modern Science (2000):
The Intelligent Design movement starts with the recognition that "In the beginning was the
Word," and "In the beginning God created." Establishing that point isn't enough, but it is
absolutely essential to the rest of the gospel message. ... The first thing that has to be done is to
get the Bible out of the discussion. ...This is not to say that the biblical issues are unimportant;
the point is rather that the time to address them will be after we have separated materialist
prejudice from scientific fact.[85]
Johnson's words bolster the claims of those critics who cite Johnson's admission that the ultimate
goal of the campaign is getting "the issue of intelligent design, which really means the reality of God, before
the academic world and into the schools."[77]
Amid this political and religious controversy the clear, categorical and oft-repeated view of
established national and international scientific organizations remains that there is no scientific controversy
over teaching evolution in public schools.
[edit] University course

George Mason University Biology Department introduced a 1-credit course on the creation/evolution
controversy, and Emmett Holman, an associate professor of philosophy from the university, found that as
students learn more about biology, they find objections to evolution less convincing. He concluded that
"teaching the controversy" would undermine creationists’ criticisms, and that the scientific community’s
resistance to this approach was bad public relations. Rather than being taught in a mainstream science
course, it would be a separate elective course, probably taught by a scientist but called a course on
"philosophy of science", "history of science", or "politics of science and religion".[86]
Biologist Tom A. Langen argues in a journal letter entitled "What is right with ‘teaching the
controversy’?" that teaching students about this controversy will help them understand the demarcation
between science and other ways of obtaining knowledge about nature.[87] Similar positions have been
expressed by atheists Julian Baggini[88] and Aaron Sloman.[89]
[edit] See also

• Creation and evolution in public education
• Darwin on Trial
• Howard Ahmanson, Jr
• Flying Spaghetti Monster
[edit] References
1. ^ Forrest, Barbara (May,2007) (PDF). Understanding the Intelligent Design Creationist
Movement: Its True Nature and Goals. A Position Paper from the Center for Inquiry, Office of Public
Policy. Washington, D.C.: Center for Inquiry, Inc..
http://www.centerforinquiry.net/uploads/attachments/intelligent-design.pdf. Retrieved 2007-08-06 .
2. ^ a b Does Seattle group "teach controversy" or contribute to it? Linda Shaw. The Seattle
Times, March 31, 2005.
3. ^ Small Group Wields Major Influence in Intelligent Design Debate ABC News, November 9,
2005
4. ^ "ID's home base is the Center for Science and Culture at Seattle's conservative Discovery
Institute. Meyer directs the center; former Reagan adviser Bruce Chapman heads the larger institute,
with input from the Christian supply-sider and former American Spectator owner George Gilder (also
a Discovery senior fellow). From this perch, the ID crowd has pushed a "teach the controversy"
approach to evolution that closely influenced the Ohio State Board of Education's recently proposed
science standards, which would require students to learn how scientists "continue to investigate and
critically analyze" aspects of Darwin's theory." Chris Mooney. The American Prospect. December 2,
2002 Survival of the Slickest: How anti-evolutionists are mutating their message
5. ^ Teaching Intelligent Design: What Happened When? by William A. Dembski"The clarion
call of the intelligent design movement is to "teach the controversy." There is a very real controversy
centering on how properly to account for biological complexity (cf. the ongoing events in Kansas),
and it is a scientific controversy."
6. ^ Nick Matzke's analysis shows how teaching the controversy using the Critical Analysis of
Evolution model lesson plan is a means of teaching all the intelligent design arguments without using
the intelligent design label.No one here but us Critical Analysis-ists... Nick Matzke. The Panda's
Thumb, July 11, 2006
7. ^ Not in Our Classrooms: Why Intelligent Design Is Wrong for Our Schools by Eugenie Scott,
Glenn Branch. Beacon Press, 2006. Page 30.
8. ^ Key Resources for Parents and School Board Members Discovery Institute staff. August
21, 2007.
9. ^ CSC Questions about Science Education Policy Discovery Institute staff.
10.^ Not in Our Classrooms: Why Intelligent Design Is Wrong for Our Schools by Eugenie Carol
Scott, Glenn Branch. Beacon Press, 2006.Page 35.
11.^ Teaching the Origins Controversy: A Guide for the Perplexed. Special Discovery Institute
Report David K. DeWolf. Discovery Institute, August 20, 1999.
12.^ "The Board relied solely on legal advice from two organizations with demonstrably
religious, cultural, and legal missions, the Discovery Institute and the TMLC."Ruling, page 131
Kitzmiller v. Dover.
13.^ Patricia O’Connell Killen, a religion professor at Pacific Lutheran University in Tacoma
whose work centers around the regional religious identity of the Pacific Northwest, recently wrote that
"religiously inspired think tanks such as the conservative evangelical Discovery Institute" are part of
the "religious landscape" of that area. [1]
14.^ Wedge Document Discovery Institute, 1999.
15.^ a b "That this controversy is one largely manufactured by the proponents of creationism and
intelligent design may not matter, and as long as the controversy is taught in classes on current
affairs, politics, or religion, and not in science classes, neither scientists nor citizens should be
concerned." Intelligent Judging — Evolution in the Classroom and the Courtroom George J. Annas,
New England Journal of Medicine, Volume 354:2277-2281 May 25, 2006
16.^ a b c "Some bills seek to discredit evolution by emphasizing so-called "flaws" in the theory
of evolution or "disagreements" within the scientific community. Others insist that teachers have
absolute freedom within their classrooms and cannot be disciplined for teaching non-scientific
"alternatives" to evolution. A number of bills require that students be taught to "critically analyze"
evolution or to understand "the controversy." But there is no significant controversy within the
scientific community about the validity of the theory of evolution. The current controversy surrounding
the teaching of evolution is not a scientific one." AAAS Statement on the Teaching of Evolution
American Association for the Advancement of Science. February 16, 2006
17.^ a b "Such controversies as do exist concern the details of the mechanisms of evolution, not
the validity of the over-arching theory of evolution, which is one of the best supported theories in all of
science." Science and Creationism: A View from the National Academy of Sciences, Second Edition
United States National Academy of Sciences
18.^ "ID's backers have sought to avoid the scientific scrutiny which we have now determined
that it cannot withstand by advocating that the controversy, but not ID itself, should be taught in
science class. This tactic is at best disingenuous, and at worst a canard." Ruling, Kitzmiller v. Dover
Area School District, page 89
19.^ Understanding the Intelligent Design Creationist Movement: Its True Nature and Goals. A
Position Paper from the Center for Inquiry, Office of Public Policy Barbara Forrest. May, 2007.
20.^ Finding the Evolution in Medicine National Institutes of Health
21.^ "ID has failed to gain acceptance in the scientific community" Ruling, page 64 Kitzmiller v.
Dover.
22.^ "Not a single expert witness over the course of the six week trial identified one major
scientific association, society or organization that endorsed ID as science."reoRuling, page 70
Kitzmiller v. Dover.
23.^ Kitzmiller v. Dover Area School District, Conclusion (pages 136-138)
24.^ a b "has the effect of implicitly bolstering alternative religious theories of origin by
suggesting that evolution is a problematic theory even in the field of science." . . . The effect of
Defendants’ actions in adopting the curriculum change was to impose a religious view of biological
origins into the biology course, in violation of the Establishment Clause. Conclusion, Page 134 of 139
25.^ a b "To Debate or Not to Debate Intelligent Design?" by Gerald Graff, Inside Higher Ed,
September 28, 2005.
26.^ The Crusade Against Evolution, Evan Ratliff, October 2004, Wired magazine
27.^ Teaching the Controversy: Darwinism, Design and the Public School Science Curriculum
David K. DeWolf, Stephen C. Meyer, Mark E. DeForrest. Foundation for Thought and Ethics, October
1, 1999
28.^ Battle on Teaching Evolution Sharpens Peter Slevin. Washington Post, March 14, 2005
29.^ Forrest and Gross(2004) p206
30.^ Turn out the lights, the "Teach the controversy" party’s over
31.^ Creationism in 2001: A State-by-State Report People For the American Way. (PDF file)
32.^ Intelligent Design Network.org
33.^ Intelligent Design: Teach the Controversy? Dann P. Siems, Assistant Professor Biology &
Integrative Studies, Bemidji State University
34.^ NSTA Position Statement: The Teaching of Evolution
35.^ Defending science education against intelligent design: a call to action American Society
for Clinical Investigation, Journal of Clinical Investigation. 116:1134-1138 (2006)
36.^ Context Ruling, Kitzmiller v. Dover Area School District. Pages 17-35
37.^ Ruling, Kitzmiller v. Dover Area School District, Case No. 04cv2688. December 20, 2005
38.^ Ruling, Whether ID Is Science, Kitzmiller v. Dover Area School District, Case No.
04cv2688. December 20, 2005
39.^ Evolution’s Backers in Kansas Start Counterattack Ralph Blumenthal. The New York
Times, August 1, 2006.
40.^ How to Make Sure Children Are Scientifically Illiterate Lawrence M. Krauss. The New York
Times, August 15, 2006.
41.^ Ruling - context, pg. 32 Kitzmiller v. Dover Area School District.
42.^ Chris Mooney (August 30, 2005). The Republican War on Science. Basic Books.
http://www.waronscience.com/excerpt.php?p=2.
43.^ "In a country in which more than 50 percent of adults consistently tell pollsters that they
believe God created humans in their present form within the past 10,000 years, however, there will
undoubtedly be a fourth wave that will feature yet another strategy to promote creationism by
questioning evolution. It looks as if this next wave will jettison the creationist and intelligent-design
baggage and concentrate exclusively on a "teach the controversy" strategy." Intelligent Judging —
Evolution in the Classroom and the Courtroom George J. Annas, New England Journal of Medicine,
Volume 354:2277-2281 May 25, 2006
44.^ a b Show Me The Science Daniel C. Dennett. New York Times.
45.^ Intelligent Design in Public School Science Curricula: A Legal Guidebook David K. DeWolf,
Stephen C. Meyer, Mark E. DeForrest 1999, Foundation for Thought and Ethics.
46.^ Father of intelligent design by Kim Minugh, Sacramento Bee, May 11, 2006
47.^ a b Ohio: Here We Go Again Richard B. Hoppe. The Panda's Thumb. July 6, 2006
48.^ ID Legislation in Michigan Ed Brayton. Dispatches from the Culture Wars, June 7, 2006
49.^ Critical Analysis of Evolution is Not the Same as Teaching Intelligent Design Casey Luskin.
Intelligent Design The Future, July 11, 2006.
50.^ No one here but us Critical Analysis-ists... Nick Matzke. The Panda's Thumb, July 11, 2006
51.^ Testimony, Aralene Callahan Kitzmiller v. Dover Area School District September 27, 2005
52.^ Testimony, Julie Smith Kitzmiller v. Dover Area School District September 28, 2005
53.^ Defending science education against intelligent design: a call to action Journal of Clinical
Investigation 116:1134-1138 (2006). American Society for Clinical Investigation.
54.^ "Moreover, Board members and teachers opposing the curriculum change and its
implementation have been confronted directly. First, Casey Brown testified that following her
opposition to the curriculum change on October 18, 2004, Buckingham called her an atheist and
Bonsell told her that she would go to hell. Second, Angie Yingling was coerced into voting for the
curriculum change by Board members accusing her of being an atheist and un- Christian. In addition,
both Bryan Rehm and Fred Callahan have been confronted in similarly hostile ways, as have
teachers in the DASD."Ruling, conclusion: Effect of Board’s Actions on Plaintiffs, pg. 130 Kitzmiller v.
Dover Area School District.
55.^ Kitzmiller v. Dover Area School District, Ruling, Pages 124-130
56.^ In July 2006 a moderator of the blog of intelligent design proponent William A. Dembski,
uncommondescent.com, endorsed bullying the children of the plaintiffs in the Kitzmiller v. Dover Area
School District trial and committing vandalism to drive them out of town and that he intends to publish
their names on the Web to that end.[2][3][4][5]
57.^ Dover gets a million-dollar bill Christina Kauffman. The York Dispatch, February 22, 2006
58.^ Robertson: PA Voters Rejected God CBS News, November 11, 2005
59.^ The Pennsylvania Controversy Phillip E. Johnson, Phillip Johnson's Weekly Wedge
Update. June 11, 2001
60.^ Icons of Evolution exposed on CNN Phillip E. Johnson, Phillip Johnson's Weekly Wedge
Update. May 2001
61.^ Passing the Torch Phillip E. Johnson, Phillip Johnson's Weekly Wedge Update. April 9,
2002
62.^ "ID proponents support their assertion that evolutionary theory cannot account for life’s
complexity by pointing to real gaps in scientific knowledge, which indisputably exist in all scientific
theories, but also by misrepresenting well-established scientific propositions." Ruling - whether ID is
science, pg. 83 Kitzmiller v. Dover Area School District.
63.^ Intelligent design group is just a religious front by Fred Barton, Lansing State Journal.
September 11, 2005
64.^ Battle on Teaching Evolution Sharpens By Peter Slevin Washington Post, March 14, 2005
65.^ Politicized Scholars Put Evolution on the Defensive By Jodi Wilgoren, New York Times,
August 21, 2005
66.^ List of scientific societies rejecting intelligent design
67.^ Ruling, Kitzmiller v. Dover page 83.
68.^ Statement on Teaching Evolution National Association of Biology Teachers, 2004.
69.^ One side can be wrong The Guardian. September 1, 2005.
70.^ The Evolution Wars Claudia Wallis. TIME magazine. August 15, 2005.
71.^ Battle on Teaching Evolution Sharpens Peter Slevin. Washington Post, March 14, 2005.
72.^ New Rules Bill Maher. Real Time with Bill Maher, HBO, August 19, 2005.
73.^ Meyer's Hopeless Monster Alan Gishlick, Nick Matzke, and Wesley R. Elsberry.
TalkReason.org, 2005.
74.^ Teach the Controversy Stephen C. Meyer. Cincinnati Enquirer, March 30, 2002.
75.^ About the NCSE National Science Teachers Association
76.^ Analysis of the Discovery Institute's "Bibliography of Supplementary Resources for Ohio
Science Instruction" National Center for Science Education (PDF file)
77.^ a b Let's Be Intelligent About Darwin Elizabeth Nickson. Christianity.ca, February, 2004.
78.^ Witness For The Prosecution, Darwin on Trial author brings together anti-Darwin coalition
to bring down evolution Joel Belz. World Magazine, Volume 11, Number 28, p. 18. November 30,
1996.
79.^ Defeating Darwinism by Opening Minds. Phillip E. Johnson. 1997. pp. 91-92
80.^ Berkeley’s Radical An Interview with Phillip E. Johnson Touchstone Magazine interview,
June 2002.
81.^ Missionary Man, Rob Boston, Church & State, April 1999
82.^ The "Wedge Document": So What? Discovery Institute.
83.^ "Creation Conflict in Schools" National Center for Science Education.
84.^ What is The Center for the Renewal of Science & Culture All About?
The Mission of The Center for Renewal of Science & Culture
85.^ The Wedge Breaking the Modernist Monopoly on Science Phillip E. Johnson. ARN.org.
86.^ AAAS Dialogue on Science, Ethics, and Religion, 20 April 2006, Emmett Holman,
Associate Professor of Philosophy from George Mason University, retrieved 2007-04-29
87.^ Langen, Tom A. (2004). "What is right with ‘teaching the controversy’?". Trends in Ecology
& Evolution 19 (3): 114–115. doi:10.1016/j.tree.2003.12.005. PMID 16701239.
88.^ Baggini, Julian (2007-06-15). "Why we should learn Intelligent Design". Times Educational
Supplement (TSL Education Ltd). http://www.tes.co.uk/search/story/?story_id=2397963. Retrieved
2008-06-27.
89.^ Sloman, Aaron. "Why scientists and philosophers of science should teach intelligent design
(ID) alongside the theory of evolution". http://www.cs.bham.ac.uk/~axs/id/. Retrieved 2008-06-27.

This article's use of external links may not follow Wikipedia's policies or guidelines.
Please improve this article by removing excessive and inappropriate external links.
(September 2009)
• David Morris, Alternet, 23 May 2005, "Having Fun With Intelligent Design"
• Peter Slevin, Washington Post, March 14, 2005, "Battle on Teaching Evolution Sharpens"
• Evan Ratliff, Wired, October 2004, "The Crusade Against Evolution"
• Discovery Institute, October 13, 2004, "Wired magazine reporter criticized for agenda driven
reporting - critique of Wired article and list of alleged misrepresentations
• Gregg Easterbrook, Wired, December 2002, "The New Convergence"
• Faith and Reason an overview of the Fall 1998 television documentary presented by PBS
dealing with religion and science.
• Teach the Controversy Stephen C. Meyer, Cincinnati Enquirer, March 30, 2002
• No Need to Fear Teaching the Controversy, from the Discovery Institute
• Reprint of Washington Post OpEd piece approving of teaching the controversy
• The "Wedge Document": "So What?" (An explanation by the Discovery Institute)
• The "Wedge" Archives at the Access Research Network website.
• Intelligent Design and that Vast Right-wing Conspiracy
• What's wrong with 'teaching the controversy'?
• The Wedge Strategy Three Years Later
• The Discovery Institute
• Critiques of Anti-Evolutionist Phillip Johnson's Views
• Resolution disparaging ID and ID politics, by the board of the American Association for the
Advancement of Science
• National Center for Science Education resources on ID
• "Intelligent Design" Not Accepted by Most Scientists
• Science and Creationism: A View from the National Academy of Sciences by the Steering
Committee on Science and Creationism, National Academy of Sciences, addressing the issue of
intelligent design in the guise of creationism.
• The "Intelligent Design" of a Monkey Trial: A Case of Hidden Agendas by Bob Weitzel. At the
axisoflogic.com website.
• Should We “Teach the Controversy”? Jason Rosenhouse csicop.org (Committee for the
Scientific Investigation of Claims of the Paranormal)
• State Your Case Chris Mooney. csicop.org (Committee for the Scientific Investigation of
Claims of the Paranormal) 25 October 2004
• Evolution Controversy in Our Schools A letter sent to Academy members by President of the
National Academy of Sciences, Bruce Alberts 4 March 2005.
• The Newest Evolution of Creationism, Intelligent design is about politics and religion, not
science. Barbara Forrest. Natural History magazine, April, 2002, page 80
• Analysis of the Discovery Institute's Bibliography of Supplementary Resources for Ohio
Science Education NCSE staff, National Center for Science Education website
• Should Creationism Be Taught in the Public Schools? (PDF) Robert T. Pennock. March 2002
• Back to School with the Religious Right A report by People For the American Way
Foundation
[edit] Audio and video

• How to Teach the Controversy Legally By the Discovery Institute
• The BBC's Robert Pigott: Changes to teaching evolution in Ohio
• "Intelligent Design" Rivals Evolution in Ohio High Schools
• Kansas Schools Struggle with Evolution and Creationism
• Ohio State Board of Education proposed new standards for teaching science
• Textbook Battles
• Why the debate over creationism is dividing the USA
Retrieved from "http://en.wikipedia.org/wiki/Teach_the_Controversy"
Categories: Christian fundamentalism | Intelligent design movement | Religion and education |

Religion and politics | Textbook controversies | Intelligent design controversies | Discovery Institute
campaigns | Denialism
W000
Symbiosis

"Symbiology" redirects here. For the study or use of things that represent other things by association,
resemblance, or convention, see Symbology.
This article is about the biological phenomenon. For other uses, see Symbiosis (disambiguation). For
the Marvel character, see Symbiote (comics).
In a symbiotic commensalism, the clownfish feeds on small invertebrates which otherwise potentially
could harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone.
Symbiosis (from Ancient Greek sýn "with" and bíōsis "living")[1] is close and often long-term
interactions between different biological species. In 1877 Bennett used the word symbiosis (which previously
had been used of people living together in community) to describe the mutualistic relationship in lichens.[2] In
1879 by the German mycologist Heinrich Anton de Bary, defined it as "the living together of unlike
organisms."[3][4]
The definition of symbiosis is in flux,[when?] and the term has been applied to a wide range of
biological interactions. The symbiotic relationship may be categorized as mutualistic, commensal, or parasitic
in nature.[5][6] Some symbiotic relationships are obligate, meaning that both symbionts entirely depend on
each other for survival. For example, many lichens consist of fungal and photosynthetic symbionts that
cannot live on their own.[3][7][8][9] Others are facultative, meaning that they can but do not have to live with
the other organism.
Symbiotic relationships include those associations in which one organism lives on another
(ectosymbiosis, such as mistletoe), or where one partner lives inside the other (endosymbiosis, such as
lactobacilli and other bacteria in humans or zooxanthelles in corals). Symbiotic relationships may be either
obligate, i.e., necessary for the survival of at least one of the organisms involved, or facultative, where the
relationship is beneficial but not essential for survival of the organisms.[10][11]
Contents
[hide]
• 1 Physical interaction
• 2 Mutualism
• 3 Commensalism
• 4 Parasitism
• 5 Amensalism
• 6 Symbiosis and evolution
• 6.1 Vascular Plants
• 6.2 Symbiogenesis
• 6.3 Co-evolution
• 7 Notes
• 8 See also
• 9 References
[edit] Physical interaction
Alder tree root nodule

Endosymbiosis is any symbiotic relationship in which one symbiont lives within the tissues of the
other, either in the intracellular space or extracellularly.[11][12] Examples are rhizobia, nitrogen-fixing
bacteria that live in root nodules on legume roots; actinomycete nitrogen-fixing bacteria called Frankia, which
live in alder tree root nodules; single-celled algae inside reef-building corals; and bacterial endosymbionts
that provide essential nutrients to about 10%–15% of insects.
Ectosymbiosis, also referred to as exosymbiosis, is any symbiotic relationship in which the symbiont
lives on the body surface of the host, including the inner surface of the digestive tract or the ducts of exocrine
glands.[11][13] Examples of this include ectoparasites such as lice, commensal ectosymbionts such as the
barnacles that attach themselves to the jaw of baleen whales, and mutualist ectosymbionts such as cleaner
fish.
[edit] Mutualism
Main article: Mutualism (biology)
Hermit crab, Calcinus laevimanus, with sea anemone.
Mutualism is any relationship between individuals of different species where both individuals derive a
benefit.[14] Generally, only lifelong interactions involving close physical and biochemical contact can properly
be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one
but facultative for the other, or facultative for both. Many biologists restrict the definition of symbiosis to close
mutualist relationships.
An Egyptian Plover picking the teeth of a Nile crocodile
A large percentage of herbivores have mutualistic gut fauna that help them digest plant matter, which
is more difficult to digest than animal prey.[10] Coral reefs are the result of mutualisms between coral
organisms and various types of algae that live inside them.[15] Most land plants and land ecosystems rely on
mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting
minerals from the ground.[16]
An example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among
the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish,
and in turn the stinging tentacles of the anemone protect the clownfish from its predators. A special mucus on
the clownfish protects it from the stinging tentacles.[17]
Another example is the goby fish, which sometimes lives together with a shrimp. The shrimp digs and
cleans up a burrow in the sand in which both the shrimp and the goby fish live. The shrimp is almost blind,
leaving it vulnerable to predators when above ground. In case of danger the goby fish touches the shrimp
with its tail to warn it. When that happens both the shrimp and goby fish quickly retract into the burrow.[18]
One of the most spectacular examples of obligate mutualism is between the siboglinid tube worms
and symbiotic bacteria that live at hydrothermal vents and cold seeps. The worm has no digestive tract and is
wholly reliant on its internal symbionts for nutrition. The bacteria oxidize either hydrogen sulfide or methane
which the host supplies to them. These worms were discovered in the late 1980s at the hydrothermal vents
near the Galapagos Islands and have since been found at deep-sea hydrothermal vents and cold seeps in all
of the world's oceans.[19]
There are also many types of tropical and sub-tropical ants that have evolved very complex
relationships with certain tree species.[20]
[edit] Commensalism
Phoretic mites on a fly (Pseudolynchia canariensis).

Main article: Commensalism
Commensalism describes a relationship between two living organisms where one benefits and the
other is not significantly harmed or helped. It is derived from the English word commensal used of human
social interaction. The word derives from the medieval Latin word, formed from com- and mensa, meaning
"sharing a table".[14][21]
Commensal relationships may involve one organism using another for transportation (phoresy) or for
housing (inquilinism), or it may also involve one organism using something another created, after its death
(metabiosis). Examples of metabiosis are hermit crabs using gastropod shells to protect their bodies and
spiders building their webs on plants.
[edit] Parasitism
Flea bites on a human is an example of parasitism (the flea as parasite to the human host in this
case).
Main article: Parasitism
A parasitic relationship is one in which one member of the association benefits while the other is
harmed.[22] Parasitic symbioses take many forms, from endoparasites that live within the host's body to
ectoparasites that live on its surface. In addition, parasites may be necrotrophic, which is to say they kill their
host, or biotrophic, meaning they rely on their host's surviving. Biotrophic parasitism is an extremely
successful mode of life. Depending on the definition used, as many as half of all animals have at least one
parasitic phase in their life cycles, and it is also frequent in plants and fungi. Moreover, almost all free-living
animals are host to one or more parasite taxa. An example of a biotrophic relationship would be a tick
feeding on the blood of its host.
[edit] Amensalism
Amensalism is the type of symbiotic relationship that exists where one species is inhibited or
completely obliterated and one is unaffected. This type of symbiosis is relatively uncommon in rudimentary
reference texts, but is omnipresent in the natural world. An example is a sapling growing under the shadow of
a mature tree. The mature tree can begin to rob the sapling of necessary sunlight and, if the mature tree is
very large, it can take up rainwater and deplete soil nutrients. Throughout the process the mature tree is
unaffected. Indeed, if the sapling dies, the mature tree gains nutrients from the decaying sapling. Note that
these nutrients become available because of the sapling's decomposition, rather than from the living sapling.
[edit] Symbiosis and evolution
Leafhoppers protected by an army of meat ants

While historically, symbiosis has received less attention than other interactions such as predation or
competition,[23] it is increasingly recognised as an important selective force behind evolution,[10][24] with
many species having a long history of interdependent co-evolution.[25] In fact, the evolution of all eukaryotes
(plants, animals, fungi, and protists) is believed under the endosymbiotic theory to have resulted from a
symbiosis between various sorts of bacteria.[10][26][27]
[edit] Vascular Plants

Up to 80% of vascular plants worldwide form symbiotic relationships with fungi, for example, in
arbuscular mycorrhiza.[28]
[edit] Symbiogenesis
The biologist Lynn Margulis, famous for her work on endosymbiosis, contends that symbiosis is a
major driving force behind evolution. She considers Darwin's notion of evolution, driven by competition, as
incomplete and claims that evolution is strongly based on co-operation, interaction, and mutual dependence
among organisms. According to Margulis and Dorion Sagan, "Life did not take over the globe by combat, but
by networking."[29]
[edit] Co-evolution
Symbiosis played a major role in the co-evolution of flowering plants and the animals that pollinate
them. Many plants that are pollinated by insects, bats, or birds have highly specialized flowers modified to
promote pollination by a specific pollinator that is also correspondingly adapted. The first flowering plants in
the fossil record had relatively simple flowers. Adaptive speciation quickly gave rise to many diverse groups
of plants, and, at the same time, corresponding speciation occurred in certain insect groups. Some groups of
plants developed nectar and large sticky pollen, while insects evolved more specialized morphologies to
access and collect these rich food sources. In some taxa of plants and insects the relationship has become
dependent,[30] where the plant species can only be pollinated by one species of insect.[31]
[edit] Notes
1. ^ σύν, βίωσις. Henry George Liddell, Robert Scott. A Greek-English Lexicon at Perseus
Project
2. ^ "symbiosis". Oxford English Dictionary. Oxford University Press. 2nd ed. 1989.
3. ^ a b Wilkinson 2001
4. ^ Douglas 1994, p. 1
5. ^ Dethlefsen L, McFall-Ngai M, Relman DA (2007), "An ecological and evolutionary
perspective on human-microbe mutualism and disease", Nature 449 (7164): 811–808,
doi:10.1038/nature06245, PMID 17943117.
6. ^ Paszkowski U. (2006), "Mutualism and parasitism: the yin and yang of plant symbioses",
Curr Opin Plant Biol 9 (4): 364–370, doi:10.1016/j.pbi.2006.05.008, PMID 16713732.
7. ^ Isaac 1992, p. 266
8. ^ Saffo 1993
9. ^ Douglas, Angela E. (2010), The symbiotic habit, New Jersey: Princeton University Press,
p. 4, ISBN 978-0-691-11341-8
10.^ a b c d Moran 2006
11.^ a b c Ahmadjian & Paracer 2000, p. 12
12.^ Sapp 1994, p. 142
13.^ Nardon & Charles 2002
14.^ a b Ahmadjian & Paracer 2000, p. 6
15.^ Toller, Rowan & Knowlton 2001
16.^ Harrison 2005
17.^ Lee 2003
18.^ Facey, Helfman & Collette 1997
19.^ Cordes 2005
20.^ Piper, Ross (2007), Extraordinary Animals: An Encyclopedia of Curious and Unusual
Animals, Greenwood Press.
21.^ Nair 2005
22.^ Ahmadjian & Paracer 2000, p. 7
23.^ Townsend, Begon & Harper 1996
24.^ Wernegreen 2004
25.^ Ahmadjian & Paracer 2000, pp. 3–4
26.^ Brinkman 2002
27.^ Golding & Gupta 1995
28.^ Schüßler, A. et al. (2001). "A new fungal phlyum, the Glomeromycota: phylogeny and
evolution". Mycol. Res. 105 (12): 1416. http://journals.cambridge.org/action/displayAbstract?
fromPage=online&aid=95091.
29.^ Sagan & Margulis 1986
30.^ Harrison 2002
31.^ Danforth & Ascher 1997
[edit] See also

• aposymbiotic
• aquaponics
• decompiculture
• list of symbiotic organisms
• list of symbiotic relationships
• multigenomic organism
• Symbiogenesis
• Symbiosis (chemical)
[edit] References
• Ahmadjian, Vernon; Paracer, Surindar (2000), Symbiosis: an introduction to biological
associations, Oxford [Oxfordshire]: Oxford University Press, ISBN 0-195-11806-5
• Burgess, Jeremy (1994), Forum: What's in it for me, New Scientist,
http://media.newscientist.com/article/mg14119115.200-forum-whats-in-it-for-me--jeremy-burgess-
examines-therole-of-cooperation-within-natures-competitive-ways-.html
• Boucher, Douglas H (1988), The Biology of Mutualism: Ecology and Evolution , New York:
Oxford University Press, ISBN 0195053923
• Cordes, E.E.; Arthur, M.A.; Shea, K.; Arvidson, R.S.; Fisher, C.R. (2005), "Modeling the
mutualistic interactions between tubeworms and microbial consortia", PLoS Biol 3 (3): 1–10,
doi:10.1371/journal.pbio.0030077, PMID 15736979
• Brinkman, F.S.L.; Blanchard, J.L.; Cherkasov, A.; Av-gay, Y.; Brunham, R.C.; Fernandez,
R.C.; Finlay, B.B.; Otto, S.P.; Ouellette, B.F.F.; Keeling, P.J.; Others, (2002), "Evidence That Plant-
Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae,
Cyanobacteria, and the Chloroplast", Genome Research 12 (8): 1159–1167, doi:10.1101/gr.341802,
PMID 12176923, PMC 186644, http://www.csa.com/partners/viewrecord.php?
requester=gs&collection=ENV&recid=5449063, retrieved 2007-09-30
• Danforth, B.N.; Ascher, J. (1997), "Flowers and Insect Evolution", Science 99 (2559): 42,
doi:10.1126/science.283.5399.143a, PMID 17741328,
http://www.sciencemag.org/cgi/reprint/283/5399/143a.pdf, retrieved 2007-09-25
• Douglas, A. E. (1994), Symbiotic interactions, Oxford [Oxfordshire]: Oxford University Press,
ISBN 0-19-854294-1
• Facey, Douglas E.; Helfman, Gene S.; Collette, Bruce B. (1997), The diversity of fishes,
Oxford: Blackwell Science, ISBN 0-86542-256-7
• Golding, RS; Gupta, RS (1995), "Protein-based phylogenies support a chimeric origin for the
eukaryotic genome", Mol. Biol. Evol. 12 (1): 1–6, PMID 7877484
• Harrison, Rhett (2002), "Balanced mutual use (symbiosis)", Quarterly journal Biohistory 10
(2), https://www.brh.co.jp/en/experience/journal/32/ss_3.html, retrieved 2007-09-23
• Harrison, Maria J. (2005), "Signaling in the arbuscular mycorrhizal symbiosis", Annu. Rev.
Microbiol. 59: 19–42, doi:10.1146/annurev.micro.58.030603.123749, PMID 16153162
• Lee, J. (2003), "Amphiprion percula" (On-line), Animal Diversity Web,
http://animaldiversity.ummz.umich.edu/site/accounts/information/Amphiprion_percula.html, retrieved
2007-09-29
• Isaac, Susan (1992), Fungal-plant interactions, London: Chapman & Hall, ISBN 0-412-
36470-0
• Isaak, Mark (2004), CB630: Evolution of obligate mutualism, TalkOrigins Archive,
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W000
Dolphin

For other uses, see Dolphin (disambiguation).
Bottlenose dolphin breaching in the bow wave of a boat
Dolphins are marine mammals that are closely related to whales and porpoises. There are almost
forty species of dolphin in seventeen genera. They vary in size from 1.2 m (4 ft) and 40 kg (90 lb) (Maui's
dolphin), up to 9.5 m (30 ft) and 10 tonnes (9.8 LT; 11 ST) (the orca or killer whale). They are found
worldwide, mostly in the shallower seas of the continental shelves, and are carnivores, mostly eating fish and
squid. The family Delphinidae is the largest in the Cetacean order, and evolved relatively recently, about ten
million years ago, during the Miocene. Dolphins are among the most intelligent animals, and their often
friendly appearance and seemingly playful attitude have made them popular in human culture.
Contents
[hide]
• 1 Etymology
• 2 Taxonomy
• 2.1 Hybridization
• 3 Evolution and anatomy
• 3.1 Evolution
• 3.2 Anatomy
• 3.3 Senses
• 4 Behavior
• 4.1 Social behavior
• 4.2 Reproduction and sexuality
• 4.3 Feeding
• 4.4 Vocalizations
• 4.5 Jumping and playing
• 4.6 Sleeping
• 5 Threats
• 5.1 Natural threats
• 5.2 Human threats
• 6 Relationships with humans
• 6.1 Mythology
• 6.2 Popular culture
Etymology
The name is originally from Greek δελφίς (delphís), "dolphin",[1] which was related to the Greek
δελφύς (delphus), "womb".[2] The animal's name can therefore be interpreted as meaning "a 'fish' with a
womb".[3] The name was transmitted via the Latin delphinus[4] (the romanization of the later Greek δελφῖνος
- delphinos[5]), which in Middle Latin became dolfinus and in Old French daulphin, which reintroduced the ph
into the word. The term mereswine has also historically been used.[6]
The word is used in a few different ways. It can mean:
• any member of the family Delphinidae (oceanic dolphins),
• any member of the families Delphinidae and Platanistoidea (oceanic and river dolphins),
• any member of the suborder Odontoceti (toothed whales; these include the above families
and some others),
• and is used casually as a synonym for bottlenose dolphin, the most common and familiar
species of dolphin.
This article uses the second definition and does not describe porpoises (suborder Odontoceti, family
Phocoenidae). Orcas and some closely related species belong to the Delphinidae family and therefore
qualify as dolphins, even though they are called whales in common language. A group of dolphins is called a
"school" or a "pod". Male dolphins are called "bulls", females "cows" and young dolphins are called "calves".
[7]
Taxonomy
Common dolphin
Bottlenose dolphin
Spotted Dolphin
Commerson's Dolphin
Dusky Dolphin
Killer Whales, also known as Orcas

The Boto, or Amazon River Dolphin
• Suborder Odontoceti, toothed whales
• Family Delphinidae, oceanic dolphins
• Genus Delphinus
• Long-Beaked Common Dolphin, Delphinus capensis
• Short-Beaked Common Dolphin, Delphinus delphis
• Genus Tursiops
• Common Bottlenose Dolphin, Tursiops truncatus
• Indo-Pacific Bottlenose Dolphin, Tursiops aduncus
• Genus Lissodelphis
• Northern Rightwhale Dolphin, Lissodelphis borealis
• Southern Rightwhale Dolphin, Lissodelphis peronii
• Genus Sotalia
• Tucuxi, Sotalia fluviatilis
• Costero, Sotalia guianensis
• Genus Sousa
• Indo-Pacific Hump-backed Dolphin, Sousa chinensis
• Chinese White Dolphin (the Chinese variant), Sousa
chinensis chinensis
• Atlantic Humpbacked Dolphin, Sousa teuszii
• Genus Stenella
• Atlantic Spotted Dolphin, Stenella frontalis
• Clymene Dolphin, Stenella clymene
• Pantropical Spotted Dolphin, Stenella attenuata
• Spinner Dolphin, Stenella longirostris
• Striped Dolphin, Stenella coeruleoalba
• Genus Steno
• Rough-Toothed Dolphin, Steno bredanensis
• Genus Cephalorhynchus
• Chilean Dolphin, Cephalorhynchus eutropia
• Commerson's Dolphin, Cephalorhynchus commersonii
• Heaviside's Dolphin, Cephalorhynchus heavisidii
• Hector's Dolphin, Cephalorhynchus hectori
• Genus Grampus
• Risso's Dolphin, Grampus griseus
• Genus Lagenodelphis
• Fraser's Dolphin, Lagenodelphis hosei
• Genus Lagenorhynchus
• Atlantic White-Sided Dolphin, Lagenorhynchus acutus
• Dusky Dolphin, Lagenorhynchus obscurus
• Hourglass Dolphin, Lagenorhynchus cruciger
• Pacific White-Sided Dolphin, Lagenorhynchus obliquidens
• Peale's Dolphin, Lagenorhynchus australis
• White-Beaked Dolphin, Lagenorhynchus albirostris
• Genus Orcaella
• Australian Snubfin Dolphin, Orcaella heinsohni
• Irrawaddy Dolphin, Orcaella brevirostris
• Genus Peponocephala
• Melon-headed Whale, Peponocephala electra
• Genus Orcinus
• Killer Whale (Orca), Orcinus orca
• Genus Feresa
• Pygmy Killer Whale, Feresa attenuata
• Genus Pseudorca
• False Killer Whale, Pseudorca crassidens
• Genus Globicephala
• Long-finned Pilot Whale, Globicephala melas
• Short-finned Pilot Whale, Globicephala macrorhynchus
• Genus †Australodelphis
• †Australodelphis mirus
• Family Platanistidae
• Ganges and Indus River Dolphin, Platanista gangetica with two subspecies
• Ganges River Dolphin (or Susu), Platanista gangetica gangetica
• Indus River Dolphin (or Bhulan), Platanista gangetica minor
• Family Iniidae
• Amazon River Dolphin (or Boto), Inia geoffrensis
• Family Lipotidae
• Baiji (or Chinese River Dolphin), Lipotes vexillifer (possibly extinct, since
December 2006)
• Family Pontoporiidae
• La Plata Dolphin (or Franciscana), Pontoporia blainvillei
Six species in the family Delphinidae are commonly called "whales", but genetically are dolphins.
They are sometimes called blackfish.
• Melon-headed Whale, Peponocephala electra
• Killer Whale (Orca), Orcinus orca
• Pygmy Killer Whale, Feresa attenuata
Wolphin Kawili'Kai at the Sea Life Park in Hawaii.
• False Killer Whale, Pseudorca crassidens
• Long-finned Pilot Whale, Globicephala melas
• Short-finned Pilot Whale, Globicephala macrorhynchus
Hybridization
In 1933, three strange dolphins beached off the Irish coast; they appeared to be hybrids between
Risso's and bottlenose dolphins.[8] This mating was later repeated in captivity, producing a hybrid calf. In
captivity, a bottlenose and a rough-toothed dolphin produced hybrid offspring.[9] A common-bottlenose
hybrid lives at SeaWorld California.[10] Other dolphin hybrids live in captivity around the world or have been
reported in the wild, such as a bottlenose-Atlantic spotted hybrid.[11] The best known hybrid is the wolphin, a
false killer whale-bottlenose dolphin hybrid. The wolphin is a fertile hybrid. Two wolphins currently live at the
Sea Life Park in Hawaii; the first was born in 1985 from a male false killer whale and a female bottlenose.
Wolphins have also been observed in the wild.[12]
Evolution and anatomy
The anatomy of a dolphin, showing its skeleton, major organs, tail, and body shape
Pacific white-sided dolphin skeleton (missing pelvic bones), on exhibit at The Museum of Osteology,
Oklahoma City, Oklahoma
Evolution
See also: Evolution of cetaceans
Dolphins, along with whales and porpoises, are descendants of terrestrial mammals, most likely of
the Artiodactyl order. The ancestors of the modern day dolphins entered the water roughly fifty million years
ago, in the Eocene epoch.
Hind limb buds are apparent on an embryo of a spotted dolphin in the fifth week of development as
small bumps (hind limb buds) near the base of the tail. The pin is approximately 2.5 cm (1.0 in) long.
Modern dolphin skeletons have two small, rod-shaped pelvic bones thought to be vestigial hind
limbs. In October 2006, an unusual bottlenose dolphin was captured in Japan; it had small fins on each side
of its genital slit, which scientists believe to be a more pronounced development of these vestigial hind limbs.
[13]
Anatomy
Dolphins have a streamlined fusiform body, adapted for fast swimming. The tail fin, called the fluke,
is used for propulsion, while the pectoral fins together with the entire tail section provide directional control.
The dorsal fin, in those species that have one, provides stability while swimming.
Though it varies by species, basic coloration patterns are shades of grey, usually with a lighter
underside, often with lines and patches of different hue and contrast.
The head contains the melon, a round organ used for echolocation. In many species, elongated jaws
form a distinct beak; species such as the bottlenose have a curved mouth which looks like a fixed smile.
Some species have up to 250 teeth. Dolphins breathe through a blowhole on top of their head. The trachea is
anterior to the brain. The dolphin brain is large and highly complex, and is different in structure from that of
most land mammals.
Unlike most mammals, dolphins do not have hair, except for a few hairs around the tip of their
rostrum which they lose shortly before or after birth.[14] The only exception to this is the Boto river dolphin,
which has persistent small hairs on the rostrum.[15]
Dolphins' reproductive organs are located on the underside of the body. Males have two slits, one
concealing the penis and one further behind for the anus. The female has one genital slit, housing the vagina
and the anus. A mammary slit is positioned on either side of the female's genital slit.
A recent study at the U.S. National Marine Mammal Foundation revealed dolphins are the only
animals other than humans that develop a natural form of type 2 diabetes, which may lead to a better
understanding of the disease and new treatments for both humans and dolphins.[16]
Senses
Most dolphins have acute eyesight, both in and out of the water, and they can hear frequencies ten
times or more above the upper limit of adult human hearing.[17] Though they have a small ear opening on
each side of their head, it is believed hearing underwater is also, if not exclusively, done with the lower jaw,
which conducts sound to the middle ear via a fat-filled cavity in the lower jaw bone. Hearing is also used for
echolocation, which all dolphins have. Dolphin teeth are believed to function as antennae to receive incoming
sound and to pinpoint the exact location of an object.[18] The dolphin's sense of touch is also well-developed,
with free nerve endings densely packed in the skin, especially around the snout, pectoral fins and genital
area. However, dolphins lack an olfactory nerve and lobes, and thus are believed to have no sense of smell.
[19] They do have a sense of taste and show preferences for certain kinds of fish. Since dolphins spend most
of their time below the surface, tasting the water could function like smelling, in that substances in the water
can signal the presence of objects that are not in the dolphin’s mouth.
Though most dolphins do not have hair, they do have hair follicles that may perform some sensory
function.[20] The small hairs on the rostrum of the Boto river dolphin are believed to function as a tactile
sense possibly to compensate for the Boto's poor eyesight.[21]
Behavior
A pod of Indo-Pacific bottlenose dolphins in the Red Sea.
See also: Whale surfacing behaviour
Dolphins are often regarded as one of Earth's most intelligent animals, though it is hard to say just
how intelligent. Comparing species' relative intelligence is complicated by differences in sensory apparatus,
response modes, and nature of cognition. Furthermore, the difficulty and expense of experimental work with
large aquatic animals has so far prevented some tests and limited sample size and rigor in others. Compared
to many other species, however, dolphin behavior has been studied extensively, both in captivity and in the
wild. See cetacean intelligence for more details.
Social behavior
Dolphins surfing at Snapper Rocks, Queensland, Australia

Dolphins are social, living in pods of up to a dozen individuals. In places with a high abundance of
food, pods can merge temporarily, forming a superpod; such groupings may exceed 1,000 dolphins.
Individuals communicate using a variety of clicks, whistles and other vocalizations. They make ultrasonic
sounds for echolocation. Membership in pods is not rigid; interchange is common. However, dolphins can
establish strong social bonds; they will stay with injured or ill individuals, even helping them to breathe by
bringing them to the surface if needed.[22] This altruism does not appear to be limited to their own species
however. The dolphin Moko in New Zealand has been observed guiding a female Pygmy Sperm Whale
together with her calf out of shallow water where they had stranded several times.[23] They have also been
seen protecting swimmers from sharks by swimming circles around the swimmers[24][25] or charging the
sharks to make them go away.[26]
Dolphins also display culture, something long believed to be unique to humans (and possibly other
primate species). In May 2005, a discovery in Australia found Indo-Pacific bottlenose dolphins (Tursiops
aduncus) teaching their young to use tools. They cover their snouts with sponges to protect them while
foraging. This knowledge is mostly transferred by mothers to daughters, unlike simian primates, where
knowledge is generally passed on to both sexes. Using sponges as mouth protection is a learned behavior.
[27] Another learned behavior was discovered among river dolphins in Brazil, where some male dolphins use
weeds and sticks as part of a sexual display.[28]
Dolphins engage in acts of aggression towards each other. The older a male dolphin is, the more
likely his body is to be covered with bite scars. Male dolphins engage in such acts of aggression apparently
for the same reasons as humans: disputes between companions and competition for females. Acts of
aggression can become so intense that targeted dolphins sometimes go into exile as a result of losing a fight.
Male bottlenose dolphins have been known to engage in infanticide. Dolphins have also been known
to kill porpoises for reasons which are not fully understood, as porpoises generally do not share the same
diet as dolphins, and are therefore not competitors for food supplies.[29]
Reproduction and sexuality

Dolphin copulation happens belly to belly; though many species engage in lengthy foreplay, the
actual act is usually brief, but may be repeated several times within a short timespan. The gestation period
varies with species; for the small Tucuxi dolphin, this period is around 11 to 12 months, while for the orca, the
gestation period is around 17 months. They usually become sexually active at a young age, even before
reaching sexual maturity. The age of sexual maturity varies by species and gender.
Dolphins are known to have sex for reasons other than reproduction, sometimes also engaging in
homosexual behavior.[30] Various species sometimes engage in sexual behavior including copulation with
other dolphin species.[30] Sexual encounters may be violent, with male dolphins sometimes showing
aggressive behavior towards both females and other males.[30][31] Occasionally, dolphins behave sexually
towards other animals, including humans.[32]
Feeding
Various methods of feeding exist among and within species, some apparently exclusive to a single
population. Fish and squid are the main food, but the false killer whale and the orca also feed on other
marine mammals.
One common feeding method is herding, where a pod squeezes a school of fish into a small volume,
known as a bait ball. Individual members then take turns plowing through the ball, feeding on the stunned
fish. Coralling is a method where dolphins chase fish into shallow water to more easily catch them. In South
Carolina, the Atlantic bottlenose dolphin takes this further with "strand feeding", driving prey onto mud banks
for easy access.[33] In some places, orcas come to the beach to capture sea lions. Some species also
whack fish with their flukes, stunning them and sometimes knocking them out of the water.
Reports of cooperative human-dolphin fishing date back to the ancient Roman author and natural
philosopher Pliny the Elder.[34] A modern human-dolphin partnership currently operates in Laguna, Santa
Catarina, Brazil. Here, dolphins drive fish towards fishermen waiting along the shore and signal the men to
cast their nets. The dolphins’ reward is the fish that escape the nets.[35][36]
Vocalizations
Spectrogram of dolphin vocalizations, with whistles, whines, and clicks are visible as upside down
V's, horizontal striations, and vertical lines, respectively.
Cacaphony of Dolphins
Recording of dolphins
whistling, whining, and clicking.
Dolphins are capable of making a broad range of sounds using nasal airsacs located just below the
blowhole. Roughly three categories of sounds can be identified: frequency modulated whistles, burst-pulsed
sounds and clicks. Dolphins communicate with their whistles and burst-pulsed sounds, though the nature and
extent of that ability is not known. At least some dolphin species can identify themselves using a signature
whistle.[37] The clicks are directional and are for echolocation, often occurring in a short series called a click
train. The click rate increases when approaching an object of interest. Dolphin echolocation clicks are
amongst the loudest sounds made by marine animals.[38]
Jumping and playing
Pacific white-sided dolphins breaching

Dolphins occasionally leap above the water surface, and sometimes perform acrobatic figures (e.g.
the spinner dolphin). Scientists are not certain about the purpose(s) of the acrobatics. Possibilities include
locating schools of fish by looking at above-water signs like feeding birds, communicating with other
dolphins, dislodging parasites or simple amusement.
Play is an important part of dolphin culture. Dolphins play with seaweed and play-fight with other
dolphins. At times they harass other local creatures, like seabirds and turtles. Dolphins enjoy riding waves
and frequently surf coastal swells and the bow waves of boats, at times “leaping” between the dual bow
waves of a moving catamaran. Occasionally, they playfully interact with swimmers. Captive dolphins have
been observed in aquariums engaging in complex play behavior which involves the creation and
manipulation of bubble rings.[39][40][41][42]
Sleeping
Generally, dolphins sleep with only one brain hemisphere in slow-wave sleep at a time, thus
maintaining enough consciousness to breathe and to watch for possible predators and other threats. Earlier
sleep stages can occur simultaneously in both hemispheres.[43][44][45] In captivity, dolphins seemingly
enter a fully asleep state where both eyes are closed and there is no response to mild external stimuli.
Respiration is automatic; a tail kick reflex keeps the blowhole above the water if necessary. Anesthetized
dolphins initially show a tail kick reflex.[46] Though a similar state has been observed with wild Sperm
Whales, it is not known if dolphins in the wild reach this state.[47] The Indus river dolphin has a different
sleep method from other dolphin species. Living in water with strong currents and potentially dangerous
floating debris, it must swim continuously to avoid injury. As a result, this species sleeps in very short bursts
which last between 4 and 60 seconds.[48]
Threats
Natural threats
Except for humans (discussed below), dolphins have few natural enemies. Some species or specific
populations have none, making them apex predators. For most of the smaller species of dolphins, only a few
of the larger sharks, such as the bull shark, dusky shark, tiger shark and great white shark are a potential
risk, especially for calves. Some of the larger dolphinic species, especially orcas (killer whales), may also
prey smaller dolphins, but this seems rare. Dolphins also suffer from a wide variety of diseases and
parasites.[citation needed]
Human threats
See also: Dolphin drive hunting and Cetacean bycatch
Dead Atlantic white-sided dolphins in Hvalba on the Faroe Islands, killed in a drive hunt
Some dolphin species face an uncertain future, especially some river dolphin species such as the
Amazon river dolphin, and the Ganges and Yangtze river dolphin, which are critically or seriously
endangered. A 2006 survey found no individuals of the Yangtze river dolphin, which now appears to be
functionally extinct.[49]
Pesticides, heavy metals, plastics, and other industrial and agricultural pollutants that do not
disintegrate rapidly in the environment concentrate in predators such as dolphins.[50] Injuries or deaths due
to collisions with boats, especially their propellers, are also common.
Various fishing methods, most notably purse seine fishing for tuna and the use of drift and gill nets,
unintentionally kill many dolphins.[51] Accidental by-catch in gill nets and incidental captures in antipredator
nets that protect marine fish farms are common and pose a risk for mainly local dolphin populations.[52][53]
In some parts of the world, such as Taiji in Japan and the Faroe Islands, dolphins are traditionally considered
as food, and are killed in harpoon or drive hunts.[54] Dolphin meat is high in mercury, and may thus pose a
health danger to humans when consumed.[55]
Dolphin safe labels attempt to reassure consumers fish and other marine products have been caught
in a dolphin-friendly way. The original deal with "Dolphin safe" labels was brokered in the 1980s between
marine activists and the major tuna companies, and involved decreasing incidental dolphin kills by up to 50%
by changing the type of nets being used to catch the tuna. It should be noted that the dolphins are only netted
while fishermen are in pursuit of smaller tuna. Albacore are not netted this way, which makes albacore the
only truly dolphin-safe tuna.
Loud underwater noises, such as those resulting from naval sonar use, live firing exercises, or
certain offshore construction projects, such as wind farms, may be harmful to dolphins, increasing stress,
damaging hearing, and causing decompression sickness by forcing them to surface too quickly to escape the
noise.[56][57]
Relationships with humans
Mythology
Fresco of Dolphins, ca. 1600 BC, from Knossos, Crete.

A sketch of the goddess Ganga on her Vahana (mount) Makara.
See also: Dolphins in mythology
Dolphins have long played a role in human culture. Dolphins are common in Greek mythology and
there are many coins from ancient Greece which feature a man or boy or deity riding on the back of a
dolphin.[58] The Ancient Greeks welcomed dolphins; spotting dolphins riding in a ship’s wake was
considered a good omen. In Hindu mythology, the Ganges River Dolphin is associated with Ganga, the deity
of the Ganges river.
Popular culture
A military dolphin
In more recent times, the 1963 Flipper movie and the subsequent 1964 television series, popularized
dolphins in Western society. The series, created by Ivan Tors, portrayed a dolphin as a kind of seagoing
Lassie. Flipper was a Bottlenose Dolphin who understood commands and always behaved heroically. Flipper
was remade in 1996. In the 1990s science fiction television series seaQuest DSV featured a bottle-nose
named Darwin who could communicate using a vocoder, a fictional invention which translated clicks and
whistles to English and back. The 1993 movie Free Willy made a star of the Orca playing Willy, Keiko. The
1977 horror movie Orca paints a less friendly picture of the species. Here, a male Orca takes revenge on
fishermen after the killing of his mate. The 1973 movie The Day of the Dolphin portrayed kidnapped dolphins
performing a naval military assassination using explosives. This was also explored in the similarly named
Simpsons Treehouse of Horror episode, Night of the Dolphin, where Lisa frees a dolphin at a aquarium
attraction and unwittingly initiates their plan to overthrow the land-dwellers and live in their place. In The
Hitchhiker's Guide to the Galaxy series, dolphins are the second most intelligent species on Earth (after
mice).
Dolphinaria
See also: Dolphinarium
The renewed popularity of dolphins in the 1960s resulted in the appearance of many dolphinaria
around the world, making dolphins accessible to the public. Criticism and animal welfare laws forced many to
close, although hundreds still exist around the world. In the United States, the best known are the SeaWorld
marine mammal parks. Since the late 1960s, SeaWorld’s Shamu orca shows have become popular. In 1988,
SeaWorld had Southwest Airlines paint three aircraft in "Shamu" colors to promote their parks.
Welfare
Organizations such as the Mote Marine Laboratory rescue and rehabilitate sick, wounded, stranded
or orphaned dolphins, while others, such as the Whale and Dolphin Conservation Society and Hong Kong
Dolphin Conservation Society, work on dolphin conservation and welfare. India has declared the Dolphin as
their national aquatic animal in an attempt to protect the endangered Ganges River Dolphin. The Vikramshila
Gangetic Dolphin Sanctuary has been created in the Ganges river for the protection of the animals.
Various scientists to have researched Dolphin behaviour have proposed that their unusually high
intelligence compared to other animals means that dolphins should be seen as non-human persons that
should have their own specific rights, and that it is morally unacceptable to keep them captive for
entertainment purposes, or to kill them; either intentionally for consumption or as by-catch.[59] [60]
Therapy
Dolphins are an increasingly popular choice of animal-assisted therapy for psychological problems
and developmental disabilities. For example, a 2005 study found dolphins an effective treatment for mild to
moderate depression.[61] However, this study was criticized on several grounds. For example, it is not
known whether dolphins are more effective than common pets.[62] Reviews of this and other published
dolphin-assisted therapy (DAT) studies have found important methodological flaws and have concluded that
there is no compelling scientific evidence that DAT is a legitimate therapy or that it affords more than fleeting
mood improvement.[63]
Military
See also: Military dolphin
A number of militaries have employed dolphins for various purposes from finding mines to rescuing
lost or trapped humans. The military use of dolphins, however, drew scrutiny during the Vietnam War when
rumors circulated that the United States Navy was training dolphins to kill Vietnamese divers.[64] The United
States Navy denies that at any point dolphins were trained for combat. Dolphins are still being trained by the
United States Navy on other tasks as part of the U.S. Navy Marine Mammal Program. The Russian military is
believed to have closed its marine mammal program in the early 1990s. In 2000 the press reported that
dolphins trained to kill by the Soviet Navy had been sold to Iran.[65]
Literature
Dolphins are also common in contemporary literature, especially science fiction novels. Dolphins play
a military role in William Gibson's short story Johnny Mnemonic, in which cyborg dolphins find submarines
and decode encrypted information. Dolphins play a role as sentient patrollers of the sea enhanced with a
deeper empathy toward humans in Anne McCaffrey's The Dragonriders of Pern series. In the Known Space
universe of author Larry Niven, dolphins play a significant role as fully recognised "legal entities". More
humorous is Douglas Adams’ The Hitchhiker's Guide to the Galaxy series of picaresque novels, in which
dolphins are the second most intelligent creatures on Earth (after mice, followed by humans) and try in vain
to warn humans of Earth’s impending destruction. Their story is told in So Long, and Thanks for All the Fish .
Much more serious is their major role in David Brin's Uplift series. A talking Dolphin named "Howard" helps
Hagbard Celine and his submarine crew fight the evil Illuminati in Robert Shea and Robert Anton Wilson's
Illuminatus Trilogy.
Dolphins appear frequently in non-science fiction literature. In the book The Music of Dolphins by
author Karen Hesse, dolphins raise a girl from the age of four until the coast guard eventually discovers her.
Fantasy author Ken Grimwood wrote dolphins into his 1995 novel Into the Deep about a marine biologist
struggling to crack the code of dolphin intelligence, including chapters written from a dolphinian viewpoint.
Art
Dolphins are a popular artistic motif, dating back to ancient times. Examples include the Triton
Fountain by Bernini and depictions of dolphins in the ruined Minoan palace at Knossos and on Minoan
pottery.
Cuisine
Dolphin meat is consumed in a small number of countries world-wide, which include Japan[66] and
Peru (where it is referred to as chancho marino, or "sea pork")[67]. While Japan may be the best-known and
most controversial example, only a very small minority of the population has ever sampled it.
Dolphin meat is dense and such a dark shade of red that it almost appears black. Fat is located in a
layer of blubber between the meat and the skin. When dolphin meat is eaten in Japan, it is often cut into thin
strips and eaten raw as sashimi, garnished with onion and either horseradish or grated garlic, much as with
sashimi of whale or horse meat (basashi). When cooked, dolphin meat is cut into bite-size cubes and then
batter-fried or simmered in a miso sauce with vegetables. Cooked dolphin meat has a flavor very similar to
beef liver.
See also
• Bottlenose Dolphin Research Institute
• Dolphin Research Center
• Whale and Dolphin Conservation Society
• Environmental Investigation Agency
References
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2. ^ δελφύς, Henry George Liddell, Robert Scott, A Greek-English Lexicon, on Perseus Digital
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05.pdf. Retrieved September 18, 2007.
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17, 2006.
33.^ U.S. Department of Commerce, National Oceanic and Atmospheric Administration,
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34.^ M.B. Santos, R. Fernández, A. López, J.A. Martínez and G.J. Pierce (2007). "Variability in
the diet of bottlenose dolphin, Tursiops truncatus, in Galician waters, north-western Spain, 1990–
2005". http://journals.cambridge.org/production/action/cjoGetFulltext?fulltextid=703604. Retrieved
April 3, 2007.
35.^ "Brazil's sexiest secret The Telegraph". The Daily Telegraph (London): p. 1. March 8, 2006.
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36.^ Dr. Moti Nissani (2007). "Bottlenose Dolphins in Laguna Requesting a Throw Net
Supporting material for Dr. Nissani's presentation at the 2007 International Ethological Conference".
http://www.youtube.com/watch?v=ECk0yMifmzw. Retrieved February 13, 2008.
37.^ the dolphin communication project. "Atlantic Spotted Dolphin vocalizations, chapter
Delphinid vocalizations". http://www.dolphincommunicationproject.org/DissPDFs/Chapter4.pdf,.
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38.^ Au, W. W. L. (1993). The Sonar of Dolphins. New York: Springer. ISBN 3540978356.
39.^ "EXTRA: Dolphins Blow Bubble Rings Underwater". ABC News. March 11, 2009.
http://abcnews.go.com/video/playerIndex?id=7062663. (with video).
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ISBN 9780822567677. http://books.google.com/books?id=5Buh9FtAG8AC.
41.^ Bayrock, Fiona; Conahan, Carolyn (2009). Bubble Homes and Fish Farts. Charlesbridge
Publishing. p. 29. ISBN 9781570916694. http://books.google.com/books?id=gArY6N3KIb4C.
42.^ Brenda McCowan; Lori Marino; Erik Vance; Leah Walke; Diana Reiss (2000). "Bubble Ring
Play of Bottlenose Dolphins (Tursiops truncatus):Implications for Cognition". Journal of Comparative
Psychology l14 (1): 98. doi:10.1037//0735-7036.114.1.98.
http://faculty.vetmed.ucdavis.edu/faculty/bjmccowan/Pubs/McCowanetal.JCP.2000.pdf.
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44.^ Mukhametov, Lev (1984). "Sleep in marine mammals". Experimental Brain Research 8
(suppl.): 227–238.
45.^ Dallas Grasby (1994). , L.M. Mukhametov, "Excerpts from "Sleep in marine mammals”".
Experimental Brain Research 8 (suppl.). http://www.bio.net/bionet/mm/neur-sci/1994-
August/003910.html , L.M. Mukhametov,. Retrieved February 11, 2008.
46.^ James G. McCormick (PhD), Department of Anesthesiology, Wake Forest University
School of Medicine, Winston-Salem, North Carolina (2007). "Behavioral Observations of Sleep and
Anesthesia in the Dolphin: Implications for Bispectral Index Monitoring of Unihemispheric Effects in
Dolphins". http://www.anesthesia-analgesia.org/cgi/content/full/104/1/239#F199. Retrieved February
11, 2008.
47.^ BBC (February 20, 2008). "Sperm whales caught 'cat napping'". BBC News.
http://news.bbc.co.uk/1/hi/scotland/edinburgh_and_east/7254522.stm. Retrieved April 9, 2008.
48.^ G. Neil Martin, Neil R. Carlson, William Buskist (1997), Psychology, third edition, page 383.
49.^ Douglas Williams for Shanghai Daily (2006). "Yangtze dolphin may be extinct".
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rs_say.htm. Retrieved December 9, 2006.
50.^ TED: Stephen Palumbi: Following the mercury trail
51.^ Clover, Charles. (2004). The End of the Line: How overfishing is changing the world and
what we eat. Ebury Press, London.. ISBN 0-09-189780-7.
52.^ Díaz López, Bruno; Shirai, J.A. (2006). "Bottlenose dolphin ( Tursiops truncatus) presence
and incidental capture in a marine fish farm on the north-eastern coast of Sardinia (Italy)". Journal of
Marine Biological Ass. UK 87: 113–117. doi:10.1017/S0025315407054215.
53.^ Díaz López, Bruno (2006). "Interactions between Mediterranean bottlenose dolphins
(Tursiops truncatus) and gillnets off Sardinia, Italy". ICES Journal of Marine Science 63: 946–951.
doi:10.1016/j.icesjms.2005.06.012.
54.^ Matsutani, Minoru (September 23, 2009). "Details on how Japan's dolphin catches work".
Japan Times. p. 3. http://search.japantimes.co.jp/cgi-bin/nn20090923f1.html.
55.^ Johnston, Eric (September 23, 2009). "Mercury danger in dolphin meat". Japan Times. p. 3.
http://search.japantimes.co.jp/cgi-bin/nn20090923f2.html.
56.^ CBC news (October 9, 2003). "Navy sonar may be killing whales, dolphins". CBC News.
http://www.cbc.ca/health/story/2003/10/09/sonar031009.html. Retrieved October 27, 2008.
57.^ "Npower renewables Underwater noise & vibration, section 9.4".
http://www.natwindpower.co.uk/northhoyle/pdfs/fepa/chapter9.pdf. Retrieved October 27, 2008.
58.^ "Taras". http://dougsmith.ancients.info/feac50tar.html. Retrieved 3 October 2010.
59.^ Thomas I. White (2007). In defense of dolphins: the new moral frontier. Blackwell Public
Philosophy Series. ISBN 978-1-4051-5778-0.
60.^ Jonathan Leake and Helen Brooks for The Sunday Times (2010), Scientists say dolphins
should be treated as 'non-human persons', article retrieved January 4, 2010.
61.^ "Randomised controlled trial of animal facilitated therapy with dolphins in the treatment of
depression". 2005. http://bmj.bmjjournals.com/cgi/content/full/bmj;331/7527/1231.
62.^ Biju Basil, Maju Mathews (2005). "Methodological concerns about animal-facilitated
therapy with dolphins". BMJ 331 (7529): 1407. doi:10.1136/bmj.331.7529.1407. PMID 16339258.
PMC 1309662. http://www.bmj.com/cgi/content/full/331/7529/1407.
63.^ Lori Marino, Scott O. Lilienfeld (2007). "Dolphin-Assisted Therapy: more flawed data and
more flawed conclusions" (PDF). Anthrozoos 20 (3): 239–49. doi:10.2752/089279307X224782.
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64.^ PBS - Frontline. "The Story of Navy dolphins".
http://www.pbs.org/wgbh/pages/frontline/shows/whales/etc/navycron.html. Retrieved June 8, 2008.
65.^ BBC News (March 8, 2000). "Iran buys kamikaze dolphins".
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66.^ "Dolphin slaughter turns sea red as Japan hunting season returns". The Guardian
(London). 2009-09-14. http://www.guardian.co.uk/world/2009/sep/14/dolphin-slaughter-hunting-
japan-taiji. Retrieved 24 May 2010.
67.^ Hall, Kevin G. (2003), "Dolphin meat widely available in Peruvian stores: Despite protected
status, `sea pork' is popular fare", The Seattle Times,
http://www.thefreelibrary.com/Dolphin+meat+widely+available+in+Peruvian+stores+Despite+protect
ed...-a0102897976, retrieved 7 Dec 2010
Further reading
• Carwardine, M., Whales, Dolphins and Porpoises, Dorling Kindersley, 2000. ISBN 0-7513-
2781-6
• Williams, Heathcote, Whale Nation, New York, Harmony Books, 1988. ISBN 9780517569320
External links
Wikimedia Commons has media related to: Dolphin
Wikispecies has information related to: Delphinidae
Look up dolphin in Wiktionary, the free dictionary.
Cetaceans portal
Conservation, research and news:
• De Rohan, Anuschka. Why dolphins are deep thinkers, The Guardian, July 3, 2003.
• The Dolphin Institute
• Digital Library of Dolphin Development Cetacean origins, Thewissen Lab
• The Oceania Project, Caring for Whales and Dolphins
• Tursiops.org: Current Cetacean-related news
Photos:
• Red Sea Spinner Dolphin - Photo gallery
• PBS NOVA: Dolphins: Close Encounters
• David's Dolphin Images
• Images of Wild Dolphins in the Red Sea
Retrieved from "http://en.wikipedia.org/wiki/Dolphin"
Categories: Cetaceans | Marine mammals | National symbols of Anguilla | National symbols of

Barbados | National symbols of Malta | Toothed whales | Greek loanwords
W000
American Museum of Natural History


American Museum of Natural History
Established 1869
Location Central Park West at 79th Street, New York City, United States
Type Natural History
Visitor figures about 4 million visits annually[1][2]
Director Ellen V. Futter
M7, M10, M11, M79, B and C at the 81 Street - Museum of Natural

Public transit access
History subway station
Website http://www.amnh.org
The American Museum of Natural History (abbreviated as AMNH), located on the Upper West Side
of Manhattan in New York City, United States, is one of the largest and most celebrated museums in the
world. Located in park-like grounds across the street from Central Park, the Museum comprises 25
interconnected buildings that house 46 permanent exhibition halls, research laboratories, and its renowned
library.
The collections contain over 32 million specimens, of which only a small fraction can be displayed at
any given time. The Museum has a scientific staff of more than 200, and sponsors over 100 special field
expeditions each year.[3]
Contents
[hide]
• 1 History
• 2 Exhibition halls
• 2.1 Hall of Ocean Life
• 2.2 Human Biology and Evolution
• 2.3 Halls of Minerals and Gems
• 2.4 Hall of Meteorites
• 2.5 Fossil Halls
• 2.6 The Art of the Diorama: Recreating Nature
• 3 Rose Center and Planetarium
• 4 Library
• 5 Research activities
• 6 Educational outreach
• 7 Surroundings
• 8 In popular culture
• 9 Neighboring area
• 10 Images
• 11 See also
• 12 References
[edit] History
The Museum was founded in 1869. Prior to construction of the present complex, the Museum was
housed in the older Arsenal building in Central Park. Theodore Roosevelt, Sr., the father of the 26th U.S.
President, was one of the founders along with John David Wolfe, William T. Blodgett, Robert L. Stuart,
Andrew H. Green, Robert Colgate, Morris K. Jesup, Benjamin H. Field, D. Jackson Steward, Richard M.
Blatchford, J. Pierpont Morgan, Adrian Iselin, Moses H. Grinnell, Benjamin B. Sherman, A. G. Phelps Dodge,
William A. Haines, Charles A. Dana, Joseph H. Choate, Henry G. Stebbins, Henry Parish, and Howard
Potter. The founding of the Museum realized the dream of naturalist Dr. Albert S. Bickmore. Bickmore, a one-
time student of Harvard zoologist Louis Agassiz, lobbied tirelessly for years for the establishment of a natural
history museum in New York. His proposal, backed by his powerful sponsors, won the support of the
Governor of New York, John Thompson Hoffman, who signed a bill officially creating the American Museum
of Natural History on April 6, 1869.[4]
In 1874, the cornerstone was laid for the Museum's first building, which is now hidden from view by
the many buildings in the complex that today occupy most of Manhattan Square. The original Victorian
Gothic building, which was opened in 1877, was designed by Calvert Vaux and J. Wrey Mould, both already
closely identified with the architecture of Central Park.[5]:19-20 It was soon eclipsed by the south range of
the Museum, designed by J. Cleaveland Cady, an exercise in rusticated brownstone neo-Romanesque,
influenced by H. H. Richardson.[6] It extends 700 feet (210 m) along West 77th Street,[7] with corner towers
150 feet (46 m) tall. Its pink brownstone and granite, similar to that found at Grindstone Island in the St.
Lawrence River, came from quarries at Picton Island, New York.[8] The entrance on Central Park West, the
New York State Memorial to Theodore Roosevelt, completed by John Russell Pope in 1936, is an overscaled
Beaux-Arts monument.[9] It leads to a vast Roman basilica, where visitors are greeted with a cast of a
skeleton of a rearing Barosaurus defending her young from an Allosaurus. The Museum is also accessible
through its 77th street foyer, renamed the "Grand Gallery" and featuring a fully suspended Haida canoe. The
hall leads into the oldest extant exhibit in the Museum, the hall of Northwest Coast Indians.[10]
The old 77th Street Entrance of the Museum

Since 1930 little has been added to the original building. The Museum's south front, spanning 77th
Street from Central Park West to Columbus Avenue was cleaned, repaired and re-emerged in 2009. Steven
Reichl, a spokesman for the Museum, said that work would include restoring 650 black-cherry window
frames and stone repairs. The Museum’s consultant on the latest renovation is Wiss, Janney, Elstner
Associates, Inc., an architectural and engineering firm with headquarters in Northbrook, IL.[6]
The museum's first two presidents were John David Wolfe (1870–1872) and Robert L. Stuart (1872–
1881), both among the museum's founders. The museum was not put on a sound footing until the
appointment of the third president, Morris K. Jesup (also one of the original founders), in 1881. Jesup was
president for over 25 years, overseeing its expansion and much of its golden age of exploration and
collection. The fourth president, Henry Fairfield Osborn, was appointed in 1906 on the death of Jesup.
Osborn consolidated the museum's expansion, developing it into one of the world's foremost natural history
museums. F. Trubee Davison was president from 1933 to 1951, with A. Perry Osborn as Acting President
from 1941 to 1946. Alexander M. White was president from 1951 to 1968. Gardner D. Stout was president
from 1968 to 1975. Robert G. Goelet from 1975 to 1988. George D. Langdon, Jr. from 1988 to 1993. Ellen V.
Futter has been president of the museum since 1993.[11]
Famous names associated with the Museum include the paleontologist and geologist Henry Fairfield
Osborn; the dinosaur-hunter of the Gobi Desert, Roy Chapman Andrews (one of the inspirations for Indiana
Jones);[5]:97-8 George Gaylord Simpson; biologist Ernst Mayr; pioneer cultural anthropologists Franz Boas
and Margaret Mead; explorer and geographer Alexander H. Rice, Jr.; and ornithologist Robert Cushman
Murphy. J. P. Morgan was also among the famous benefactors of the Museum.
[edit] Exhibition halls
Model of a Blue Whale in the Milstein Family Hall of Ocean Life

The Museum boasts habitat dioramas of African, Asian and North American mammals, a full-size
model of a Blue Whale suspended in the Milstein Family Hall of Ocean Life, sponsored by the family of Paul
Milstein (reopened in 2003), a 62 foot (19 m) Haida carved and painted war canoe from the Pacific
Northwest, a massive 31 ton piece of the Cape York meteorite, and the Star of India, the largest star sapphire
in the world.[12] The circuit of an entire floor is devoted to vertebrate evolution.
The Museum has extensive anthropological collections: Asian People, Pacific People, Man in Africa,
American Indian collections, general Native American collections, and collections from Mexico and Central
America.
[edit] Hall of Ocean Life
The Hall of Ocean Life opened in 1933 and was renovated in 1969 and later 2003. In the first of
these renovations the hall's star attraction appeared; the 94-foot (29 m)-long[13] blue whale model, which is
suspended from the ceiling behind its dorsal fin. It was redesigned dramatically in the 2003 renovation: its
flukes and fins were readjusted, a navel was added, and was repainted from a dull gray to various rich
shades of blue. Other notable exhibits in this hall include the Andros Coral Reef Diorama, which is the only
two-level diorama in the Western Hemisphere.[14]
[edit] Human Biology and Evolution
Hall of African Peoples

The Bernard and Anne Spitzer Hall of Human Origins, formerly The Hall of Human Biology and
Evolution, opened on February 10, 2007.[15] Originally known under the name "Hall of the Age of Man", at
the time of its original opening in 1921 it was the only major exhibition in the United States to present an in-
depth investigation of human evolution.[16] The displays traced the story of Homo sapiens, illuminated the
path of human evolution and examined the origins of human creativity.
Many of the celebrated displays from the original hall can still be viewed in the present expanded
format. These include life-size dioramas of our human predecessors Australopithecus afarensis, Homo
ergaster, Neanderthal, and Cro-Magnon, showing each species demonstrating the behaviors and capabilities
that scientists believe they were capable of. Also displayed are full-sized casts of important fossils, including
the 3.2-million-year-old Lucy skeleton and the 1.7-million-year-old Turkana Boy, and Homo erectus
specimens including a cast of Peking Man.
The hall also features replicas of ice age art found in the Dordogne region of southwestern France.
The limestone carvings of horses were made nearly 26,000 years ago and are considered to represent the
earliest artistic expression of humans.[17]
[edit] Halls of Minerals and Gems

The Harry Frank Guggenheim Hall of Minerals houses hundreds of unusual geological specimens. It
adjoins the Morgan Memorial Hall of Gems showcasing many rare, and valuable gemstones.
On display are many renowned samples that are chosen from among the Museum's more than
100,000 pieces. Included among these are the Patricia Emerald, a 632 carat (126 g), 12 sided stone that is
considered to be one of the world's most fabulous emeralds. It was discovered during the 1920s in a mine
high in the Colombian Andes and was named for the mine-owner's daughter. The Patricia is one of the few
large gem-quality emeralds that remains uncut.[18] Also on display is the 563 carat (113 g) Star of India, the
largest, and most famous, star sapphire in the world. It was discovered over 300 years ago in Sri Lanka, most
likely in the sands of ancient river beds from where star sapphires continue to be found today. It was donated
to the Museum by the financier J.P. Morgan. The thin, radiant, six pointed star, or asterism, is created by
incoming light that reflects from needle-like crystals of the mineral rutile which are found within the sapphire.
The Star of India is polished into the shape of a cabochon, or dome, to enhance the star's beauty.[19] Among
other notable specimens on display are a 596 pound (270 kg) topaz, a 4.5 ton specimen of blue
azurite/malachite ore that was found in the Copper Queen Mine in Bisbee, Arizona at the turn of the century;
[20] and a rare, 100 carat (20 g) orange-colored padparadschan sapphire from Sri Lanka, considered "the
mother of all pads."[21]
On October 29, 1964, the Star of India, along with several other precious gems including the Eagle
Diamond and the de Long Ruby, was stolen from the Museum by several thieves.[22] The group of burglars,
which included Jack Murphy, gained entrance by climbing through a bathroom window they had unlocked
hours before the Museum was closed. The Star of India and other gems were later recovered from a locker in
a Miami bus station, but the Eagle Diamond was never found; it may have been recut or lost.[23]
Labradorite specimen Quartz var. agate geode M

Assorted faceted and polished
minerals
[edit] Hall of Meteorites
Willamette Meteorite
The Arthur Ross Hall of Meteorites contains some of the finest specimens in the world including
Ahnighito, a section of the 200 ton Cape York meteorite which was found at the location of the same name in
Greenland. The meteorite's great weight—at 34 tons, it is the largest meteorite on display at any museum in
the world[24]—requires support by columns that extend through the floor and into the bedrock below the
Museum.[25]
The hall also contains extra-solar nanodiamonds (diamonds with dimensions on the nanometer level)
more than 5 billion years old. These were extracted from a meteorite sample through chemical means, and
they are so small that a quadrillion of these fit into a volume smaller than a cubic centimeter.[26]
[edit] Fossil Halls
Hall of Saurischian Dinosaurs

Most of the Museum's collections of mammalian and dinosaur fossils remain hidden from public view.
They are kept in numerous storage areas located deep within the Museum complex. Among these, the most
significant storage facility is the ten story Childs Frick Building which stands within an inner courtyard of the
Museum. During construction of the Frick, giant cranes were employed to lift steel beams directly from the
street, over the roof, and into the courtyard, in order to ensure that the classic museum façade remained
undisturbed. The predicted great weight of the fossil bones led designers to add special steel reinforcement
to the building's framework, as it now houses the largest collection of fossil mammals and dinosaurs in the
world. These collections occupy the basement and lower seven floors of the Frick Building, while the top
three floors contain laboratories and offices. It is inside this particular building that many of the Museum's
intensive research programs into vertebrate paleontology are carried out.
Other areas of the Museum contain repositories of life from thousands and millions of years in the
past. The Whale Bone Storage Room is a cavernous space in which powerful winches come down from the
ceiling to move the giant fossil bones about. Upstairs in the Museum attic there are yet more storage facilities
including the Elephant Room, and downstairs from that space one can find the tusk vault and boar vault.
[5]:119-20
Skeleton of Styracosaurus
The great fossil collections that are open to public view occupy the entire fourth floor of the Museum
as well as a separate exhibit that is on permanent display in the Theodore Roosevelt Memorial Hall, the
Museum's main entrance. The fourth floor exhibits allow the visitor to trace the evolution of vertebrates by
following a circuitous path that leads through several Museum buildings. On the 77th street side of the
Museum the visitor begins in the Orientation Center and follows a carefully marked path, which takes the
visitor along an evolutionary tree of life. As the tree "branches" the visitor is presented with the familial
relationships among vertebrates. This evolutionary pathway is known as a cladogram.
To create a cladogram, scientists look for shared physical characteristics to determine the
relatedness of different species. For instance, a cladogram will show a relationship between amphibians,
mammals, turtles, lizards, and birds since these apparently disparate groups share the trait of having 'four
limbs with movable joints surrounded by muscle', making them tetrapods. A group of related species such as
the tetrapods is called a "clade". Within the tetrapod group only lizards and birds display yet another trait:
"two openings in the skull behind the eye". Lizards and birds therefore represent a smaller, more closely
related clade known as diapsids. In a cladogram the evolutionary appearance of a new trait for the first time
is known as a "node". Throughout the fossil halls the nodes are carefully marked along the evolutionary path
and these nodes alert us to the appearance of new traits representing whole new branches of the
evolutionary tree. Species showing these traits are on display in alcoves on either side of the path. A video
projection on the Museum's fourth floor introduces visitors to the concept of the cladogram, and is popular
among children and adults alike.
Many of the fossils on display represent unique and historic pieces that were collected during the
Museum's golden era of worldwide expeditions (1880s to 1930s).[4] On a smaller scale, expeditions continue
into the present and have resulted in additions to the collections from Vietnam, Madagascar, South America,
and central and eastern Africa.
The fourth-floor halls include the Hall of Vertebrate Origins, Hall of Saurischian Dinosaurs
(recognized by their grasping hand, long mobile neck, and the downward/forward position of the pubis bone,
they are forerunners of the modern bird),[27] Hall of Ornithischian Dinosaurs (defined for a pubic bone that
points toward the back), Hall of Primitive Mammals, and Hall of Advanced Mammals.
Anatotitan fossil skeletons

Among the many outstanding fossils on display include:
• Tyrannosaurus rex: Composed almost entirely of real fossil bones, it is mounted in a
horizontal stalking pose beautifully balanced on powerful legs. The specimen is actually composed of
fossil bones from two T. rex skeletons discovered in Montana in 1902 and 1908 by the legendary
dinosaur hunter Barnum Brown.[28]
• Mammuthus: Larger than its relative the woolly mammoth, these fossils are from an animal
that lived 11 thousand years ago in Indiana.[29]
• Apatosaurus (Brontosaurus): This giant specimen was discovered at the end of the 19th
century. Although most of its fossil bones are original, the skull is not, since none was found on site.
It was only many years later that the first Apatosaurus skull was discovered and so a plaster cast of
that skull was made and placed on the Museum's mount. A Camarasaurus skull had been used
mistakenly until a correct skull was found.[30]
• Brontops: Extinct mammal distantly related to the horse and rhinoceros. It lived 35 million
years ago in what is now South Dakota. It is noted for its magnificent and unusual pair of horns.[31]
• Two skeletons of Anatotitan, a large herbivorous ornithopod dinosaur.
• On September 26, 2007, an 80-million-year-old, 2-feet-in-diameter fossil of ammonite made
its debut at the Museum. Neil Landman, curator, said that it became extinct 65 million years ago, at
the time of the dinosaurs. Korite International donated it after its discovery in Alberta, Canada.[32]
There are also a Triceratops and a Stegosaurus on display, among many other specimens.
[edit] The Art of the Diorama: Recreating Nature
Gorilla diorama in Akeley Hall of African Mammals

Grizzly bear diorama
Nature diorama
Renowned naturalists, artists, photographers, taxidermists and other Museum personnel have
blended their talents to create the great habitat dioramas which can be found in halls throughout the
Museum. Born in an era of black-and-white photography, when wildlife photography was in its earliest
stages, the dioramas have themselves become major historic attractions. Notable among them is the Akeley
Hall of African Mammals which opened in 1936.[33] The enormous hall showcases the vanishing wildlife of
Africa, in spaces where the human presence is notably absent, and includes hyperrealistic depictions of
elephants, hippopotamuses, lions, gorillas, zebras, and various species of antelope, including the rarely-seen
aquatic sitatunga.[34] Some of the displays are up to 18 feet (5 m) in height and 23 feet (7 m) in depth.
Carl Akeley was an outstanding taxidermist employed at the Field Museum in Chicago when the
American Museum of Natural History sent him to Africa to collect elephant hides. Akeley fell in love with the
rainforests of Africa and decried the encroachment of farming and civilization into formerly pristine natural
habitats. Fearing the permanent loss of these natural areas, Akeley was motivated to educate the American
public by creating the hall that bears his name. Akeley died in 1926 from infection while exploring the Kivu
Volcanoes in his beloved Belgian Congo, an area near to that depicted by the hall's gorilla diorama.[5]:79
With the 1942 opening of the Hall of North American Mammals, diorama art reached a pinnacle. It
took more than a decade to create the scenes depicted in the hall which includes a 432 square foot (40 m²)
diorama of the American bison.
Today, although the art of diorama has ceased to be a major exhibition technique, dramatic
examples of this art form are still occasionally employed. In 1997 Museum artists and scientists traveled to
the Central African Republic to collect samples and photographs for the construction of a 3,000 square
foot (300 m²) recreation of a tropical West African rainforest, the Dzanga-Sangha rain forest diorama in the
Hall of Biodiversity.[35]
Other notable dioramas, some dating back to the 1930s have been restored in the Milstein Hall of
Ocean Life. The hall is a 29,000 square foot (2,700 m²) bi-level room that includes a delicately mounted
94 foot (29 m) long model of a Blue Whale swimming beneath and around video projection screens and
interactive computer stations. Among the hall's notable dioramas is the "sperm whale and giant squid", which
represents a true melding of art and science since an actual encounter between these two giant creatures at
over one half mile depth has never been witnessed. Another celebrated diorama in the hall represents the
"Andros coral reef" in the Bahamas, a two-story-high diorama that features the land form of the Bahamas and
the many inhabitants of the coral reef found beneath the water's surface.
[edit] Rose Center and Planetarium
Rose Center for Earth and Space

Main article: Rose Center for Earth and Space
The Hayden Planetarium, connected to the Museum, is now part of the Rose Center for Earth and
Space, housed in a glass cube containing the spherical Space Theater, designed by James Stewart Polshek.
[36] The Heilbrun Cosmic Pathway is one of the most popular exhibits in the Rose Center, which opened
February 19, 2000.[15]
The original Hayden Planetarium was founded in 1933 with a donation by philanthropist Charles
Hayden. Opened in 1935,[37] it was demolished and replaced in 2000 by the $210 million Frederick Phineas
and Sandra Priest Rose Center for Earth and Space. Designed by James Stewart Polshek, the new building
consists of a six-story high glass cube enclosing a 87-foot (27 m) illuminated sphere that appears to float —
although it is actually supported by truss work. James Polshek has referred to his work as a "cosmic
cathedral".[38] The Rose center and its adjacent plaza, both located on the north facade of the Museum, are
regarded as some of Manhattan's most outstanding recent architectural additions. The facility encloses
333,500 square feet (30,980 m2) of research, education, and exhibition space as well as the Hayden
planetarium. Also located in the facility is the Department of Astrophysics, the newest academic research
department in the Museum. Further, Polshek designed the 1,800-square-foot (170 m 2) Weston Pavilion, a
43-foot (13 m) high transparent structure of "water white" glass along the Museum's west facade. This
structure, a small companion piece to the Rose Center, offers a new entry way to the Museum as well as
opening further exhibition space for astronomically related objects. The planetarium's former magazine, The
Sky, merged with "The Telescope", to become the leading astronomy magazine Sky & Telescope.[39]
Tom Hanks provided the voice-over for the first planetarium show during the opening of the new
Rose Center for Earth & Space in the Hayden Planetarium in 2000. Since then such celebrities as Whoopi
Goldberg, Robert Redford, Harrison Ford and Maya Angelou have been featured.
[edit] Library
Main article: Library of the American Museum of Natural History
From its founding, the Library of the American Museum of Natural History has grown into one of the
world's great natural history collections. In its early years, the Library expanded its collection mostly through
such gifts as the John C. Jay conchological library, the Carson Brevoort library on fishes and general
zoology, the ornithological library of Daniel Giraud Elliot, the Harry Edwards entomological library, the Hugh
Jewett collection of voyages and travel and the Jules Marcou geology collection. In 1903 the American
Ethnological Society deposited its library in the Museum and in 1905 the New York Academy of Sciences
followed suit by transferring its collection of 10,000 volumes. Today, the Library's collections contain over
550,000 volumes of monographs, serials, pamphlets, reprints, microforms, and original illustrations, as well
as film, photographic, archives and manuscripts, fine art, memorabilia and rare book collections. The Library
collects materials covering such subjects as mammalogy, earth and planetary science, astronomy and
astrophysics, anthropology, entomology, herpetology, ichthyology, paleontology, ethology, ornithology,
mineralogy, invertebrates, systematics, ecology, oceanography, conchology, exploration and travel, history of
science, museology, bibliography, genomics, and peripheral biological sciences. The collection is rich in
retrospective materials — some going back to the 15th century — that are difficult to find elsewhere.[40]
[edit] Research activities

The Museum has a scientific staff of more than 200, and sponsors over 100 special field expeditions
each year. Many of the fossils on display represent unique and historic pieces that were collected during the
Museum's golden era of worldwide expeditions (1880s to 1930s). Examples of some of these expeditions,
financed in whole or part by the AMNH are: Jesup North Pacific Expedition, the Whitney South Seas
Expedition, the Roosevelt-Rondon Scientific Expedition, the Crocker Land Expedition, and the expeditions to
Madagascar and New Guinea by Richard Archbold. On a smaller scale, expeditions continue into the
present. The Museum also publishes several peer-reviewed journals, including the Bulletin of the American
Museum of Natural History.[41]
[edit] Educational outreach

AMNH's education programs include outreach to schools in New York city by the Moveable Museum.
[42][43][44][45][46][47][48][49][50][51][52][53][54]
[edit] Surroundings
The Museum is located at 79th Street and Central Park West, accessible via the B C trains of the
New York City Subway. There is a low-level floor direct access to the Museum via the 81st Street - Museum
of Natural History subway station on the IND Eighth Avenue Line at the south end of the upper platform
(where the uptown trains arrive).
The Museum also houses the stainless steel time capsule designed after a competition won by
Santiago Calatrava, which was sealed at the end of 2000 to mark the millennium. It takes the form of a folded
saddle-shaped volume, symmetrical on multiple axes, that explores formal properties of folded spherical
frames, which Calatrava described as a flower.[55] It stands on a pedestal outside the Museum's Columbus
Avenue entrance. The capsule is to remain sealed until the year 3000.
[edit] In popular culture
The Theodore Roosevelt Rotunda, the main ticketing lobby

• In J. D. Salinger's book The Catcher in the Rye, the protagonist Holden Caulfield at one point
finds himself heading towards the Museum, reflecting on past visits and remarking that what he likes
is the permanence of the exhibits there.[56]
• In many episodes of the Time Warp Trio on Discovery Kids, Joe, Sam, and Fred are in the
Museum; in one episode they see it 90 years into the future.
• On early seasons of Friends, Ross Geller works at the Museum.
• The museum in the film Night at the Museum (2006) is based on a 1993 book that was set at
the AMNH (The Night at the Museum). The interior scenes were shot at a sound stage in Vancouver,
British Columbia, but exterior shots of the museum's façade were done at the actual AMNH. The
museum in the film itself features a Hall of African Mammals, a Hall of Reptiles is mentioned, "Gems
and Minerals" can be seen on a sign, there is a brief scene featuring the Milstein Hall of Ocean Life
and the Blue Whale model, and it is dedicated to Teddy Roosevelt. AMNH officials have credited the
movie with increasing the number of visitors during the holiday season in 2006 by almost 20%.
According to Museum president Ellen Futter, there were 50,000 more visits over the previous year
during the 2006 holiday season.[57] Its 2009 sequel was partially set in this museum.
• The Museum appeared in the film The Nanny Diaries.
• The Museum has appeared repeatedly in the fiction of dark fantasy author Caitlín R. Kiernan,
including appearances in her fifth novel Daughter of Hounds, her work on the DC/Vertigo comic book
The Dreaming (#47, "Trinket"), and many of her short stories, including "Valentia" and "Onion" (both
collected in To Charles Fort, With Love, 2005).
• A scene in John Boorman's Exorcist II: The Heretic is set before one of the dioramas.
• Several scenes in the 2004 movie The Day After Tomorrow were set in the Museum's halls.
• As the "New York Museum of Natural History", the Museum is a favorite setting in many
Douglas Preston and Lincoln Child novels, including Relic, Reliquary, The Cabinet of Curiosities, and
The Book of the Dead. F.B.I. Special Agent Aloysius X. L. Pendergast plays a major role in all of
these thrillers. Preston was actually manager of publications at the Museum before embarking upon
his fiction writing career.
• The title of Noah Baumbach's 2005 film The Squid and the Whale refers to a diorama in the
Milstein Hall of Ocean Life. The diorama is shown at the end of the film.
• Other novels in which the AMNH is featured include Murder at the Museum of Natural
History by Michael Jahn (1994), Funny Bananas: The Mystery in the Museum by Georgess
McHargue (1975), The Bone Vault by Linda Fairstein (2003) and a brief scene in Motherless
Brooklyn by Jonathan Lethem (1999).
• An ending for the film We're Back! A Dinosaur's Story shows all four dinosaurs finally
reaching the AMNH.
• Portions of the Sony PlayStation game Parasite Eve take place within the AMNH.
• The AMNH is featured in the film An American Tail: The Treasure of Manhattan Island. Fievel
Mousekewitz and Tony Toponi go to the AMNH to meet Dr. Dithering to decipher a treasure map
they have found in an abandoned subway.
• The AMNH appears as a Resistance-controlled building in the Sierra game Manhunter: New
York.
• A scene from the biographic film Malcolm X was filmed in the Hall of African Mammals.
• The AMNH is featured in the video game Grand Theft Auto IV where it is known as the
Liberty State Natural History Museum.
• In the fourth volume of Mirage's Teenage Mutant Ninja Turtles, Michelangelo acts as a tour
guide for visiting aliens. His first assignment is the Saurian Regenta Seri and her Styracodon
bodyguards who wish to see the Museum, specifically the dinosaur exhibit.
• The Museum was the setting for the 1970 novel The Great Dinosaur Robbery by David
Forrest, but was not featured in the film adaptation One of Our Dinosaurs Is Missing, which was set
in the Natural History Museum in London, England.
• In 2009, the Museum hosted the live finale of the second season of The Celebrity Apprentice.
• In a second season episode of The Spectacular Spider-Man titled "Destructive Testing",
Spider-Man fights Kraven the Hunter in the Museum.
• An episode of Mad About You entitled "Natural History" is set in the museum.
• The museum is featured in the Dinosaur King episode The Big Apple Grapple
• The museum is featured in the How I Met Your Mother episode Natural History, although it is
renamed the Natural History Museum.
[edit] Neighboring area
The museum is situated in a 17-acre (69,000 m2) park known as "Theodore Roosevelt Park". The
park contains pleasant park benches, beautiful gardens and fields, and a dog run. This small park has made
the area around the museum very desirable and some of the most expensive real estate in the Upper West
Side (even more so after the completion of the renovation of the southern-facing museum facade) lies in this
area. In 2007 it was not uncommon to see museum facing apartments sell for as much as $2000 per square
foot. Additionally, the museum is surrounded by many gourmet restaurants that have outdoor cafes where
patrons can sit outside and enjoy the view.
[edit] Images
Bengal Tiger at the

Diorama in Akeley Diorama in Akeley Diorama in Akeley
American Museum of
Hall of African Mammals Hall of African Mammals Hall of African Mammals
Natural History
Butterfly Display in Milstein Tibet God Vajrapani
Conservatory Hall of Ocean Life statue Tibetan Kalachakra
statue
The Museum's south

range, in the 1920's South front
[edit] See also

• List of museums and cultural institutions in New York City
• Education in New York City
• Margaret Mead Film Festival
[edit] References
1. ^ "America's 25 Most Visited Museums". USA Today. 2007-10-04.
http://www.usatoday.com/travel/destinations/2007-09-28-most-visited-museums-forbes_N.htm.
2. ^ America's 25 Most Visited Museums ForbesTraveler.com. Made September 21, 2007.
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http://www.youtube.com/watch?v=x0NZzEQ3xno. Retrieved 2010-12-03.
48.^ "Moveable Museum". National Lab Day. http://www.nationallabday.org/resources/all?filter
%5Bprovided_by%5D=American+Museum+of+Natural+History. Retrieved 2010-12-03.
49.^ "Moveable Museum". Stuyvesant Town Events. http://www.stuytown.com/#/events.
50.^ "At Staten Island School, a Moving Way to Learn". SILive.com. 3-Oct-10.
http://www.silive.com/northshore/index.ssf/2008/10/at_staten_island_school_a_movi.html. Retrieved
2010-12-03.
51.^ "Dinosaurs, Moveable Museums, and Science!". United States Department of Education. 8-
Nov-10. http://www.ed.gov/oese-news/dinosaurs-moveable-museums-and-science. Retrieved 2010-
12-03.
52.^ "AMERICAN MUSEUM OF NATURAL HISTORY BRINGS DINOSAURS "EXHIBIT-ON-
WHEELS" TO LOCAL PRESCHOOLERS". Educational Alliance.
http://www.edalliance.org/index.php?
src=news&submenu=ArtGalleriesUpcoming&srctype=detail&category=Early
%20Childhood&refno=72. Retrieved 2010-12-03.
53.^ "AMNH Moveable at Family Fun Day". Family Health Resource Center & Patient Library.
http://www.nyupatientlibrary.org/hassenfeld/news/6-30-08/amnh-moveable-museum-family-fun-day.
54.^ "M.O.N.H (sic) Moveable Museum". ColoriumLaboratorium.
http://coloriumlaboratorium.com/m-o-n-h-moveable-museum. Retrieved 2010-12-03.
55.^ "Design Is Selected for Times Capsule". The New York Times. 1999-12-02.
http://query.nytimes.com/gst/fullpage.html?res=9A00EFDF1F3FF931A35751C1A96F958260.
56.^ Salinger, J. D. (1951). The Catcher in the Rye. New York: Back Bay Books. pp. 157–8.
ISBN 0316769177.
57.^ Dominguez, Robert; Cullen, Christopher (2007-01-04). "'NIGHT' MAKES HISTORY HOT".
Daily News (New York).

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W000
List of lemur species


The Ring-tailed Lemur (Lemur catta) is one of 101 recognized species and subspecies of lemur
found only in Madagascar.
Lemurs are strepsirrhine primates, all species of which are endemic to Madagascar. They include the
smallest primate in the world, Madame Berthe's Mouse Lemur, which weighs 30 grams (1.1 oz), and range
up to the size of the Indri, which can weigh as much as 9.5 kilograms (21 lb). However, recently extinct
species grew much larger. As of 2010, five families, 15 genera, and 101 species and subspecies of lemur are
formally recognized.[1] Of the 101 species and subspecies, the International Union for Conservation of
Nature (IUCN) has classified eight as Critically Endangered, 18 as Endangered, 15 as Vulnerable, four as
Near Threatened, eight as Least Concern, 41 as Data Deficient, and seven have yet to be evaluated.[2] From
2000 through 2008, 39 new species were described and nine other taxa resurrected.[3]
The number of lemur species is likely to continue growing in the coming years, as field studies,
cytogenetic and molecular genetic research continues.[3] There is not complete agreement over the latest
revisions to lemur taxonomy, with some experts preferring an estimated 50 lemur species.[4] The debates
are likely to continue, as some scholars label the explosive growth of species numbers as taxonomic
inflation. In many cases, classifications will ultimately depend upon which species concept is used.[5] In the
case of the lemurs of Madagascar, which have suffered extensively from deforestation and habitat
fragmentation, nearly 25% of all species are either Endangered or Critically Endangered, most have yet to be
extensively studied, and nearly all populations are in decline. For these reasons, taxonomists and
conservationists favor splitting them into separate species to develop an effective strategy for the
conservation of the full range of lemur diversity.[3] Implicitly, this means that full species status will help grant
genetically distinct populations added environmental protection.
At least 17 species and eight genera are believed to have become extinct in the 2,000 years since
humans first arrived in Madagascar.[6][7] All known extinct species were large, ranging in weight from 10 to
200 kg (22 to 440 lb). The largest known subfossil lemur was Archaeoindris fontoynonti, a giant sloth lemur,
which weighed more than a modern female gorilla. The extinction of the largest lemurs is often attributed to
predation by humans and possibly habitat destruction.[6] Since all extinct lemurs were not only large (and
thus ideal prey species), but also slow-moving (and thus more vulnerable to human predation), their
presumably slow-reproducing and low-density populations were least likely to survive the introduction of
humans.[6] Gradual changes in climate have also been blamed, and may have played a minor role; however
since the largest lemurs also survived the climatic changes from previous ice ages and only disappeared
following the arrival of humans, it is unlikely that climatic change was largely responsible.[6]
There is strong evidence of extensive declines in extant populations since the introductions of
humans, particularly among the larger and more specialized lemurs.[6] As long as habitats continue to shrink,
degrade and fragment, extinctions are likely to continue.
Contents
[hide]
• 1 Taxonomic classification
• 2 Extant species
• 2.1 Family: Cheirogaleidae
• 2.2 Family: Lemuridae
• 2.3 Family: Lepilemuridae
• 2.4 Family: Indriidae
• 2.5 Family: Daubentoniidae
• 3 Extinct species
• 4 Footnotes
• 5 Notes
• 6 References
• 8 See also
[edit] Taxonomic classification

Further information: Lemur taxonomic and phylogenetic classification
Lemurs are classified under eight families, three of which are extinct:
The Silky Sifaka, one of the most endangered primates in the world.
Mouse lemurs are the smallest primates in the world.

As of 2010 there are 5 species and 3 subspecies of bamboo lemurs recognized.
• Family: †Archaeolemuridae : monkey lemurs
• Genus: †Archaeolemur (2 extinct species)
• Genus: †Hadropithecus (1 extinct species)
• Family: Cheirogaleidae
• Genus: Allocebus: Hairy-eared Dwarf Lemur (1 extant species)
• Genus: Cheirogaleus: dwarf lemurs (5 extant species)
• Genus: Microcebus: mouse lemurs (18 extant species)
• Genus: Mirza: giant mouse lemurs (2 extant species)
• Genus: Phaner: fork-marked lemurs (4 extant species)
• Family: Daubentoniidae: Aye-aye
• Genus: Daubentonia (1 extant species, 1 extinct species)
• Family: Indriidae
• Genus: Avahi: woolly lemurs (9 extant species)
• Genus: Indri: Indri (1 extant species)
• Genus: Propithecus: sifakas (9 extant species)
• Family: Lemuridae
• Genus: Eulemur: true lemurs (12 extant species)
• Genus: Hapalemur: bamboo lemurs (5 extant species, 3 extant subspecies)
• Genus: Lemur: Ring-tailed Lemur (1 extant species)
• Genus: †Pachylemur (2 extinct species)
• Genus: Prolemur: Greater Bamboo Lemur (1 extant species)
• Genus: Varecia: ruffed lemurs (2 extant species, 3 extant subspecies)
• Family: Lepilemuridae: sportive lemurs
• Genus: Lepilemur (26 extant species)
• Family: †Megaladapidae: koala lemurs
• Genus: †Megaladapis (3 extinct species)
• Family: †Palaeopropithecidae: sloth lemurs
• Genus: †Archaeoindris (1 extinct species)
• Genus: †Babakotia (1 extinct species)
• Genus: †Mesopropithecus (3 extinct species)
• Genus: †Palaeopropithecus (3 extinct species)
The placement of lemurs within the order Strepsirrhini is currently under debate, although both sides
agree upon the same phylogenetic tree. The following table demonstrates the differences between the two
taxonomies.
3 infraorders, 2 superfamilies[8] 1 infraorder, 2 superf
• Order Primates • Order Primates

• Suborder Strepsirrhini: non-tarsier prosimians • Suborder Strepsirrhin
• Infraorder Chiromyiformes (Aye-aye) • Infraorder Lem
• Infraorder Lemuriformes • Super
• Superfamily Cheirogaleoidea •
• Family Cheirogaleidae •
• Superfamily Lemuroidea •
• Family †Archaeolemuridae •
• Family Indriidae •
• Family Lemuridae •
• Family Lepilemuridae •
• Family †Megaladapidae •
• Family †Pala
†Palaeopropithecidae • Super
• Infraorder Lorisiformes • Suborder Haplorrhini:
• Suborder Haplorrhini: tarsiers, monkeys and apes
[edit] Extant species

Main article: Lemur
All lemurs belong to the suborder Strepsirrhini within the order Primates. The 101 extant species and
subspecies are divided among 5 families and 15 genera. They range in weight from 30 g (1.1 oz) (Madame
Berthe's Mouse Lemur) to as much as 9.5 kg (21 lb) (Indri). Most are highly arboreal and activity patterns
range widely from nocturnal to diurnal to cathemeral. Having diversified over millions of years to fill every
ecological niche, diets also vary widely, though fruit, leaves, and insects make up the majority of the diet for
most species.
[edit] Family: Cheirogaleidae

Family Cheirogaleidae consists of the mouse lemurs (smallest of all primates), the dwarf lemurs, and
the fork-marked lemurs and their allies. There are 30 extant species.
The Gray Mouse Lemur is one of as many as 16 tiny, nocturnal mouse lemur species.
Fork-marked lemurs are the largest of the cheirogaleids.
Scientific name Common Average
Classified Conservation status
name size
Allocebus Hairy-eared 1875, 00065 ! 0!

trichotis Dwarf Lemur Günther 65–90 g (2.3–3.2
oz)
Data Deficient
0!
00250 !
Cheirogaleus Furry-eared 1870, A.
250–500 g (8.8–
crossleyi Dwarf Lemur Grandidier
18 oz)[d]
Data Deficient
1!
00350 !
Cheirogaleus Greater Dwarf 1812, É.
350–400 g (12–14
major Lemur Geoffroy
oz)
Least Concern
1!
00120 !
Cheirogaleus Fat-tailed 1812, É.
120–270 g (4.2–
medius Dwarf Lemur Geoffroy
9.5 oz)
Least Concern
Cheirogaleus Lesser Iron- 2000, unknown 0!

minusculus gray Dwarf Lemur Groves
Data Deficient
0!
Cheirogaleus Sibree's Dwarf 1896,
unknown
sibreei Lemur Forsyth Major
Data Deficient
4!
Microcebus Madame 2000, 00030 !
berthae Berthe's Mouse Lemur Rasoloarison et al. 30 g (1.1 oz)
Endangered
0!
Microcebus Bongolava 2007, 00078 !
bongolavensis Mouse Lemur Olivieri et al. 54 g (1.9 oz)[d]
Data Deficient
0!
Microcebus Danfoss' 2007, 00078 !
danfossi Mouse Lemur Olivieri et al. 63 g (2.2 oz)[d]
Data Deficient
Microcebus Reddish-gray 1910, 00046 ! 1!

griseorufus Mouse Lemur Kollman 46–79 g (1.6–2.8
oz)
Least Concern
0!
Microcebus Jolly's Mouse 2006, Louis 00060 !
jollyae Lemur et al. 60 g (2.1 oz)[d]
Data Deficient
0!
00045 !
Microcebus Goodman's 2005, Roos
45–48 g (1.6–1.7
lehilahytsara Mouse Lemur and Kappeler
oz)
Data Deficient
Microcebus MacArthur's 2008,

unknown -1 !Not Evaluated
macarthurii Mouse Lemur Radespiel et al.
0!
2006,
Microcebus Claire's 00078 !
Andriantompohavan
mamiratra Mouse Lemur 61 g (2.2 oz)[d]
a et al.
Data Deficient
Microcebus Mittermeier's 2006, Louis 00040 ! 0!

mittermeieri Mouse Lemur et al. 40 g (1.4 oz)[d]
Data Deficient
1!
Microcebus Gray Mouse 00060 !
1777, Miller
murinus Lemur 60 g (2.1 oz)
Least Concern
0!
00043 !
Microcebus Pygmy Mouse
1852, Peters 43–55 g (1.5–1.9
myoxinus Lemur
oz)
Data Deficient
4!
00056 !
Microcebus Golden-brown 1998,
56–87 g (2.0–3.1
ravelobensis Mouse Lemur Zimmerman et al.
oz)
Endangered
Microcebus Brown Mouse 1834, É. 00040 ! 1!

rufus Lemur Geoffroy 40–50 g (1.4–1.8
oz)
Least Concern
4!
00038 !
Microcebus Sambirano 2000,
38–50 g (1.3–1.8
sambiranensis Mouse Lemur Rasoloarison et al.
oz)
Endangered
0!
Microcebus Simmons' 2006, Louis 00078 !
simmonsi Mouse Lemur et al. 78 g (2.8 oz)[d]
Data Deficient
4!
00045 !
Microcebus Northern 2000,
45–77 g (1.6–2.7
tavaratra Rufous Mouse Lemur Rasoloarison et al.
oz)
Endangered
Microcebus Arnhold's 2008, E. 00049 !

0 !Not Evaluated
arnholdi Mouse Lemur Lewis, Jr. et al. 49.7 g (1.75 oz)
2006,
Microcebus Margot 00041 !
Andriantompohavan 0 !Not Evaluated
margotmarshae Marsh's Mouse Lemur 41 g (1.4 oz)
a et al.
Mirza coquereli Coquerel's 1867, A. 00300 ! 2!

300–320 g (11–11
Giant Mouse Lemur Grandidier
oz)
Near Threatened
0!
00287 !
Northern 2005,
Mirza zaza 287–299 g (10.1–
Giant Mouse Lemur Kappeler & Roos
10.5 oz)
Data Deficient
3!
Amber 1991, 00350 !
Phaner
Mountain Fork-marked Groves and 350–500 g (12–18
electromontis
Lemur Tattersall oz)[d]
Vulnerable
1!
00350 !
Masoala Fork- 1839,
Phaner furcifer 350–500 g (12–18
marked Lemur Blainville
oz)[d]
Least Concern
Phaner Pale Fork- 1991, 00330 ! 1!

pallescens marked Lemur Groves and 330 g (12 oz)
Tattersall
Least Concern
3!
1991, 00350 !
Pariente's
Phaner parienti Groves and 350–500 g (12–18
Fork-marked Lemur
Tattersall oz)[d]
Vulnerable
[edit] Family: Lemuridae

Family Lemuridae consists of the Ring-tailed Lemur, the brown lemurs, the bamboo lemurs and the
ruffed lemurs. There are 21 extant species and six subspecies.
The Red-fronted Lemur, like other brown lemurs, is sexually dichromatic (the sexes have different
colorations).
The Ring-tailed Lemur is highly social and is the most popularly known lemur species.
Ruffed lemurs are the largest of the extant lemurids.
Scientific name Common name Average
Classified Conservation statu
size
3!
02200 !
Eulemur White-fronted 1796, É.
2.2–2.6 kg (4.9–
albifrons Brown Lemur Geoffroy
5.7 lb)
Vulnerable
4!
1890,
Eulemur Gray-headed 02000 !2–
Grandidier and Milne-
cinereiceps[b] Lemur 2.5 kg (4.4–5.5 lb)
Edwards
Endangered
3!
02250 !
Collared Brown 1812, É.
Eulemur collaris 2.25–2.5 kg (5.0–
Lemur Geoffroy
5.5 lb)
Vulnerable
Eulemur Crowned Lemur 1842, Gray 01100 ! 3!

1.1–1.3 kg (2.4–
coronatus
2.9 lb)
Vulnerable
4!
01800 !
Eulemur
Sclater's Lemur 1867, Gray 1.8–1.9 kg (4.0–
flavifrons
4.2 lb)
Endangered
2!
Common Brown 1812, É. 02000 !2–
Eulemur fulvus
Lemur Geoffroy 3 kg (4.4–6.6 lb)
Near Threatene
3!
Eulemur 02000 !2–
Black Lemur 1766, Linnaeus
macaco 2.9 kg (4.4–6.4 lb)
Vulnerable
Eulemur Mongoose 1766, Linnaeus 01100 ! 3!

1.1–1.6 kg (2.4–
mongoz Lemur
3.5 lb)
Vulnerable
3!
01600 !
Eulemur Red-bellied 1850, I.
1.6–2.4 kg (3.5–
rubriventer Lemur Geoffroy
5.3 lb)
Vulnerable
2!
02200 !
Eulemur Red-fronted
1833, Bennett 2.2–2.3 kg (4.9–
rufifrons[a] Lemur
5.1 lb)
Near Threatene
0!
02200 !
Eulemur rufus[a] Red Lemur 1799, Audebert 2.2–2.3 kg (4.9–
5.1 lb)
Data Deficient
Eulemur Sanford's Brown 1932, Archbold 01800 ! 4!

sanfordi Lemur 1.8–1.9 kg (4.0–
4.2 lb)
Endangered
5!
01100 !
Hapalemur Lac Alaotra
1975, Rumpler 1.1–1.4 kg (2.4–
alaotrensis Bamboo Lemur
3.1 lb)
Critically Endange
4!
01300 !
Hapalemur Golden Bamboo 1987, Meier et
1.3–1.7 kg (2.9–
aureus Lemur al.
3.7 lb)
Endangered
0!
Hapalemur Beanamalao 2007, 00967 !
griseus gilberti Bamboo Lemur Rabarivola et al. 0.967 kg (2.13 lb)
Data Deficient
Hapalemur Eastern Lesser 1795, Link 00700 ! 3!

griseus griseus Bamboo Lemur 0.7–1 kg (1.5–2.2
lb)
Vulnerable
00700 !
Hapalemur Ranomafana 2007,
0.7–0.85 kg (1.5– -1 !Not Evaluate
griseus ranomafanensis Bamboo Lemur Rabarivola et al.
1.9 lb)
3!
00750 !
Hapalemur Southern Lesser 1987, Warter,
0.75–1.05 kg (1.7–
meridionalis Bamboo Lemur et al.
2.3 lb)[d]
Vulnerable
3!
Hapalemur Western Lesser 01000 !
1975, Rumpler
occidentalis Bamboo Lemur 1 kg (2.2 lb)
Vulnerable
02300 ! 2!
Ring-tailed
Lemur catta 1756, Linnaeus 2.3–3.5 kg (5.1–
Lemur
7.7 lb)
Near Threatene
5!
02200 !
Greater
Prolemur simus 1871, Gray 2.2–2.5 kg (4.9–
Bamboo Lemur
5.5 lb)
Critically Endange
4!
03300 !
Red Ruffed 1812, É.
Varecia rubra 3.3–3.6 kg (7.3–
Lemur Geoffroy
7.9 lb)
Endangered
5!
03100 !
Varecia Southern Black- 1953, Osman
3.1–3.6 kg (6.8–
variegata editorum and-white Ruffed Lemur Hill
7.9 lb)
Critically Endange
Varecia White-belted 1833, A. Smith 03100 ! 5!

variegata subcincta Black-and-white Ruffed 3.1–3.6 kg (6.8–
Lemur 7.9 lb)
Critically Endange
5!
03100 !
Varecia Black-and-white
1792, Kerr 3.1–3.6 kg (6.8–
variegata variegata Ruffed Lemur
7.9 lb)
Critically Endange
[edit] Family: Lepilemuridae

Family Lepilemuridae consists solely of the sportive lemurs. As of 2010, there are 26 extant species.
The Sahamalaza Sportive Lemur is one of 25 species of sportive lemur.
Common name Average
Scientific name Classified Conservation statu
size
0!
2006, 00765 !
Antafia Sportive
Lepilemur aeeclis Andriaholinirina et 0.765–0.97 kg
Lemur
al. (1.69–2.1 lb)[d]
Data Deficient
0!
Lepilemur Ahmanson's 2006, Louis, 00610 !
ahmansonorum Sportive Lemur Jr. 0.61 kg (1.3 lb)[d]
Data Deficient
4!
Lepilemur Ankarana 1975, 00750 !
ankaranensis Sportive Lemur Rumpler & Albignac 0.75 kg (1.7 lb)
Endangered
0!
Betsileo 2006, Louis, 01150 !
Lepilemur betsileo
Sportive Lemur Jr. 1.15 kg (2.5 lb)[d]
Data Deficient
Lepilemur dorsalis Gray-backed 1870, Gray 00500 ! 0!

Sportive Lemur 0.5 kg (1.1 lb)
Data Deficient
3!
Lepilemur Milne-Edwards' 1894, 01000 !
edwardsi Sportive Lemur Forsyth Major 1 kg (2.2 lb)
Vulnerable
0!
Lepilemur Fleurete's 2006, Louis, 00980 !
fleuretae Sportive Lemur Jr. 0.98 kg (2.2 lb)[d]
Data Deficient
0!
Lepilemur Grewcock's 2006, Louis, 00780 !
grewcockorum Sportive Lemur Jr. 0.78 kg (1.7 lb)[d]
Data Deficient
0!
Lepilemur Hubbard's 2006, Louis, 00990 !
hubbardorum Sportive Lemur Jr. 0.99 kg (2.2 lb)[d]
Data Deficient
0!
Lepilemur James' Sportive 2006, Louis, 00780 !
jamesorum Lemur Jr. 0.78 kg (1.7 lb)[d]
Data Deficient
0!
Lepilemur White-footed 1894, 00600 !
leucopus Sportive Lemur Forsyth Major 0.6 kg (1.3 lb)
Data Deficient
0!
00800 !
Lepilemur Small-toothed 1894,
0.8–1.0 kg (1.8–
microdon Sportive Lemur Forsyth Major
2.2 lb)
Data Deficient
0!
Daraina 2006, Louis, 00720 !
Lepilemur milanoii
Sportive Lemur Jr. 0.72 kg (1.6 lb)[d]
Data Deficient
0!
Lepilemur Mittermeier's 2006,
unknown
mittermeieri Sportive Lemur Rabarivola et al.
Data Deficient
Lepilemur Weasel Sportive 1851, I. 01000 ! 0!

mustelinus Lemur Geoffroy 1 kg (2.2 lb)
Data Deficient
0!
Otto's Sportive 2007, Craul
Lepilemur otto unknown
Lemur et al.
Data Deficient
0!
Petter's Sportive 2006, Louis, 00630 !
Lepilemur petteri
Lemur Jr. 0.63 kg (1.4 lb)[d]
Data Deficient
0!
2006, 00660 !
Lepilemur Randrianasolo's
Andriaholinirina et 0.66–0.88 kg
randrianasoloi Sportive Lemur
al. (1.5–1.9 lb)[d]
Data Deficient
0!
00760 !
Lepilemur Red-tailed 1867, A.
0.76–0.95 kg
ruficaudatus Sportive Lemur Grandidier
(1.7–2.1 lb)
Data Deficient
Lepilemur Sahamalaza 2006, 00687 ! 0!

sahamalazensis Sportive Lemur Andriaholinirina et 0.687–0.892 kg
al. (1.51–1.97 lb)[d]
Data Deficient
0!
Lepilemur Scott's Sportive 2008, Lei et
unknown
scottorum Lemur al.
Data Deficient
0!
Seal's Sportive 2006, Louis, 00950 !
Lepilemur seali
Lemur Jr. 0.95 kg (2.1 lb)[d]
Data Deficient
5!
Lepilemur Northern 1975, 00750 !
septentrionalis Sportive Lemur Rumpler & Albignac 0.75 kg (1.7 lb)
Critically Endange
0!
Lepilemur Hawks' Sportive 2006, Louis, 00880 !
tymerlachsonorum Lemur Jr. 0.88 kg (1.9 lb)[d]
Data Deficient
0!
Lepilemur Wright's 2006, Louis, 00950 !
wrightae Sportive Lemur Jr. 0.95 kg (2.1 lb)[d]
Data Deficient
Lepilemur Holland's 2009, 00990 !

0 !Not Evaluated
hollandorum Sportive Lemur Ramaromilanto et al. 0.99 kg (2.2 lb)[d]
[edit] Family: Indriidae

Family Indriidae consists of the Indri (the largest extant lemur), the woolly lemurs and the sifakas.
There are 19 extant species.
The Indri is one of the two largest extant lemurs.
Sifakas are vertical clingers and jumpers and are represented by 9 species.
Average
Scientific name Common name Classified Conservatio
size
0
2007,
Betsileo Woolly
Avahi betsileo Andriantompohavana et unknown
Lemur
al.
Data D
4
Cleese's Woolly 2005, Thalmann 00830 !
Avahi cleesei
Lemur and Geissmann 0.83 kg (1.8 lb)[d]
Endan
1
00900 !
Eastern Woolly
Avahi laniger 1788, Gmelin 0.9–1.3 kg (2.0–
Lemur
2.9 lb)
Least C
Avahi Southern Woolly 2006, Zaramody unknown 0

meridionalis Lemur et al.
Data D
Moore's Woolly
Avahi mooreorum 2008, Lei et al. unknown -1 !Not E
Lemur
4
00700 !
Avahi Western Woolly 1898, von
0.7–0.9 kg (1.5–
occidentalis Lemur Lorenz-Liburnau
2.0 lb)
Endan
0
Peyrieras' Woolly 2006, Zaramody
Avahi peyrierasi unknown
Lemur et al.
Data D
0
Avahi Ramanantsoavana's 2006, Zaramody
unknown
ramanantsoavani Woolly Lemur et al.
Data D
0
00700 !
Sambirano Woolly 2000, Thalmann
Avahi unicolor 0.7–1 kg (1.5–2.2
Lemur and Geissmann
lb)[d]
Data D
4
06000 !6–
Indri indri Indri 1788, Gmelin
9.5 kg (13–21 lb)
Endan
5
Propithecus 1871, A. 05000 !5–
Silky Sifaka
candidus Grandidier 6 kg (11–13 lb)
Critically E
4
03700 !
Propithecus 1867, A.
Coquerel's Sifaka 3.7–4.3 kg (8.2–
coquereli Grandidier
9.5 lb)
Endan
4
03500 !
Propithecus 1871, Milne-
Crowned Sifaka 3.5–4.3 kg (7.7–
coronatus Edwards
9.5 lb)
Endan
3
Propithecus Van der Decken's 1870, A. 03000 !3–
deckenii Sifaka Grandidier 4.5 kg (6.6–9.9 lb)
Vulne
4
Propithecus 06000 !6–
Diademed Sifaka 1832, Bennett
diadema 8.5 kg (13–19 lb)
Endan
4
Propithecus Milne-Edwards' 1871, A. 05000 !5–
edwardsi Sifaka Grandidier 6.5 kg (11–14 lb)
Endan
5
04300 !
Propithecus
Perrier's Sifaka 1931, Lavauden 4.3–5 kg (9.5–11
perrieri
lb)
Critically E
4
03400 !
Propithecus Golden-crowned
1988, Simons 3.4–3.6 kg (7.5–
tattersalli Sifaka
7.9 lb)
Endan
3
Propithecus 1867, A. 03000 !3–
Verreaux's Sifaka
verreauxi Grandidier 3.5 kg (6.6–7.7 lb)
Vulne
[edit] Family: Daubentoniidae

Family Daubentoniidae contains only one surviving species, of the Aye-aye. Wide ranging genetic
studies have shown that it separated from the ancestral lemurs long before any other branch of the modern
Lemuriformes.[3]
The Aye-aye has many physical traits unique for a primate and is represented by a single extant
species.
Common Average
Scientific name Classified Conservation status
name size
2!
Daubentonia 1788, 2.5 kg
Aye-aye
madagascariensis Gmelin (5.5 lb) [25
Near Threatened
[edit] Extinct species
Main article: Subfossil lemur
All known extinct lemurs from Madagascar are known from recent, subfossil remains.[253]
Conditions for fossilization were not ideal on the island, so little is known about ancestral lemur populations.
All known extinct lemurs are thought to have died out after the arrival of humans.
Common Estimated Extinction

Scientific name name Family date
size
160000 !
Archaeoindris Sloth
Palaeopropithecidae 160–200 kg (350– 1600 CE
fontoynonti lemurs [256
440 lb)
Monkey
Archaeolemur 015000 ! 1047–
lemurs (or Baboon Archaeolemuridae
edwardsi 15–25 kg (33–55 lb) 1280 CE
lemurs)
Monkey
Archaeolemur 015000 ! 1047–
majori 15–25 kg (33–55 lb) 1280 CE
lemurs)
Babakotia radofilai Sloth Palaeopropithecidae 016000 ! 3050

lemurs 16–20 kg (35–44 lb) BCE[c]
Daubentonia Giant Aye- 014000 ! 891–1027

Daubentoniidae
robusta aye 14 kg (31 lb) CE
Monkey
Hadropithecus 027000 ! 444–772
stenognathus 27–35 kg (60–77 lb) CE
lemurs)
040000 !
Megaladapis Koala 1280–
Megaladapidae 40–80 kg (88–180
edwardsi lemurs 1420 CE
lb)
040000 !
grandidieri lemurs 1420 CE
lb)
040000 !
madagascariensis lemurs 1420 CE
lb)
Mesopropithecus Sloth 010000 ! 245–429

Palaeopropithecidae
dolichobrachion lemurs 10–14 kg (22–31 lb) CE

Palaeopropithecidae
globiceps lemurs 10–14 kg (22–31 lb) CE
Palaeopropithecidae
pithecoides lemurs 10–14 kg (22–31 lb) CE
Pachylemur 010000 ! 1280–

Pachylemur Lemuridae
insignis 10–13 kg (22–29 lb) 1420 CE
010000 ! 1280–
Pachylemur jullyi Pachylemur Lemuridae
10–13 kg (22–29 lb) 1420 CE
027000 !
Palaeopropithecus Sloth 1300–
Palaeopropithecidae 25–50 kg (55–110
ingens lemurs 1620 CE
lb)
Palaeopropithecus Sloth 035000 !

Palaeopropithecidae unknown
kelyus lemurs 35 kg (77 lb)
027000 !
Palaeopropithecus Sloth 1300–
Palaeopropithecidae 25–50 kg (55–110
maximus lemurs 1620 CE
lb)
[edit] Footnotes
• a In 2008, the Red Lemur, Eulemur rufus, was split into two species, Eulemur rufus (Red
Lemur) and Eulemur rufifrons (Red-fronted Lemur). Also, Eulemur rufus was previously known as the
Red-fronted lemur, but was renamed the Red Lemur, while Eulemur rufifrons assumed its former
name.[3]
• b Formerly referred to as Eulemur albocollaris or White-collared Brown Lemur, but was
changed in 2008.[3]
• c This extinction date for Babakotia radofilai is based on a single radiocarbon date from one
specimen. For this reason, it is hard to tell when this species became extinct or how it is related to
other lemur species.[254]
• d Average weights reported for this species are based on very small sample sizes or are
general ranges for its genus and thus require further research.
[edit] Notes
1. ^ Mittermeier et al. 2010, pp. 101–103
2. ^ Mittermeier et al. 2010, pp. 86–87
3. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af ag ah ai aj ak al am an ao ap aq ar as at au
av aw ax ay az ba bb bc bd be bf bg bh bi bj bk bl bm bn bo bp bq br bs bt bu bv bw bx by bz ca cb cc cd ce cf cg ch ci cj
ck cl cm cn co cp cq cr cs ct cu cv cw cx
Mittermeier, R. A.; Ganzhorn, J. U.; Konstant, W. R.; Glander, K.;
Tattersall, I.; Groves, C. P.; Rylands, A. B.; Hapke, A. et al. (2008). "Lemur Diversity in Madagascar"
(PDF). International Journal of Primatology 29 (6): 1607–1656. doi:10.1007/s10764-008-9317-y.
http://www.aeecl.org/documents/28.pdf. edit
4. ^ Yoder, A.D. (2007). "Lemurs: a quick guide". Current Biology 17 (20): 866–868.
http://www.biology.duke.edu/yoderlab/reprints/2007YoderCB.pdf.
5. ^ Tattersall, I. (2007). "Madagascar's Lemurs: Cryptic diversity or taxonomic inflation?".
Evolutionary Anthropology: Issues, News, and Reviews 16: 12–23. doi:10.1002/evan.20126. edit
6. ^ a b c d e Mittermeier, pp. 50–51
7. ^ a b Gommery, D.; Ramanivosoa, B.; Tombomiadana-Raveloson, S.; Randrianantenaina, H.;
Kerloc’h, P. (2009). "A new species of giant subfossil lemur from the North-West of Madagascar
(Palaeopropithecus kelyus, Primates)". Comptes Rendus Palevol 8 (5): 471–480.
doi:10.1016/j.crpv.2009.02.001. Lay summary (27 May 2009). edit
8. ^ Groves, C. (2005). "Strepsirrhini". In Wilson, D. E., & Reeder, D. M, eds. Mammal Species
of the World (3rd ed.). Baltimore: Johns Hopkins University Press. ISBN 0-801-88221-4.
OCLC 62265494. http://www.bucknell.edu/msw3/browse.asp?id=12100002.
9. ^ Godinot, M. (2006). "Lemuriform Origins as Viewed from the Fossil Record". Folia
Primatologica 77 (6): 446–464. doi:10.1159/000095391. PMID 17053330. edit
10.^ Cartmill 2010, pp. 10–30
11.^ Mittermeier, pp. 130–135
12.^ Groves, C. (2005). "Allocebus trichotis". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. p. 111. ISBN 0-801-
88221-4. OCLC 62265494. http://www.bucknell.edu/msw3/browse.asp?id=12100007.
13.^ Andrainarivo, C., Andriaholinirina, V. N., Feistner, A., Felix, T., Ganzhorn, J., Garbutt, N.,
Golden, C., Konstant, B., Louis Jr., E., Meyers, D., Mittermeier, R. A., Perieras, A., Princee, F.,
Rabarivola, J. C., Rakotosamimanana, B., Rasamimanana, H., Ratsimbazafy, J., Raveloarinoro, G.,
Razafimanantsoa, A., Rumpler, Y., Schwitzer, C., Thalmann, U., Wilmé, L. & Wright, P. (2008).
Allocebus trichotis. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January
2009.
15.^ Garbutt, pp. 103–104
16.^ Groves, C. (2005). "Cheirogaleus crossleyi". In Wilson, D. E., & Reeder, D. M, eds.
Mammal Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. pp. 111–112.
ISBN 0-801-88221-4. OCLC 62265494. http://www.bucknell.edu/msw3/browse.asp?id=12100010.
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January 2009.
19.^ Groves, C. (2005). "Cheirogaleus major". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Cheirogaleus major. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
22.^ Groves, C. (2005). "Cheirogaleus medius". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Cheirogaleus medius. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
24.^ Mittermeier, p. 166
25.^ Groves, C. (2005). "Cheirogaleus minusculus". In Wilson, D. E., & Reeder, D. M, eds.
Mammal Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. p. 112. ISBN 0-
801-88221-4. OCLC 62265494. http://www.bucknell.edu/msw3/browse.asp?id=12100013.
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28.^ Groves, C. (2005). "Cheirogaleus sibreei". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. ISBN 0-801-88221-4.
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January 2009.
31.^ Groves, C. (2005). "Microcebus berthae". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Microcebus berthae. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
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33.^ Garbutt, pp. 98–99
34.^ Hoffmann, M. (2008). Microcebus bongolavensis. In: IUCN 2008. IUCN Red List of
Threatened Species. Downloaded on 1 January 2009.
35.^ Garbutt, p. 99
36.^ Hoffmann, M. (2008). Microcebus danfossorum. In: IUCN 2008. IUCN Red List of
38.^ Groves, C. (2005). "Microcebus griseorufus". In Wilson, D. E., & Reeder, D. M, eds.
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January 2009.
40.^ Hoffmann, M. (2008). Microcebus jollyae. In: IUCN 2008. IUCN Red List of Threatened
Species. Downloaded on 1 January 2009.
42.^ Roos, C., Kappeler, P. & Hoffmann, M. (2008). Microcebus lehilahytsara. In: IUCN 2008.
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43.^ Garbutt, pp. 97–98
44.^ Hoffmann, M. (2008). Microcebus mamiratra. In: IUCN 2008. IUCN Red List of Threatened
45.^ Hoffmann, M. (2008). Microcebus mittermeieri. In: IUCN 2008. IUCN Red List of
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Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. p. Microcebus murinus.
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50.^ Groves, C. (2005). "Microcebus myoxinus". In Wilson, D. E., & Reeder, D. M, eds. Mammal
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53.^ Groves, C. (2005). "Microcebus ravelobensis". In Wilson, D. E., & Reeder, D. M, eds.
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56.^ Groves, C. (2005). "Microcebus rufus". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Microcebus rufus. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January
2009.
59.^ Groves, C. (2005). "Microcebus sambiranensis". In Wilson, D. E., & Reeder, D. M, eds.
Microcebus sambiranensis. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
61.^ Hoffmann, M. (2008). Microcebus simmonsi. In: IUCN 2008. IUCN Red List of Threatened
63.^ Groves, C. (2005). "Microcebus tavaratra". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Microcebus tavaratra. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
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65.^ a b Louis, E. E.; Engberg, S. E.; McGuire, S. M.; McCormick, M. J.; Randriamampionona,
R.; Ranaivoarisoa, J. F.; Bailey, C. A.; Mittermeier, R. A. et al. (2008). "Revision of the Mouse
Lemurs, Microcebus (Primates, Lemuriformes), of Northern and Northwestern Madagascar with
Descriptions of Two New Species at Montagne d'Ambre National Park and Antafondro Classified
Forest" (PDF). Primate Conservation 23: 19–38. doi:10.1896/052.023.0103. http://www.primate-
sg.org/PDF/PC23.new.microcebus.V3.pdf. re edit
67.^ Groves, C. (2005). "Mirza coquereli". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Razafimanantsoa, A., Roos, C., Rumpler, Y., Schwitzer, C., Thalmann, U., Wilmé, L. & Wright, P.
(2008). Mirza coquereli. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
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70.^ Hoffmann, M. (2008). Mirza zaza. In: IUCN 2008. IUCN Red List of Threatened Species.
Downloaded on 1 January 2009.
71.^ a b c Garbutt, pp. 111–114
72.^ a b Mittermeier, pp. 181–182
73.^ Groves, C. (2005). "Phaner electromontis". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Phaner electromontis. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
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76.^ Groves, C. (2005). "Phaner furcifer". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Phaner furcifer. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January
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79.^ Groves, C. (2005). "Phaner pallescens". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Phaner pallescens. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January
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81.^ Groves, C. (2005). "Phaner parienti". In Wilson, D. E., & Reeder, D. M, eds. Mammal
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84.^ Groves, C. (2005). "Eulemur albifrons". In Wilson, D. E., & Reeder, D. M, eds. Mammal
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87.^ Groves, C. (2005). "Eulemur cinereiceps". In Wilson, D. E., & Reeder, D. M, eds. Mammal
88.^ Andrainarivo, C., Andriaholinirina, V.N., Feistner, A., Felix, T., Ganzhorn, J., Garbutt, N.,
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Rabarivola, J.C., Rakotosamimanana, B., Rasamimanana, H., Ratsimbazafy, J., Raveloarinoro, G.,
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90.^ Groves, C. (2005). "Eulemur collaris". In Wilson, D. E., & Reeder, D. M, eds. Mammal
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(2008). Eulemur macaco ssp. flavifrons. In: IUCN 2008. IUCN Red List of Threatened Species.
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104.^ Groves, C. (2005). "Eulemur mongoz". In Wilson, D. E., & Reeder, D. M, eds. Mammal
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151.^ Garbutt, pp. 130–131
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170.^ Garbutt, p. 134
171.^ Hoffmann, M. (2008). Lepilemur hubbardorum. In: IUCN 2008. IUCN Red List of
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175.^ Groves, C. (2005). "Lepilemur leucopus". In Wilson, D. E., & Reeder, D. M, eds. Mammal
176.^ Hoffmann, M. (2008). Lepilemur leucopus. In: IUCN 2008. IUCN Red List of Threatened
178.^ Groves, C. (2005). "Lepilemur microdon". In Wilson, D. E., & Reeder, D. M, eds. Mammal
179.^ Hoffmann, M. (2008). Lepilemur microdon. In: IUCN 2008. IUCN Red List of Threatened
180.^ Garbutt, p. 122
181.^ Hoffmann, M. (2008). Lepilemur milanoii. In: IUCN 2008. IUCN Red List of Threatened
182.^ Hoffmann, M. (2008). Lepilemur mittermeieri. In: IUCN 2008. IUCN Red List of
Threatened Species. Downloaded on 3 May 2009.
184.^ Groves, C. (2005). "Lepilemur mustelinus". In Wilson, D. E., & Reeder, D. M, eds.
Mammal Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. pp. 118–119.
Lepilemur mustelinus. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
186.^ Hoffmann, M. (2008). Lepilemur otto. In: IUCN 2008. IUCN Red List of Threatened
187.^ Garbutt, pp. 134–135
188.^ Hoffmann, M. (2008). Lepilemur petteri. In: IUCN 2008. IUCN Red List of Threatened
189.^ Garbutt, p. 132
190.^ Hoffmann, M. (2008). Lepilemur randrianasoloi. In: IUCN 2008. IUCN Red List of
192.^ Groves, C. (2005). "Lepilemur ruficaudatus". In Wilson, D. E., & Reeder, D. M, eds.
193.^ Garbutt, pp. 127–128
194.^ Olivieri, G., Schwitzer, C., Schwitzer, N. & Craul, M. (2008). Lepilemur sahamalazensis.
In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January 2009.
195.^ Garbutt, pp. 120–121
196.^ Hoffmann, M. (2008). Lepilemur seali. In: IUCN 2008. IUCN Red List of Threatened
198.^ Groves, C. (2005). "Lepilemur septentrionalis". In Wilson, D. E., & Reeder, D. M, eds.
Lepilemur septentrionalis. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
200.^ Garbutt, pp. 126–127
201.^ Hoffmann, M. (2008). Lepilemur tymerlachsonorum. In: IUCN 2008. IUCN Red List of
202.^ Garbutt, pp. 119–120
203.^ Hoffmann, M. (2008). Lepilemur wrightae. In: IUCN 2008. IUCN Red List of Threatened
204.^ Ramaromilanto, B.; Lei, R.; Engberg, S.E.; Johnson, S.E.; Sitzmann, B.D.; Louis, Jr., E.E.
(2009). "Description of a new sportive lemur, Holland's or Mananara-Nord sportive lemur, from
Mananara-Nord Biosphere Reserve, Madagascar". Occasional Papers (Museum of Texas Tech
University) (286): 1–22. ISSN 0149-175X.
http://www.nsrl.ttu.edu/publications/opapers/ops/OP286.pdf. Retrieved 2009-05-23.
205.^ Hoffmann, M. (2008). Avahi betsileo. In: IUCN 2008. IUCN Red List of Threatened
207.^ Thalmann, U., Geissmann, T. & Hoffmann, M. (2008). Avahi cleesei. In: IUCN 2008. IUCN
Red List of Threatened Species. Downloaded on 1 January 2009.
209.^ Groves, C. (2005). "Avahi laniger". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Razafimanantsoa, A., Rumpler, Y., Schwitzer, C., Thalmann, U., Wilmé, L. & Wright, P. (2008). Avahi
laniger. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January 2009.
211.^ Hoffmann, M. (2008). Avahi meridionalis. In: IUCN 2008. IUCN Red List of Threatened
213.^ Groves, C. (2005). "Avahi occidentalis". In Wilson, D. E., & Reeder, D. M, eds. Mammal
occidentalis. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January 2009.
215.^ Hoffmann, M. (2008). Avahi peyrierasi. In: IUCN 2008. IUCN Red List of Threatened
216.^ Hoffmann, M. (2008). Avahi ramanantsoavanai. In: IUCN 2008. IUCN Red List of
218.^ Garbutt, pp. 180–181
219.^ Groves, C. (2005). "Avahi unicolor". In Wilson, D. E., & Reeder, D. M, eds. Mammal
unicolor. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January 2009.
222.^ Groves, C. (2005). "Indri indri". In Wilson, D. E., & Reeder, D. M, eds. Mammal Species of
the World (3rd ed.). Baltimore: Johns Hopkins University Press. p. 120. ISBN 0-801-88221-4.
Razafimanantsoa, A., Rumpler, Y., Schwitzer, C., Thalmann, U., Wilmé, L. & Wright, P. (2008). Indri
indri. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1 January 2009.
225.^ Groves, C. (2005). "Propithecus candidus". In Wilson, D. E., & Reeder, D. M, eds.
Golden, C., Konstant, B., Louis Jr., E., Meyers, D., Mittermeier, R. A., Patel, E., Perieras, A., Princee,
F., Rabarivola, J. C., Rakotosamimanana, B., Rasamimanana, H., Ratsimbazafy, J., Raveloarinoro,
G., Razafimanantsoa, A., Rumpler, Y., Schwitzer, C., Thalmann, U., Wilmé, L. & Wright, P. (2008).
Propithecus candidus. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
228.^ Groves, C. (2005). "Propithecus coquereli". In Wilson, D. E., & Reeder, D. M, eds.
Propithecus coquereli. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
231.^ Groves, C. (2005). "Propithecus coronatus". In Wilson, D. E., & Reeder, D. M, eds.
Propithecus coronatus. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
234.^ Groves, C. (2005). "Propithecus deckenii". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Propithecus deckenii. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
237.^ Groves, C. (2005). "Propithecus diadema". In Wilson, D. E., & Reeder, D. M, eds.
Propithecus diadema. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
240.^ Groves, C. (2005). "Propithecus edwardsi". In Wilson, D. E., & Reeder, D. M, eds.
Propithecus edwardsi. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
243.^ Groves, C. (2005). "Propithecus perrieri". In Wilson, D. E., & Reeder, D. M, eds. Mammal
Propithecus perrieri. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
246.^ Groves, C. (2005). "Propithecus tattersalli". In Wilson, D. E., & Reeder, D. M, eds.
248.^ Groves, C. (2005). "Propithecus verreauxi". In Wilson, D. E., & Reeder, D. M, eds.
Propithecus verreauxi. In: IUCN 2008. IUCN Red List of Threatened Species. Downloaded on 1
January 2009.
251.^ Groves, C. (2005). "Daubentonia madagascariensis". In Wilson, D. E., & Reeder, D. M,
eds. Mammal Species of the World (3rd ed.). Baltimore: Johns Hopkins University Press. p. 121.
252.^ Andrainarivo, C., et. al. (2008). Daubentonia madagascariensis. In: IUCN 2008. IUCN Red
List of Threatened Species. Downloaded on 1 January 2009.
254.^ a b c d e f g h Mittermeier, pp. 44–46
255.^ a b c d e f g Nowak, pp. 89–91
256.^ William L. Jungers, Laurie R. Godfrey, Elwyn L. Simons, and Prithijit S. Chatrath (1997-
10-28). "Phalangeal curvature and positional behavior in extinct sloth lemurs (Primates,
Palaeopropithecidae)". PNAS Proceedings of the National Academy of Sciences of the United States
of America 94 (22): 11998–12001.
257.^ a b c d e Mittermeier, p. 43
258.^ a b c Nowak, pp. 91–92
260.^ Nowak, p. 92
261.^ a b c Mittermeier, pp. 46–49
262.^ a b c Nowak, p. 83
263.^ a b Nowak, p. 77
[edit] References
• Garbutt, N. (2007). Mammals of Madagascar, A Complete Guide. A&C Black Publishers.
ISBN 978-0-300-12550-4.
• Mittermeier, R.A.; Louis, E.E.; Richardson, M.; Schwitzer, C.; Langrand, O.; Rylands, A.B.;
Hawkins, F.; Rajaobelina, S. et al. (2010). Lemurs of Madagascar. Illustrated by S.D. Nash (3rd ed.).
Conservation International. ISBN 978-1-934151-23-5.
• Mittermeier, R.A.; Konstant, W.R.; Hawkins, F.; Louis, E.E.; Langrand, O.; Ratsimbazafy, J.;
Rasoloarison, R.; Ganzhorn, J.U. et al. (2006). Lemurs of Madagascar. Illustrated by S.D. Nash (2nd
ed.). Conservation International. ISBN 1-881173-88-7.
• Nowak, Ronald M. (1999). Walker's Primates of the World. Johns Hopkins University Press.
ISBN 0-8018-6251-5.
• Platt, M.; Ghazanfar, A., eds (2010). Primate Neuroethology. Oxford University Press.
ISBN 978-0195-32659-8.
• Cartmill, M. (2010). "Chapter 2: Primate Classification and Diversity". Primate
neuroethology. pp. 10–30. ISBN 9780195326598. http://books.google.com/?
id=hv28p1tCnnEC&pg=PA10&dq=lemuridae+cladogram#v=onepage&q&f=false.

• Too Many New Lemur Species? – Interview with Anne Yoder, Director of the Duke Lemur
Center
[edit] See also
• List of mammals of Madagascar
[hide]v · d · eList of mammals of Africa
Algeria · Angola · Benin · Botswana · Burkina Faso · Burundi · Cameroon ·

Cape Verde · Central African Republic · Chad · Comoros · Democratic Republic of
the Congo · Republic of the Congo · Côte d'Ivoire (Ivory Coast) · Djibouti · Egypt ·
Equatorial Guinea · Eritrea · Ethiopia · Gabon · The Gambia · Ghana · Guinea ·
Sovereign
Guinea-Bissau · Kenya · Lesotho · Liberia · Libya · Madagascar · Malawi · Mali ·
states
Mauritania · Mauritius · Morocco · Mozambique · Namibia · Niger · Nigeria ·
Rwanda · São Tomé and Príncipe · Senegal · Seychelles · Sierra Leone · Somalia ·
South Africa · Sudan · Swaziland · Tanzania · Togo · Tunisia · Uganda · Zambia ·
Zimbabwe
States with
limited Sahrawi Arab Democratic Republic · Somaliland
recognition
Dependencies, Canary Islands / Ceuta / Melilla / Plazas de soberanía (Spain) · Madeira

autonomies, (Portugal) · Mayotte / Réunion (France) · Puntland (Somalia) · Saint Helena /
other territories Ascension Island / Tristan da Cunha (United Kingdom) · Southern Sudan (Sudan) ·
Western Sahara · Zanzibar (Tanzania)
Retrieved from "http://en.wikipedia.org/wiki/List_of_lemur_species"
Categories: Regional mammals lists | Lemurs

W000
W000
Cladistics

For the scientific journal, see Cladistics (journal).
Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
Cladistics (Ancient Greek: κλάδος, klados, "branch") is a method of classifying species of organisms
into groups called clades, which consist of an ancestor organism and all its descendants (and nothing else).
For example, birds, dinosaurs, crocodiles, and all descendants (living or extinct) of their most recent common
ancestor form a clade.[1] In the terms of biological systematics, a clade is a single "branch" on the "tree of
life", a monophyletic group.
Cladistics can be distinguished from other taxonomic systems, such as phenetics, by its focus on
shared derived characters (synapomorphies). Systems developed earlier usually employed overall
morphological similarity to group species into genera, families and other higher level groups (taxa); cladistic
classifications (usually in the form of trees called cladograms) are intended to reflect the relative recency of
common ancestry or the sharing of homologous features. Cladistics is also distinguished by an emphasis on
parsimony and hypothesis testing (particularly falsificationism), leading to a claim that cladistics is more
objective than systems which rely on subjective judgements of relationship based on similarity.[2]
Cladistics originated in the work of the German entomologist Willi Hennig, who referred to it as
"phylogenetic systematics" (also the name of his 1966 book); the use of the terms "cladistics" and "clade"
was popularized by other researchers. The technique and sometimes the name have been successfully
applied in other disciplines: for example, to determine the relationships between the surviving manuscripts of
the Canterbury Tales.[3]
Cladists use cladograms — diagrams which show ancestral relations between species — to represent
the monophyletic relationships of species, termed sister-group relationships. This is interpreted as
representing phylogeny, or evolutionary relationships. Although traditionally such cladograms were
generated largely on the basis of morphological characters, genetic sequencing data and computational
phylogenetics are now very commonly used in the generation of cladograms.
Cladistics, either generally or in specific applications, has been criticized from its beginnings. A
decision as to whether a particular character is a synapomorphy or not may be challenged as involving
subjective judgements,[4] raising the issue of whether cladistics as actually practised is as objective as has
been claimed. Formal classifications based on cladistic reasoning are said to emphasize ancestry at the
expense of descriptive characteristics, and thus ignore biologically sensible, clearly defined groups which do
not fall into clades (e.g. reptiles as traditionally defined or prokaryotes).[5]
Contents
[hide]
• 1 History of cladistics
• 1.1 Cladistics as a successor to phenetics
• 2 Clades
• 2.1 Terminology for characters
• 2.2 Terminology for groups
• 2.3 Branch-based definitions of clade
• 3 Cladograms
• 4 Cladistics in taxonomy
• 4.1 Phylogenetic nomenclature contrasted with
traditional taxonomy
• 4.2 Paraphyletic groups discouraged
• 4.3 Complexity of the Tree of Life
• 4.4 PhyloCode approach to naming species
• 4.5 Example
• 4.6 Summary of advantages of phylogenetic
nomenclature
• 4.7 Summary of criticisms of phylogenetic
nomenclature
• 5 Application to other disciplines
• 6 See also
[edit] History of cladistics
The term clade was introduced in 1958 by Julian Huxley, cladistic by Cain and Harrison in 1960, and
cladist (for an adherent of Hennig's school) by Mayr in 1965.[6] Hennig referred to his own approach as
phylogenetic systematics. From the time of his original formulation until the end of the 1980s cladistics
remained a minority approach to classification. However in the 1990s it rapidly became the dominant method
of classification in evolutionary biology. Computers made it possible to process large quantities of data about
organisms and their characteristics. At about the same time the development of effective polymerase chain
reaction techniques made it possible to apply cladistic methods of analysis to biochemical and molecular
genetic features of organisms as well as to anatomical ones.[7]
[edit] Cladistics as a successor to phenetics

For some decades in the mid to late twentieth century, a commonly used methodology was phenetics
("numerical taxonomy"). This can be seen as a predecessor[8] to some methods of today's cladistics (namely
distance matrix methods such as neighbor-joining), but made no attempt to resolve phylogeny, only
similarities.
[edit] Clades
The yellow group (sauropsids) is monophyletic, the blue group (traditional reptiles) is paraphyletic,
and the red group (warm-blooded animals) is polyphyletic.
Main article: Clade
A clade is a group of taxa consisting only of an ancestor taxon and all of its descendant taxa. In the
diagram provided (a cladogram), it is hypothesized that all vertebrates, including ray-finned fishes
(Actinopterygii), had a common ancestor, and so form a clade. Within the vertebrates, all tetrapods, including
amphibians, mammals, reptiles (as traditionally defined) and birds, are hypothesized to have had a common
ancestor, and so also form a clade. The tetrapod ancestor was a descendant of the original vertebrate
ancestor, but is not an ancestor of any ray-finned fish living today.
An important caution is that any cladogram is a provisional hypothesis. Although unlikely, future
genetic or morphological evidence might suggest that ray-finned fish and amphibians share a common
ancestor that was not an ancestor of the other tetrapods. The new information would cause us to define a
ray-finned-fish-and-amphibian clade, altering the cladogram.
The relationship between clades can be described in several ways:
• A clade is basal to another clade if it contains that other clade as a subset within it. In the
example, the vertebrate clade is basal to the tetrapod and ray-finned fish clades. (Some authors have
used "basal" differently to mean a clade that is less species-rich than a sister clade, with such a
deficit being taken as an indication of 'primitiveness'. Others consider this usage to be incorrect.[9])
• A clade located within a clade is said to be nested within that clade. In the diagram, the
tetrapod clade is nested within the vertebrate clade.
• Two clades are sisters if they have an immediate common ancestor. In the diagram,
crocodiles and birds are sister clades, as are amphibians and amniotes.
[edit] Terminology for characters
The following terms are used to identify shared or distinct characters among groups:[10][11][12]
• Plesiomorphy ("close form") or ancestral state, also symplesiomorphy ("shared
plesiomorphy", i.e. "shared close form"), is a characteristic that is present at the base of a tree
(cladogram). Since a plesiomorphy that is inherited from the common ancestor may appear
anywhere in a tree, its presence provides no evidence of relationships within the tree. The traditional
definition of reptiles (the blue group in the diagram) includes being cold-blooded (i.e. not maintaining
a constant high body temperature), whereas birds are warm-blooded. Since cold-bloodedness is a
plesiomorphy, inherited from the common ancestor of traditional reptiles and birds, it should not be
used to define a group in a system based on cladistics.
• Apomorphy ("separate form") or derived state is a characteristic believed to have evolved
within the tree. It can thus be used to separate one group in the tree from the rest. Within the group
which shares the apomorphy it is a synapomorphy ("shared apomorphy", i.e. "shared separate
form"). For example, within the vertebrates, all tetrapods (and only tetrapods) have four limbs; thus,
having four limbs is an synapomorphy for tetrapods. All the tetrapods can legitimately be grouped
together because they have four limbs.
• Homoplasy is a characteristic shared by members of a tree but not present in their common
ancestor. It arises by convergence or reversion. Both mammals and birds are able to maintain a high
constant body temperature (i.e. they are 'warm-blooded'). However, the ancestors of each group did
not share this character, so it must have evolved independently. Mammals and birds should not be
grouped together on the basis that they are warm-blooded.
The terms (sym)plesiomorphy and (syn)apomorphy are relative and their application depends on the
position of a group within a tree. An apomorphy of one clade is a plesiomorphy of another contained within it.
For example, when trying to decide whether tetrapods should form a clade, an important question is whether
having four limbs is a synapomorphy of all the taxa to be included within Tetrapoda: did all the possible
members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not?
By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. The fact that
ostriches and rheas both have four limbs does not provide any support for putting them into a separate group
of 'flightless birds'. Using these two terms allows a greater precision in the discussion of homology, in
particular allowing clear expression of the hierarchical relationships among different homologies.
It can be difficult to decide whether a character is in fact the same, and thus can classified as a
synapomorphy which may identify a group, or whether it only appears to be the same, and is thus a
homoplasy which cannot identify a group. There is a danger of circular reasoning: assumptions about the
shape of a phylogenetic tree are used to justify decisions about characters, which are then used as evidence
for the shape of the tree. It has been argued that this kind of reasoning has been used by proponents of the
view that birds are nested within the theropod dinosaur clade.[13]
[edit] Terminology for groups

Three main types of group can be identified on the basis of their relationships in cladograms.[11][12]
[14] The three can be defined in two different but related ways, as shown in the table below. The first is in
terms of the shape of a set of nodes taken from a cladogram. In this approach, an 'ancestor node' is simply a
branching point in the diagram; it may or may not correspond to an actual ancestor. The second is in terms of
the characters of the taxa being classified and how these characters have been inherited. In this approach,
an ancestor is an actual taxon, whether currently known or not.
Term Node-based definition Character-based definition

Monophyly A monophyletic group of nodes A monophyletic group of taxa is
in a tree is one which includes all the characterized by one or more
nodes descended from their most recent synapomorphies: derived characters inherited
common ancestor node, plus the most by all members of the group from ancestors
recent common ancestor node, but no and not inherited by any other taxa. A
other nodes. monophyletic group is a 'clade'. A 'crown
group' is an example of a monophyletic group.
Paraphyly A paraphyletic group of nodes in A paraphyletic group of taxa is

a tree is one which is constructed by characterized by one or more
taking a monophyletic group and (sym)plesiomorphies: characters inherited
removing one or more smaller from ancestors but not present in all of their
monophyletic groups.[15] (Removing descendants. As a consequence, a
one group produces a singly paraphyletic group is truncated, in that it
paraphyletic group, removing two a excludes one or more monophyletic taxa from
doubly paraphylectic group, and so on. an initially monophyletic group. An alternative
[16]) A paraphyletic group is necessarily name is an 'evolutionary grade', refering to
non-monophyletic. the ancestral character state within the group.
A 'stem group' is an example of a paraphyletic
group.
Polyphyly A polyphyletic group of nodes in A polyphyletic group of taxa is

a tree is one which is neither characterized by by one or more
monophyletic nor paraphyletic. homoplasies: characters which have
converged or reverted so as to appear to be
the same but which have not been inherited
from common ancestors. As a consequence,
polyphyletic groups of taxa are totally artificial.
[edit] Branch-based definitions of clade

See also: Phylogenetic definitions
Three alternative ways to define a clade
The node-based definition of a monophyletic group (i.e. a clade) given above regards the lines in the
cladogram only as a way of showing connections between taxa. This is appropriate when considering only
living (extant) taxa; however, when extinct taxa are to be included in a cladogram, lines correspond to
sequences of ancestors. There are two alternative ways of defining a clade which explicitly take into account
the line below the branching point at the base of a clade.[17] These definitions are most notably set out in the
PhyloCode.
Consider how a clade combining A and B in the diagram can be defined.
• Node-based: The node-based definition specifies A+B as the last common ancestor of A and
B, and all descendants of that ancestor. It thus excludes from the clade the line below the junction of
A and B. Crown groups are a type of node-based clade.
• Branch-based: A branch-based definition specifies A+B as the first ancestor of A which is not
also an ancestor of C, and all descendants of that ancestor. It thus includes in the clade the line
below the junction of A and B. (This type of definition was originally called "stem-based", but this was
changed to avoid confusion with the term "stem group", which is parapyletic.) Total groups are a type
of branch-based clade.
• Apomorphy-based: An apomorphy-based definition specifies A+B as the first ancestor of A to
possess derived trait M homologously (that is, synapomorphically) with that trait in A, and all
descendants of that ancestor. It thus includes in the clade only that part of the line below the junction
of A and B which corresponds to ancestors possessing the apomorphy. The process of identifying
and naming groups based on apomorphies is the method that most resembles classical systematics,
with the proviso that cladistic taxa always denote a clade.
Note that these alternative definitions do not alter the classification of the tips of the tree, and so are
equivalent if only living (extant) taxa are being considered.
[edit] Cladograms
Main articles: Cladogram and Polytomy
Cladists use cladograms, diagrams which show ancestral relations between taxa, to represent the
evolutionary tree of life. Although traditionally such cladograms were generated largely on the basis of
morphological characters, molecular sequencing data and computational phylogenetics are now very
commonly used in the generation of cladograms.
The starting point of cladistic analysis is a group of species and molecular, morphological, or other
data characterizing those species. The end result is a tree-like relationship diagram called a cladogram,[18]
or sometimes a dendrogram (Greek for "tree drawing").[19] The cladogram graphically represents a
hypothetical evolutionary process. Cladograms are subject to revision as additional data become available.
The terms "evolutionary tree", and sometimes "phylogenetic tree" are often used synonymously with
cladogram[20] but others treat phylogenetic tree as a broader term that includes trees generated with a
nonevolutionary emphasis. In cladograms, all species lie at the leaves. The two taxa on either side of a split,
with a common ancestor and no additional descendents, are called "sister taxa" or "sister groups".[21] Each
subtree, whether it contains only two or a hundred thousand items, is called a "clade". Many cladists require
that all forks in a cladogram be 2-way forks. Some cladograms include 3-way or 4-way forks when there are
insufficient data to resolve the forking to a higher level of detail (see under phylogenetic tree).
For a given set of taxa, the number of distinct cladograms that can be drawn (ignoring which
cladogram best matches the taxon characteristics) is:[22]
Number of 2 3 4 5 6 7 8
taxa
Number of 1 3 15 105 945 10,395 135,135

rooted cladograms
This superexponential growth of the number of possible cladograms explains why manual creation of
cladograms becomes very difficult when the number of taxa is large. If a cladogram represents N taxa, the
number of levels (the "depth") in the cladogram is on the order of log 2(N).[23] For example, if there are 32
species of deer, a cladogram representing deer could be around 5 levels deep (because 2 5 = 32), although
this is really just the lower limit. A cladogram representing the complete tree of life, with about 10 million
species, could be about 23 levels deep. This formula gives a lower limit, with the actual depth generally a
larger value, because the various branches of the cladogram will not be uniformly deep. Conversely, the
depth may be shallower if forks larger than 2-way forks are permitted.
A cladogram tree has an implicit time axis,[24] with time running forward from the base of the tree to
the leaves of the tree. If the approximate date (for example, expressed as millions of years ago) of all the
evolutionary forks were known, those dates could be captured in the cladogram. Thus, the time axis of the
cladogram could be assigned a time scale (e.g. 1 cm = 1 million years), and the forks of the tree could be
graphically located along the time axis. Such cladograms are called scaled cladograms. Many cladograms
are not of this type, for a variety of reasons:
• They are built from species characteristics that cannot be readily dated (e.g. morphological
data in the absence of fossils or other dating information)
• When the characteristic data are DNA/RNA sequences, it is feasible to use sequence
differences to establish the relative ages of the forks, but converting those ages into actual years
requires a significant approximation of the rate of change[25]
• Even when the dating information is available, positioning the cladogram's forks along the
time axis in proportion to their dates may cause the cladogram to become difficult to understand or
hard to fit within a human-readable format
Cladistics makes no distinction between extinct and extant species,[26] and it is appropriate to
include extinct species in the group of organisms being analyzed. Cladograms that are based on DNA/RNA
generally do not include extinct species because DNA/RNA samples from extinct species are rare.
Cladograms based on morphology, especially morphological characteristics that are preserved in fossils, are
more likely to include extinct species.
[edit] Cladistics in taxonomy

Main article: Phylogenetic nomenclature
[edit] Phylogenetic nomenclature contrasted with traditional taxonomy
A highly resolved, automatically generated tree of life based on completely sequenced genomes[27]
Most taxonomists have used the traditional approaches of Linnaean taxonomy and later Evolutionary
taxonomy to organize life forms. These approaches use several fixed levels of a hierarchy, such as kingdom,
phylum, class, order, and family. Phylogenetic nomenclature does not feature those terms, because the
evolutionary tree is so deep and so complex that it is inadvisable to set a fixed number of levels.
Evolutionary taxonomy insists that groups reflect phylogenies. In contrast, Linnaean taxonomy allows
both monophyletic and paraphyletic groups as taxa. Since the early 20th century, Linnaean taxonomists have
generally attempted to make at least family- and lower-level taxa (i.e. those regulated by the codes of
nomenclature) monophyletic. Ernst Mayr in 1985 drew a distinction between the terms cladistics and
phylogeny: "It would seem to me to be quite evident that the two concepts of phylogeny (and their role in the
construction of classifications) are sufficiently different to require terminological distinction. The term
phylogeny should be retained for the broad concept of phylogeny, promoted by Darwin and adopted by most
students of phylogeny in the ensuing 90 years. The concept of phylogeny as mere genealogy should be
terminologically distinguished as cladistics. To lump the two concepts together terminologically could not
help but produce harmful equivocation." [28]
Willi Hennig's pioneering work provoked a spirited debate[29] about the relative merits of
phylogenetic nomenclature versus Linnaean or evolutionary taxonomy, which has continued down to the
present;[30] however Hennig did not advocate abandoning the Linnaean nomenclatural system. Some of the
debates in which the cladists were engaged had been running since the 19th century, but they were renewed
fervor,[31] as can be seen from the Foreword to Hennig (1979) by Rosen, Nelson, and Patterson:[32]
"Encumbered with vague and slippery ideas about adaptation, fitness, biological species and
natural selection, neo-Darwinism (summed up in the "evolutionary" systematics of Mayr and
Simpson) not only lacked a definable investigatory method, but came to depend, both for
evolutionary interpretation and classification, on consensus or authority."
Phylogenetic nomenclature strictly and exclusively follows phylogeny and has arbitrarily deep trees
with binary branching: each taxon corresponds to a clade. Linnaean taxonomy, while since the advent of
evolutionary theory following phylogeny, also may subjectively consider similarity and has a fixed hierarchy of
taxonomic ranks, and its taxa are not required to correspond to clades.
[edit] Paraphyletic groups discouraged
Many cladists discourage the use of paraphyletic groups in classification of organisms, because they
detract from cladistics' emphasis on clades (monophyletic groups). In contrast, proponents of the use of
paraphyletic groups argue that any dividing line in a cladogram creates both a monophyletic section above
and a paraphyletic section below. They also contend that paraphyletic taxa are necessary for classifying
earlier sections of the tree – for instance, the early vertebrates that would someday evolve into the family
Hominidae cannot be placed in any other monophyletic family. They also argue that paraphyletic taxa provide
information about significant changes in organisms' morphology, ecology, or life history – in short, that both
paraphyletic groups and clades are valuable notions with separate purposes.[ citation needed]
[edit] Complexity of the Tree of Life

The cladistic tree of life is a fractal:[33]
"The tree of life is inherently fractal-like in its complexity, .... Look closely at the 'lineage' of a
phylogeny ... and it dissolves into many smaller lineages, and so on, down to a very fine scale."
The overall shape of a dichotomous (bifurcating) tree is recursive; as a viewpoint zooms into the tree
of life, the same type of tree appears no matter what the scale. When extinct species are considered (both
known and unknown), the complexity and depth of the tree can be very large. Moreover the tree continues to
recreate itself by bifurcation, a series of events called fractal evolution.[34] Every single speciation event,
including all the species that are now extinct, represents an additional fork on the hypothetical, complete
cladogram of the tree of life.
The tree of life is a quasi-self-similar fractal; that is, the deep reconstruction is not as regular as the
shallow reconstruction.[35] By shallow Mishler means the most recent branching toward and at the tips, and
by deep the more ancient branches further back, which are harder to reconstruct and are missing unknown
extinct lines. In the shallow part of the tree, branching events are relatively regular; it is often possible to
estimate the times between them. In the deep part of the tree, "homology assessments" are "difficult" and the
times vary widely.[36] At this level Eldredge's and Gould's punctuated equilibrium applies, which
hypothesizes long periods of stability followed by punctuations of rapid speciation, based on the fossil record.
[edit] PhyloCode approach to naming species

A formal code of phylogenetic nomenclature, the PhyloCode,[37] is currently under development. It is
intended for use by both those who would like to abandon Linnaean taxonomy and those who would like to
use taxa and clades side by side. In several instances (see for example Hesperornithes) it has been
employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that
unambiguously places problematic groups in the evolutionary tree in a way that is consistent with current
knowledge.
[edit] Example
For example, Linnaean taxonomy contains the taxon Tetrapoda, defined morphologically as
vertebrates with four limbs (as well as animals with four-limbed ancestors, such as snakes), which is often
given the rank of superclass, and divides into the classes Amphibia, Reptilia, Aves, Mammalia.
Phylogenetic nomenclature also contains the taxon Tetrapoda (see the diagram under Clades
above), whose living members can be classified phylogenically as "the clade defined by the common
ancestor of amphibians and mammals", or more precisely the clade defined by the common ancestor of a
specific amphibian and mammal (or bird or snake). This definition gives us the Crown group tetrapods (or
Crown-Tetrapoda). A few primitive four legged ancestors (the Ichthyostegalia) fall outside Crown-Tetrapoda.
[38] An alternative is to define tetrapoda as all animals more closely related to mammals than to lungfish (our
nearest living non-tetrapod relatives). In this definition, the ichthyostegalians are included, together with a
host of fossil animals usually classed as crossopterygian fish. This wider definition is termed Pan-Tetrapoda.
A third option is to define Tetrapoda according to their apomorphy (their unique trait, i.e. having legs rather
than fins), a definition that yield the same group as the Linnaean taxon.
Non of the phylogenetic taxa as described above have a rank, and neither do its subtaxa. All the
subclades are contained within one another. The clades are not divided into several non-overlapping taxa (as
in traditional taxonomy), rather the clade is split into two clades at the first branching, a process repeated
throughout. With regards to the traditional classes, Aves and Mammalia are subclades, contained in the
subclade Amniota, while Reptilia and Amphibia are paraphyletic taxa, not clades.[39] Instead of classifying
non-mammalian, non-avian amniotes as reptiles, Amniota is divided into the two clades Sauropsida (which
contains birds and all living amniotes other than mammals, including all living traditional reptiles) and
Theropsida (mammals and the extinct mammal-like reptiles). Similarly, Amphibia can be split into the
Batrachomorpha (fossil amphibians more closely related to modern amphibians) and Reptiliomorpha, the
latter of which the amiotes is a sub-clade.[40] Ichthyostegalians and other Stem-tetrapods represent sister
groups from splits predating the Batrachomorpha/Reptilopmorpha split.[38]
Further information: Reptiles, History of Classification
[edit] Summary of advantages of phylogenetic nomenclature

Proponents of phylogenetic nomenclature enumerate key distinctions between phylogenetic
nomenclature and Linnaean taxonomy as follows:[41]
Phylogenetic Nomenclature Linnaean Taxonomy

Handles arbitrarily deep trees. Often must invent new level names (such as
superorder, suborder, infraorder, parvorder,
magnorder) to accommodate new discoveries. Biased
towards trees about 4 to 12 levels deep.
Discourages naming or use of groups that Acceptable to name and use paraphyletic
are not monophyletic groups
Primary goal is to reflect actual process of Primary goal is to group species based on
evolution morphological similarities
Assumes that the shape of the tree will New discoveries often require renaming or
change frequently with new discoveries releveling of Classes, Orders, and Kingdoms
[edit] Summary of criticisms of phylogenetic nomenclature

Critics of phylogenetic nomenclature include Ashlock,[42] Mayr,[43] and Williams.[44] Some of their
criticisms include:
Phylogenetic Nomenclature Linnaean Taxonomy
Limited to entities related by evolution or Supports groupings without reference to

ancestry evolution or ancestry
Does not include a process for naming Includes a process for giving unique names to
species species
Clade definitions emphasize ancestry at the Taxa definitions based on tangible

expense of descriptive characteristics characteristics
Ignores sensible, clearly defined paraphyletic Permits clearly defined groups such as
groups such as reptiles reptiles
Difficult to determine if a given species is in a Straightforward process to determine if a

clade or not (e.g. if clade X is defined as "most given species is in a taxon or not
recent common ancestor of A and B along with its
descendants", then the only way to determine if
species Y is in the clade is to perform a complex
evolutionary analysis)
Limited to organisms that evolved by Applicable to all organisms, regardless of

inherited traits; not applicable to organisms that evolutionary mechanism
evolved via complex gene sharing or lateral transfer
[edit] Application to other disciplines

The comparisons used to acquire data on which cladograms can be based are not limited to the field
of biology.[45] Any group of individuals or classes, hypothesized to have a common ancestor, and to which a
set of common characteristics may or may not apply, can be compared pairwise. Cladograms can be used to
depict the hypothetical descent relationships within groups of items in many different academic realms. The
only requirement is that the items have characteristics that can be identified and measured.
Recent attempts to use cladistic methods outside of biology address the reconstruction of lineages
in:
• Anthropology and archeology.[46] Compares cultures or artifacts using groups of cultural
traits or artifact features.
• Linguistics.[47] Compares languages using groups of linguistic features.
• Textual criticism or Stemmatics.[48] Compares manuscripts of the same work (original lost)
using groups of distinctive copying errors.
• Ethology.[49] Compares animal species using behavioral traits presumed hereditary.
[edit] See also

• Bauplan • Important • Phylogenomics
• Bioinformatics publications in • Phylogeography
• Biomathematics phylogenetics • Phylogenetic
• Coalescent theory • Language family comparative methods
• Computational • Maximum • Scientific
phylogenetics parsimony Classification
• Dendrogram • Molecular • Stratocladistics
• Evolution of phylogeny • Systematics
Mollusca • PhyloCode • Tree structure
• Last common • Phylogenetics • Three-taxon
ancestor • Phylogenetic analysis
network
• Phylogenetics
software

1. ^ Glossary entry "clade" Understanding Evolution. 2010. University of California Museum of
Paleontology.
2. ^ Phillips 2000
3. ^ "Canterbury Tales Project". http://www.canterburytalesproject.org. Retrieved 4 July 2009.
4. ^ James & Pourtless IV 2009, p. 21ff.
5. ^ Mayr 1974, p. 104: "Since birds and crocodilians (excluding all other living reptiles) are
derived from a common ancestor, his method [cladistics] forces the cladist to recognize a taxon for
birds and crocodilians together, even though this is a useless assemblage."
6. ^ Dupuis 1984
7. ^ Baron & Høeg 2005
8. ^ Mayr 1982, p. 221
9. ^ Krell & Cranston 2004
10.^ Patterson 1982, pp. 21–74
11.^ a b Patterson 1988
12.^ a b de Pinna 1991
13.^ James & Pourtless IV 2009, p. 25: "Synapomorphies are invoked to defend the hypothesis;
the hypothesis is invoked to defend the synapomorphies."
14.^ Patterson 1982
15.^ Many sources give a verbal definition of 'paraphyletic' which does not require the missing
groups to be monophyletic. However when diagrams are presented representing paraphyletic
groups, these invariably show the missing groups as monophyletic. See e.g. Wiley et al. 1991, p. 4.
16.^ Taylor 2003
17.^ de Queiroz & Gauthier 1994
18.^ Cracraft & Donaghue 2004, pp. 45, 78, 555
19.^ Weygoldt 1998
20.^ Singh 2004, pp. 203–4
21.^ Gould 1983, p. 357
22.^ Lowe 2004, p. 164
23.^ Aldous & Pemantle 1996
24.^ Freeman 1998, p. 380
25.^ Carroll 1997, p. 80
26.^ Scott-Ram 1990, p. 83
27.^ Letunic & Bork 2007
28.^ Mayr 1985
29.^ Wheeler 2000
30.^ Benton 2000
31.^ Hull 1988, pp. 232–276
32.^ Hennig 1979, p. ix
33.^ Mishler 2005, p. 57
34.^ Gordon 1999, p. 664
35.^ Mishler 2005, p. 62
36.^ Mishler 2005, p. 62: "In deep reconstruction problems, the branch events at issue
happened a relatively long time ago and the ... relative lengths of ... branches are often quite
different...."
37.^ Pennisi 2001
38.^ a b Clarck, J.A. (1997): Ichthyostega, Tree of Life website
39.^ Tudge 2002, p. 83
40.^ Benton 2004 – see also Taxonomic hierarchy of the vertebrates
41.^ Hennig 1975.
42.^ Ashlock 1971, Ashlock 1972, Ashlock 1974, Ashlock 1979.
43.^ Mayr 1974, Mayr 1978, Mayr & Bock 2002
44.^ Williams 1992
45.^ Mace, Clare & Shennan 2005, p. 1
46.^ Lipo et al. 2006
47.^ Oppenheimer 2006, pp. 290–300, 340–56
48.^ Robinson & O’Hara 1996
49.^ Jerison 2003, p. 254
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Systematics". University of California Museum of Paleontology.
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College. http://anthro.palomar.edu/animal/default.htm. Retrieved 21 January 2010.
• Robinson, Peter; O'Hara, Robert J. (1992). "Report on the Textual Criticism Challenge 1991".
rjohara.net. http://rjohara.net/darwin/files/bmcr. Retrieved 21 January 2010.
• Theobald, Douglas (1999-2004). "Phylogenetics Primer". The TalkOrigins Archive.
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Relevant



Retrieved from "http://en.wikipedia.org/wiki/Cladistics"
Categories: Phylogenetics
W000
Systematics

"Systematic" redirects here. For the band, see Systematic (band).
For other uses, see Systematics (disambiguation).
A comparison of phylogenetic and phenetic concepts
Biological systematics is the study of the diversification of life on the planet Earth, both past and
present, and the relationships among living things through time. Relationships are visualized as evolutionary
trees (synonyms: cladograms, phylogenetic trees, phylogenies). Phylogenies have two components,
branching order (showing group relationships) and branch length (showing amount of evolution).
Phylogenetic trees of species and higher taxa are used to study the evolution of traits (e.g., anatomical or
molecular characteristics) and the distribution of organisms (biogeography). Systematics, in other words, is
used to understand the evolutionary history of life on Earth.
"Systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) were
defined in relationship to one another as follows:[1]
Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific
names for organisms, (b) describes them, (c) preserves collections of them, (d) provides
classifications for the organisms, keys for their identification, and data on their distributions, (e)
investigates their evolutionary histories, and (f) considers their environmental adaptations. This
is a field with a long history that in recent years has experienced a notable renaissance,
principally with respect to theoretical content. Part of the theoretical material has to do with
evolutionary areas (topics e and f above), the rest relates especially to the problem of
classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above.
The term "systematics" is sometimes used synonymously with "taxonomy" and may be confused with
"scientific classification". However, Taxonomy is more specifically the identification, description, and naming
(i.e. nomenclature) of organisms[citation needed], while "classification" is focused on placing organisms
within hierarchical groups that show their relationships to other organisms. All of these biological disciplines
can be involved with extinct and extant organisms. However, systematics alone deals specifically with
relationships through time, and can be synonymous with phylogenetics, broadly dealing with the inferred
hierarchy of organisms.
Systematics uses taxonomy as a primary tool in understanding organisms, as nothing about an
organism's relationships with other living things can be understood without it first being properly studied and
described in sufficient detail to identify and classify it correctly. Scientific classifications are aids in recording
and reporting information to other scientists and to laymen. The systematist, a scientist who specializes in
systematics, must, therefore, be able to use existing classification systems, or at least know them well
enough to skillfully justify not using them.
Phenetic systematics was an attempt to determine the relationships of organisms through a measure
of similarity, considering plesiomorphies (ancestral traits) and apomorphies (derived traits) to be equally
informative. From the 20th century onwards, it was superseded by cladistics, which considers plesiomorphies
to be uninformative for an attempt to resolve the phylogeny of Earth's various organisms through time.
Today's systematists generally make extensive use of molecular biology and computer programs to study
organisms.
Systematics is fundamental to biology because it is the foundation for all studies of organisms, by
showing how any organism relates to other living things (ancestor-descendant relationships).
Systematics is also of major importance in understanding conservation issues because it attempts to
explain the Earth's biodiversity and could be used to assist in allocating limited means to preserve and
protect endangered species, by looking at, for example, the genetic diversity among various taxa of plants or
animals and deciding how much of that to preserve.
[edit] See also

• Cladistics - a popular methodology in systematics
• Phenetics - an obsolete methodology, predecessor to cladistics
• Phylogeny - what is analyzed in systematics and taxonomy
• 16S ribosomal RNA - the most intensively studied nucleic acid in phylogenetics
• Phylogenetic comparative methods - use of evolutionary trees to study biodiversity and
comparative biology
• Scientific classification - the result of research in systematics and taxonomy
• Taxonomy - a branch of the biological sciences related to systematics
[edit] References
[edit] Notes
1. ^ Michener, Charles D., John O. Corliss, Richard S. Cowan, Peter H. Raven, Curtis W.
Sabrosky, Donald S. Squires, and G. W. Wharton (1970). Systematics In Support of Biological
Research. Division of Biology and Agriculture, National Research Council. Washington, D.C. 25 pp.

• Schuh, Randall T. and Andrew V. Z. Brower. 2009. Biological Systematics: Principles and
Applications, 2nd edn. ISBN 978-0-8014-4799-0
• Simpson, Michael G. 2005. Plant Systematics. ISBN 978-0-12-644460-5

• Society of Australian Systematic Biologists
• Society of Systematic Biologists
Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of

Retrieved from "http://en.wikipedia.org/wiki/Systematics"
Categories: Evolutionary biology | Scientific classification

W000
Phylogenetics

"Phylogenesis" redirects here. For the science fiction novel, see Phylogenesis (novel).
Evolution
Adaptation
Genetic drift
Gene flow
Mutation
Natural selection
Speciation
Introduction
Evidence
History
Level of support
Modern synthesis
Social effect
Theory and fact
Cladistics
Ecological genetics
Molecular evolution
Phylogenetics
Population genetics
Systematics
In biology, phylogenetics ( /faɪlɵdʒɪˈnɛtɪks/) is the study of evolutionary relatedness among various
groups of organisms (for example, species or populations), which is discovered through molecular
sequencing data and morphological data matrices. The term phylogenetics is of Greek origin from the terms
phyle/phylon (φυλή/φῦλον), meaning "tribe, race", and genetikos (γενετικός), meaning "relative to birth" from
genesis (γένεσις, "birth"). Taxonomy, the classification, identification, and naming of organisms, has been
richly informed by phylogenetics but remains methodologically and logically distinct.[1]
The fields of phylogenetics and taxonomy overlap in the science of phylogenetic systematics – one
methodology of which is called "cladism" or "cladistics" where shared derived characters (synapomorphies)
are used to create ancestor-descendant trees (cladograms) and delimit taxa (clades).[2][3] In biological
systematics as a whole, phylogenetic analyses have become essential in researching the evolutionary tree of
life.
Contents
[hide]
• 1 Construction of a phylogenetic tree
• 2 Grouping of organisms
• 3 Molecular phylogenetics
• 4 Ernst Haeckel's recapitulation theory
• 5 Gene transfer
• 6 Taxon sampling and phylogenetic signal
• 7 Importance of missing data
• 8 Role of fossils
• 9 Homoplasy weighting
• 10 See also
• 11 References
[edit] Construction of a phylogenetic tree
Evolution is regarded as a branching process, whereby populations are altered over time and may
speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized in a
phylogenetic tree.
The problem posed by phylogenetics is that genetic data are only available for living taxa, and the
fossil records (osteometric data) contains less data and more-ambiguous morphological characters.[4] A
phylogenetic tree represents a hypothesis of the order in which evolutionary events are assumed to have
occurred.
Cladistics is the current method of choice to infer phylogenetic trees. The most commonly-used
methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference.
Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to
construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships.
All methods depend upon an implicit or explicit mathematical model describing the evolution of characters
observed in the species included, and are usually used for molecular phylogeny, wherein the characters are
aligned nucleotide or amino acid sequences.
[edit] Grouping of organisms
Phylogenetic groups, or taxa, can be monophyletic, paraphyletic, or polyphyletic.

There are some terms that describe the nature of a grouping in such trees. For instance, all birds and
reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow
in the diagram below) is called monophyletic. "Modern reptile" (cyan in the diagram) is a grouping that
contains a common ancestor, but does not contain all descendants of that ancestor (birds are excluded).
This is an example of a paraphyletic group. A grouping such as warm-blooded animals would include
only mammals and birds (red/orange in the diagram) and is called polyphyletic because the members of this
grouping do not include the most recent common ancestor.
[edit] Molecular phylogenetics

Main article: Molecular phylogenetics
The evolutionary connections between organisms are represented graphically through phylogenetic
trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly,
biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day
organisms. Fossils can aid with the reconstruction of phylogenies; however, fossil records are often too poor
to be of good help. Therefore, biologists tend to be restricted with analysing present-day organisms to identify
their evolutionary relationships. Phylogenetic relationships in the past were reconstructed by looking at
phenotypes, often anatomical characteristics. Today, molecular data, which includes protein and DNA
sequences, are used to construct phylogenetic trees.[5]
The overall goal of National Science Foundation's Assembling the Tree of Life activity (AToL) is to
resolve evolutionary relationships for large groups of organisms throughout the history of life, with the
research often involving large teams working across institutions and disciplines. Investigators are typically
supported for projects in data acquisition, analysis, algorithm development and dissemination in
computational phylogenetics and phyloinformatics. For example, RedToL aims at reconstructing the Red
Algal Tree of Life.
[edit] Ernst Haeckel's recapitulation theory
Genealogical tree suggested by Haeckel (1866)
During the late 19th century, Ernst Haeckel's recapitulation theory, or biogenetic law, was widely
accepted. This theory was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of an
organism exactly mirrors the evolutionary development of the species. Haeckel's early version of this
hypothesis [that the embryo mirrors adult evolutionary ancestors] has since been rejected, and the
hypothesis amended as the embryo's development mirroring embryos of its evolutionary ancestors. He was
accused by five professors of falsifying his images of embryos (See Ernst Haeckel). Most modern biologists
recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory,
or view them as supporting evidence for that theory. Donald I. Williamson suggested that larvae and embryos
represented adults in other taxa that have been transferred by hybridization (the larval transfer theory).[6][7]
However, Williamson's views do not represent mainstream thought in molecular biology,[8] and there is a
significant body of evidence against the larval transfer theory.[9]
[edit] Gene transfer

In general, organisms can inherit genes in two ways: vertical gene transfer and horizontal gene
transfer. Vertical gene transfer is the passage of genes from parent to offspring, and horizontal gene transfer
or lateral gene transfer occurs when genes jump between unrelated organisms, a common phenomenon in
prokaryotes.
Horizontal gene transfer has complicated the determination of phylogenies of organisms, and
inconsistencies in phylogeny have been reported among specific groups of organisms depending on the
genes used to construct evolutionary trees.
Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes)
based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages
of life with little or no horizontal gene transfer. Therefore, rRNAs are commonly recommended as molecular
clocks for reconstructing phylogenies.
This has been particularly useful for the phylogeny of microorganisms, to which the species concept
does not apply and which are too morphologically simple to be classified based on phenotypic traits.
[edit] Taxon sampling and phylogenetic signal

Owing to the development of advanced sequencing techniques in molecular biology, it has become
feasible to gather large amounts of data (DNA or amino acid sequences) to infer phylogenetic hypotheses.
For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes
(~16,000 nucleotides, in many animals). However, it has been proposed that it is more important to increase
the number of taxa in the matrix than to increase the number of characters, because the more taxa the more
robust is the resulting phylogenetic tree.[10]
This may be partly due to the breaking up of long branches. It has been argued that this is an
important reason to incorporate data from fossils into phylogenies where possible. Of course, phylogenetic
data that include fossil taxa are generally based on morphology, rather than DNA data. Using simulations,
Derrick Zwickl and David Hillis[11] found that increasing taxon sampling in phylogenetic inference has a
positive effect on the accuracy of phylogenetic analyses.
Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed
actually contain a useful phylogenetic signal, a term that is used generally to denote whether related
organisms tend to resemble each other with respect to their genetic material or phenotypic traits.[12]
Ultimately, however, there is no way to measure whether a particular phylogenetic hypothesis is accurate or
not, unless the "true" relationships among the taxa being examined are already known. The best result an
empirical systematist can hope to attain is a tree with branches well-supported by the available evidence.
[edit] Importance of missing data

In general, the more data that is available when constructing a tree, the more accurate and reliable
the resulting tree will be. Missing data is no less detrimental than simply having less data, although its impact
is greatest when most of the missing data is in a small number of taxa. The fewer characters that have
missing data, the better; concentrating the missing data across a small number of character states produces
a more robust tree.[13]
[edit] Role of fossils

Because many morphological characters involve embryological or soft-tissue characters that cannot
be fossilized, and the interpretation of fossils is more ambiguous than living taxa, it is sometimes difficult to
incorporate fossil data into phylogenies. However, despite these limitations, the inclusion of fossils is
invaluable, as they can provide information in sparse areas of trees, breaking up long branches and
constraining intermediate character states; thus, fossil taxa contribute as much to tree resolution as modern
taxa.[14]
Molecular phylogenies can reveal rates of diversification, but in order to track rates of origination,
extinction and patterns in diversification, fossil data must be incorporated.[15] Molecular techniques assume
a constant rate of diversification, which is rarely likely to be true; in some (but by no means all) cases, the
assumptions inherent in interpreting the fossil record (e.g. a complete and unbiased record) are closer to
being true than the assumption of a constant rate, making fossil insights more accurate than molecular
reconstructions.[15]
[edit] Homoplasy weighting
Certain characters are more likely to be evolved convergently than others; logically, such characters
should be given less weight in the reconstruction of a tree.[16] Unfortunately the only objective way to
determine convergence is by the construction of a tree – a somewhat circular method. Even so, weighting
homoplasious characters does indeed lead to better-supported trees.[16] Further refinement can be brought
by weighting changes in one direction higher than changes in another; for instance, the presence of thoracic
wings almost guarantees placement among the pterygote insects, although because wings are often lost
secondarily, their absence does not exclude a taxon from the group.[17]
[edit] See also

• Bauplan
• Bioinformatics
• Biomathematics
• Cladistics
• Coalescent theory
• Computational phylogenetics
• EDGE of Existence Programme
• Important publications in phylogenetics
• Language family
• Maximum parsimony
• Molecular phylogeny
• PhyloCode
• Joe Felsenstein
• Systematics
• Phylogenetic tree
• Phylogenetic network
• Phylogenetic nomenclature
• Phylogenetics software
• Phylogenetic tree viewers
• Phylogeography
• Phylodynamics
• Phylogenetic comparative methods
• Microbial phylogenetics
[edit] References
1. ^ Edwards AWF, Cavalli-Sforza LL Phylogenetics is that branch of life science,which deals
with the study of evolutionary relation among various groups of organisms,through molecular
sequencing data. (1964). Systematics Assoc. Publ. No. 6: Phenetic and Phylogenetic Classification.
ed. Reconstruction of evolutionary trees. pp. 67–76.
2. ^ Speer, Vrian (1998). "UCMP Glossary: Phylogenetics". UC Berkeley.
http://www.ucmp.berkeley.edu/glossary/glossary_1.html. Retrieved 2008-03-22.
3. ^ E.O. Wiley, D. Siegel-Causey, D.R. Brooks, V.A. Funk. 1991. The Compleat Cladist: A
Primer of Phylogenetic Procedures. Univ. Kansas Mus. Nat. Hist. (Lawrence, KS), Spec. Publ. No 19
online at Internet Archive
4. ^ Cavalli-Sforza, L. L.; Edwards, A. W. F. (1967). "Phylogenetic Analysis: Models and
Estimation Procedures". Evolution 21 (3): 550–570. doi:10.2307/2406616.
http://jstor.org/stable/2406616. edit
5. ^ Pierce, Benjamin A. (2007-12-17). Genetics: A conceptual Approach (3rd ed.). W. H.
Freeman. ISBN 978-0716-77928-5.
6. ^ Williamson DI (2003-12-31). "xviii". The Origins of Larvae (2nd ed.). Springer. pp. 261.
ISBN 978-1402-01514-4.
7. ^ Williamson DI (2006). "Hybridization in the evolution of animal form and life-cycle".
Zoological Journal of the Linnean Society 148: 585–602. doi:10.1111/j.1096-3642.2006.00236.x.
8. ^ John Timmer, "Examining science on the fringes: vital, but generally wrong", ARS
Technica, 9 November 2009
9. ^ Michael W. Hart, and Richard K. Grosberg, "Caterpillars did not evolve from
onychophorans by hybridogenesis", Proceedings of the National Academy of the Sciences , 30
October 2009 (doi: 10.1073/pnas.0910229106)
10.^ Wiens J (2006). "Missing data and the design of phylogenetic analyses". Journal of
Biomedical Informatics 39 (1): 34–42. doi:10.1016/j.jbi.2005.04.001. PMID 15922672.
11.^ Zwickl DJ, Hillis DM (2002). "Increased taxon sampling greatly reduces phylogenetic error".
Systematic Biology 51 (4): 588–598. doi:10.1080/10635150290102339. PMID 12228001.
12.^ Blomberg SP, Garland T Jr, Ives AR (2003). "Testing for phylogenetic signal in comparative
data: behavioral traits are more labile". Evolution 57 (4): 717–745. PMID 12778543. PDF
13.^ Prevosti, F. J.; Chemisquy, M. �A. A. (2009). "The impact of missing data on real
morphological phylogenies: influence of the number and distribution of missing entries". Cladistics
26: 326. doi:10.1111/j.1096-0031.2009.00289.x. edit
14.^ Cobbett, A.; Wilkinson, M.; Wills, M. (2007). "Fossils impact as hard as living taxa in
parsimony analyses of morphology". Systematic biology 56 (5): 753–766.
doi:10.1080/10635150701627296. PMID 17886145. edit
15.^ a b Quental, T.; Marshall, C. (2010). "Diversity dynamics: molecular phylogenies need the
fossil record". Trends in ecology & evolution (Personal edition) 25 (8): 434–441.
doi:10.1016/j.tree.2010.05.002. PMID 20646780. edit
16.^ a b Goloboff, P. A.; Carpenter, J. M.; Arias, J. S.; Esquivel, D. R. M. (2008). "Weighting
against homoplasy improves phylogenetic analysis of morphological data sets". Cladistics 24: 758.
doi:10.1111/j.1096-0031.2008.00209.x. edit
17.^ Goloboff, P. A. (1997). "Self-Weighted Optimization: Tree Searches and Character State
Reconstructions under Implied Transformation Costs". Cladistics 13: 225. doi:10.1111/j.1096-
0031.1997.tb00317.x. edit

• Schuh, R. T. and A. V. Z. Brower. 2009. Biological Systematics: principles and applications
(2nd edn.) ISBN 978-0-8014-4799-0

• The Tree of Life
• Interactive Tree of Life
• PhyloCode
• ExploreTree
• UCMP Exhibit Halls: Phylogeny Wing
• Filogenetica.org in Spanish
• PhyloPat, Phylogenetic Patterns
• SplitsTree, program for computing phylogenetic trees and unrooted phylogenetic networks
• Dendroscope, program for drawing phylogenetic trees and rooted phylogenetic networks
• Phylogenetic inferring on the T-REX server
• Mesquite
• Geneious Pro all-in-one phylogenetics software
• NCBI – Systematics and Molecular Phylogenetics
• What Genomes Can Tell Us About the Past – lecture on phylogenetics by Sydney Brenner
• Mikko's Phylogeny Archive
• Phylogenetic Reconstruction from Gene-Order Data
• ETE: A Python Environment for Tree Exploration This is a programming library to analyze,
manipulate and visualize phylogenetic trees. Ref.
• PhylomeDB A public database hosting thousands of gene phylogenies ranging many
different species.Ref.
Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of

Relevant

Retrieved from "http://en.wikipedia.org/wiki/Phylogenetics"
W000
Taxonomy

For the science of classifying living things, see biological classification and alpha taxonomy.
Look up taxonomy in Wiktionary, the free dictionary.
Taxonomy is the practice and science of classification. The word finds its roots in the Greek τάξις,
taxis (meaning 'order' or 'arrangement') and νόμος, nomos (meaning 'law' or 'science'). Taxonomy uses
taxonomic units, known as taxa (singular taxon).
In addition, the word is also used as a count noun: a taxonomy, or taxonomic scheme, is a particular
classification ("the taxonomy of ..."), arranged in a hierarchical structure. Typically this is organized by
supertype-subtype relationships, also called generalization-specialization relationships, or less formally,
parent-child relationships. In such an inheritance relationship, the subtype by definition has the same
properties, behaviors, and constraints as the supertype plus one or more additional properties, behaviors, or
constraints. For example: car is a subtype of vehicle, so any car is also a vehicle, but not every vehicle is a
car. Therefore a type needs to satisfy more constraints to be a car than to be a vehicle. Another example: any
shirt is also a piece of clothing, but not every piece of clothing is a shirt. Hence, a type must satisfy more
parameters to be a shirt than to be a piece of clothing.
Contents
[hide]
• 1 Applications
• 2 Taxonomy and mental classification
• 3 Various biological taxonomies
• 3.1 Phylogenetics
• 3.2 Numerical taxonomy
• 4 Non-scientific taxonomies
• 5 Military taxonomy
• 6 Economic taxonomies
• 7 Safety taxonomies
• 8 Notes
• 9 See also
• 10 References
[edit] Applications
Originally taxonomy referred only to the classifying of organisms (now sometimes known as alpha
taxonomy) or a particular classification of organisms. It is also used to refer a classification of things or
concepts, as well as to the principles underlying such a classification.
Almost anything—animate objects, inanimate objects, places, concepts, events, properties, and
relationships—may then be classified according to some taxonomic scheme. Wikipedia categories illustrate a
taxonomy schema,[1] and a full taxonomy of Wikipedia categories can be extracted by automatic means.[2]
Recently, it has been shown that a manually constructed taxonomy, such as that of computational lexicons
like WordNet, can be used to improve and restructure the Wikipedia category taxonomy.[3]
The term taxonomy is sometimes applied to relationship schemes other than parent-child
hierarchies, such as network structures with other types of relationships. In that case, they might include
single children with multi-parents, for example, "Car" might appear with both parents "Vehicle" and "Steel
Mechanisms"; technically, this merely means that 'car' is a part of several different taxonomies.[4] A
taxonomy might also be a simple organization of kinds of things into groups, or even an alphabetical list.
However, the term vocabulary is more appropriate for such a list. In current usage within Knowledge
Management, taxonomies are considered narrower than ontologies since ontologies apply a larger variety of
relation types.[5]
Mathematically, a hierarchical taxonomy is a tree structure of classifications for a given set of objects.
It is also named Containment hierarchy. At the top of this structure is a single classification, the root node,
that applies to all objects. Nodes below this root are more specific classifications that apply to subsets of the
total set of classified objects. The progress of reasoning proceeds from the general to the more specific. In
scientific taxonomies, a conflative term is always a polyseme.[6]
In contrast, in a context of legal terminology, an open-ended contextual taxonomy—a taxonomy
holding only with respect to a specific context. In scenarios taken from the legal domain, a formal account of
the open-texture of legal terms is modeled, which suggests varying notions of the "core" and "penumbra" of
the meanings of a concept. The progress of reasoning proceeds from the specific to the more general.[7]
[edit] Taxonomy and mental classification
Some have argued that the adult human mind naturally organizes its knowledge of the world into
such systems. This view is often based on the epistemology of Immanuel Kant. Anthropologists have
observed that taxonomies are generally embedded in local cultural and social systems, and serve various
social functions. Perhaps the most well-known and influential study of folk taxonomies is Émile Durkheim's
The Elementary Forms of Religious Life. A more recent treatment of folk taxonomies (including the results of
several decades of empirical research) and the discussion of their relation to the scientific taxonomy can be
found in Scott Atran's Cognitive Foundations of Natural History
[edit] Various biological taxonomies

Biological classification (sometimes known as "Linnaean taxonomy") is still generally the best known
form of taxonomy. It differs from the above in that it is an empirical science, with classifying only the final step
of a process, and a classification only the means to communicate the end results. It also includes the
prediction, discovery, description and (re)defining of taxa. It uses taxonomic ranks, including, among others,
(in order) Kingdom, Phylum, Class, Order, Family, Genus, Species (various mnemonic devices have been
used to help people remember the list of "Linnaean" taxonomic ranks. See Zoology mnemonic). In zoology,
the nomenclature for the more important ranks (superfamily to subspecies), including the allowed number of
ranks, is strictly regulated by the ICZN Code, whereas there is more latitude for names at higher ranks.
Taxonomy itself is never regulated, but is always the result of research in the scientific community. How
researchers arrive at their taxa varies; depending on the available data, and resources, methods vary from
simple quantitative or qualitative comparisons of striking features to elaborate computer analyses of large
amounts of DNA sequence data.
[edit] Phylogenetics
Today, the alternative to the traditional rank-based biological classification is phylogenetic
systematics, which is postulating phylogenetic trees (trees of descent), rather than focusing on what taxa to
delimit. The best-known form of this is cladistics.
The results of cladistic analyses are often represented as cladograms. It is held by cladists that taxa
(if recognized) must always correspond to clades, united by apomorphies (derived traits) which are
discovered by a cladistic analysis. Some cladists[who?] hold that clades are poorly expressed in rank-based
hierarchies and support the PhyloCode, a proposed ruleswork for the formal naming of clades, based on the
model of the ICZN, ICBN etc. in rank-based nomenclature.
[edit] Numerical taxonomy

In numerical taxonomy, numerical phenetics or taximetrics, the taxonomy is exclusively based on
cluster analysis and neighbor joining to best-fit numerical equations that characterize measurable traits of a
number of organisms. It results in a measure of evolutionary "distance" between species. This method has
been largely superseded by cladistic analyses today; it is liable to being misled by plesiomorphic traits.
[edit] Non-scientific taxonomies

Other taxonomies, such as those analyzed by Durkheim and Lévi-Strauss, are sometimes called folk
taxonomies to distinguish them from scientific taxonomies that focus on evolutionary relationships rather than
similarity in habitus and habits. Though phenetics arguably places much emphasis on overall similarity, it is a
quantitative analysis that attempts to reproduce evolutionary relationships of lineages and not similarities of
form taxa.
The neologism folksonomy should not be confused with "folk taxonomy", though it is obviously a
portmanteau created from the two words. "Fauxonomy" (from French faux, "false") is a pejorative neologism
used to criticize folk taxonomies for their lack of agreement with scientific findings. Baraminology is a
taxonomy used in creation science which in classifying form taxa resembles folk taxonomies.
The phrase "enterprise taxonomy" is used in business to describe a very limited form of taxonomy
used only within one organization. An example would be a certain method of classifying trees as "Type A",
"Type B" and "Type C" used only by a certain lumber company for categorising log shipments.
[edit] Military taxonomy

Military theorist Carl von Clausewitz stressed the significance of grasping the fundamentals of any
situation in the "blink of an eye" (coup d'œil). In a military context the astute tactician can immediately grasp a
range of implications and can begin to anticipate plausible and appropriate courses of action.[8] Clausewitz'
conceptual "blink" represents a tentative ontology which organizes a set of concepts within a domain.
The term "military taxonomy" encompasses the domains of weapons, equipment, organizations,
strategies, and tactics.[9] The use of taxonomies in the military extends beyond its value as an indexing tool
or record-keeping template[10] -- for example, the taxonomy-model analysis suggests a useful depiction of
the spectrum of the use of military force in a political context.[11]
A taxonomy of terms to describe various types of military operations is fundamentally affected by the
way all elements are defined and addressed—not unlike framing. For example, in terms of a specific military
operation, a taxonomic approach based on differentiation and categorization of the entities participating
would produce results which were quite different from an approach based on functional objective of an
operation (such as peacekeeping, disaster relief, or counter-terrorism).[12]
[edit] Economic taxonomies
Main article: Industry taxonomy
Taxonomies are also often used to classify economic activity, including products, companies and
industries.
Widely used industry taxonomies include the International Standard Industrial Classification (ISIC);
national and regional taxonomies such as the United States Standard Industrial Classification (SIC), the
North American Industry Classification System (NAICS), Statistical classification of economic activities in the
European Community (NACE), the United Kingdom Standard Industrial Classification of Economic Activities,
the Russian Economic Activities Classification System (OKVED); and proprietary taxonomies such as the
Industry Classification Benchmark and Global Industry Classification Standard. The international and
national taxonomies are used by official statistical agencies. The proprietary taxonomies are often used in the
financial services industry to group similar investment vehicles and to construct sectorial stock market
indices.
Pavitt's Taxonomy classifies firms by their principal sources of innovation.
[edit] Safety taxonomies

The creation of taxonomies is very important in safety science. For example there exist numerous
taxonomies to classify and analyze human error and accident causes. Examples of these include the Human
Factors Analysis and Classification System based on Reason's Swiss Cheese Model, the CREAM (Cognitive
Reliability Error Analysis Method), the taxonomy used by CIRAS (Confidential Incident Railway Analysis
System) in the UK rail industry, and others.[13]
[edit] Notes
1. ^ Zirn, Cäcilia, Vivi Nastase and Michael Strube. 2008. "Distinguishing Between Instances
and Classes in the Wikipedia Taxonomy" (video lecture). 5th Annual European Semantic Web
Conference (ESWC 2008).
2. ^ S. Ponzetto and M. Strube. 2007. "Deriving a large scale taxonomy from Wikipedia". Proc.
of the 22nd Conference on the Advancement of Artificial Intelligence, Vancouver, B.C., Canada, pp.
1440-1445.
3. ^ S. Ponzetto, R. Navigli. 2009. "Large-Scale Taxonomy Mapping for Restructuring and
Integrating Wikipedia". Proc. of the 21st International Joint Conference on Artificial Intelligence (IJCAI
2009), Pasadena, California, pp. 2083-2088.
4. ^ Jackson, Joab. "Taxonomy’s not just design, it’s an art," Government Computer News
(Washington, D.C.). September 2, 2004.
5. ^ Suryanto, Hendra and Paul Compton. "Learning classification taxonomies from a
classification knowledge based system." University of Karlsruhe; "Defining 'Taxonomy'," Straights
Knowledge website.
6. ^ Malone, Joseph L. (1988). The Science of Linguistics in the Art of Translation: Some Tools
from Linguistics for the Analysis and Practice of Translation, p. 112.
7. ^ Grossi, Davide, Frank Dignum and John-Jules Charles Meyer. (2005). "Contextual
Taxonomies" in Computational Logic in Multi-Agent Systems, pp. 33-51.
8. ^ Clausewitz, Carl. (1982). On War, p. 141; "Defining 'Taxonomy'," Straights Knowledge
website.
9. ^ Cycorp: Structured information
10.^ Fenske, Russell W. "A Taxonomy for Operations Research," Operations Research, Vol. 19,
No. 1 (Jan.-Feb., 1971), pp. 224-234;] United Nations. "Taxonomy for Recordkeeping in Field
Missions of UN Peacekeeping Operations." June 2006.
11.^ Cohen, Stuart A. and Efraim Inbar. "A taxonomy of Israel's use of military force," Journal
Comparative Strategy, Vol. 10, No. 2 (April 1991), pp. 121 - 138.
12.^ Downie, Richard D. "Defining integrated operations," Joint Force Quarterly (Washington,
D.C.). July, 2005.
13.^ Wallace,B, and Alastair Ross. Beyond Human Error: Taxonomies and Safety Science ;
(CRC Press 2006).
[edit] See also

• Biological classification
• Carolus Linnaeus, the father of systematics
• Categorization
• Conflation
• Cultigen taxonomy
• Cultivated plant taxonomy
• Celestial Emporium of Benevolent Recognition , a fictional Chinese encyclopedia with an
"impossible" taxonomic scheme.
• Chresonym
• Cladistics, the most prominent of several forms of phylogenetic systematics
• Folksonomy
• Gellish English dictionary / Taxonomy, in which the concepts are arranged as a subtype-
supertype hierarchy.
• History of plant systematics
• Hypernym
• Identification (biology)
• Jean-Baptiste Lamarck
• Knowledge representation
• Lexicon
• Life
• Linnaean taxonomy
• Nosology
• Ontology
• Ontology learning
• Phylogenetic
• Plant identification
• Plant morphology
• Sibley-Ahlquist taxonomy
• SOLO Taxonomy
• Species problem
• Systematics
• Taxocene
• Taxonomic database
[edit] References
• Atran, S. (1993) Cognitive Foundations of Natural History: Towards an Anthropology of
Science. Cambridge: Cambridge University Press. 10-ISBN 0521438713 13-ISBN 9780521438711
• Carbonell, J. G. and J. Siekmann, eds. (2005). Computational Logic in Multi-Agent Systems,
Vol. 3487. Berlin: Springer-Verlag. 13-ISBN 978-3-540-28060-6
• Clausewitz, Carl. (1982). On War (editor, Anatol Rapoport). New York: Penguin Classics. 10-
ISBN 0-140-44427-0; 13-ISBN 978-0-140-44427-8
• Malone, Joseph L. (1988). The Science of Linguistics in the Art of Translation: Some Tools
from Linguistics for the Analysis and Practice of Translation. Albany, New York: State University of
New York Press. 10-ISBN 0-887-06653-4; 13-ISBN 978-0-887-06653-5; OCLC 15856738
• *Marcello Sorce Keller, "The Problem of Classification in Folksong Research: a Short
History", Folklore, XCV(1984), no. 1, 100-104.
• Chester D Rowe and Stephen M Davis, 'The Excellence Engine Tool Kit'; ISBN 978-0-615-
24850-9

• Hjørland: Scientific classification and taxonomy. IN: The epistemological Lifeboat
• Wikispecies Main Page
• Integrated Taxonomic Information System
• Taxonomy at the National Center for Biotechnology Information
• Taxonomy at the European Bioinformatics Institute (formerly known as "New EBI Web
Taxonomy (NEWT)")
• Library of Taxonomy Resources
• Metadata? Thesauri? Taxonomies? Topic Maps! - Making sense of it all
• Taxonomies & Controlled Vocabularies Special Interest Group of the American Society for
Indexing
• Consortium of European Taxonomic Facilities
Retrieved from "http://en.wikipedia.org/wiki/Taxonomy"
Categories: Taxonomy | Classification systems | Greek loanwords | Nomenclature

W000
Molecular phylogenetics

Molecular phylogenetics ( /məˈlɛkjʊlər faɪlɵdʒɪˈnɛtɪks/), also known as molecular systematics (a
term likely discouraged to avoid confusion with molecular-biological system/structure-activity relationship), is
the use of the structure of molecules to gain information on an organism's evolutionary relationships. The
result of a molecular phylogenetic analysis is expressed in a phylogenetic tree.
Contents
[hide]
• 1 History of molecular phylogenetics
• 2 Techniques and applications
• 3 Theoretical background
• 4 Limitations of molecular systematics
• 6 See also
• 7 References
[edit] History of molecular phylogenetics

Further information: History of molecular evolution
The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile
Zuckerkandl, Emanuel Margoliash, Linus Pauling and Walter M. Fitch.[1] Applications of molecular
systematics were pioneered by Charles G. Sibley (birds), Herbert C. Dessauer (herpetology), and Morris
Goodman (primates), followed by Allan C. Wilson, Robert K. Selander, and John C. Avise (who studied
various groups). Work with protein electrophoresis began around 1956. Although the results were not
quantitative and did not initially improve on morphological classification, they provided tantalizing hints that
long-held notions of the classifications of birds, for example, needed substantial revision. In the period of
1974–1986, DNA-DNA hybridization was the dominant technique.[2]
[edit] Techniques and applications

Every living organism contains DNA, RNA, and proteins. Closely related organisms generally have a
high degree of agreement in the molecular structure of these substances, while the molecules of organisms
distantly related usually show a pattern of dissimilarity. Conserved sequences, such as mitochondrial DNA,
are expected to accumulate mutations over time, and assuming a constant rate of mutation provide a
molecular clock for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that
shows the probable evolution of various organisms. Not until recent decades, however, has it been possible
to isolate and identify these molecular structures.
The most common approach is the comparison of homologous sequences for genes using sequence
alignment techniques to identify similarity. Another application of molecular phylogeny is in DNA barcoding,
where the species of an individual organism is identified using small sections of mitochondrial DNA. Another
application of the techniques that make this possible can be seen in the very limited field of human genetics,
such as the ever more popular use of genetic testing to determine a child's paternity, as well as the
emergence of a new branch of criminal forensics focused on evidence known as genetic fingerprinting.
[edit] Theoretical background

Early attempts at molecular systematics were also termed as chemotaxonomy and made use of
proteins, enzymes, carbohydrates and other molecules which were separated and characterized using
techniques such as chromatography. These have been largely replaced in recent times by DNA sequencing
which produces the exact sequences of nucleotides or bases in either DNA or RNA segments extracted
using different techniques. These are generally considered superior for evolutionary studies since the actions
of evolution are ultimately reflected in the genetic sequences. At present it is still a long and expensive
process to sequence the entire DNA of an organism (its genome), and this has been done for only a few
species. However it is quite feasible to determine the sequence of a defined area of a particular
chromosome. Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At
any location within such a sequence, the bases found in a given position may vary between organisms. The
particular sequence found in a given organism is referred to as its haplotype. In principle, since there are four
base types, with 1000 base pairs, we could have 4 1000 distinct haplotypes. However, for organisms within a
particular species or in a group of related species, it has been found empirically that only a minority of sites
show any variation at all and most of the variations that are found are correlated, so that the number of
distinct haplotypes that are found is relatively small.
In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic
material; ideally a substantial sample of individuals of the target species or other taxon are used however
many current studies are based on single individuals. Haplotypes of individuals of closely related, but
supposedly different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from
a definitely different taxon are determined: these are referred to as an out group. The base sequences for the
haplotypes are then compared. In the simplest case, the difference between two haplotypes is assessed by
counting the number of locations where they have different bases: this is referred to as the number of
substitutions (other kinds of differences between haplotypes can also occur, for example the insertion of a
section of nucleic acid in one haplotype that is not present in another). Usually the difference between
organisms is re-expressed as a percentage divergence, by dividing the number of substitutions by the
number of base pairs analysed: the hope is that this measure will be independent of the location and length
of the section of DNA that is sequenced.
An older and superseded approach was to determine the divergences between the genotypes of
individuals by DNA-DNA hybridisation. The advantage claimed for using hybridisation rather than gene
sequencing was that it was based on the entire genotype, rather than on particular sections of DNA. Modern
sequence comparison techniques overcome this objection by the use of multiple sequences.
Once the divergences between all pairs of samples have been determined, the resulting triangular
matrix of differences is submitted to some form of statistical cluster analysis, and the resulting dendrogram is
examined in order to see whether the samples cluster in the way that would be expected from current ideas
about the taxonomy of the group, or not. Any group of haplotypes that are all more similar to one another
than any of them is to any other haplotype may be said to constitute a clade. Statistical techniques such as
bootstrapping and jackknifing help in providing reliability estimates for the positions of haplotypes within the
evolutionary trees.
[edit] Limitations of molecular systematics

Molecular systematics is an essentially cladistic approach: it assumes that classification must
correspond to phylogenetic descent, and that all valid taxa must be monophyletic.
Molecular systematics often uses the molecular clock assumption that quantitative similarity of
genotype is a sufficient measure of the recency of genetic divergence. Particularly in relation to speciation,
this assumption could be wrong if either some genotypic modification acted to prevent interbreeding between
two groups of organisms, or genetic modification proceeded at different rates in different subgroups of the
organisms.
In animals, it is often convenient to use mitochondrial DNA for molecular systematic analysis.
However, because in mammals mitochondria are inherited only from the mother, this is not fully satisfactory,
because inheritance in the paternal line might not be detected.
• Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates Incorporated. ISBN 0-87893-
177-5.
• Hillis, D. M. & Moritz, C. 1996. Molecular systematics. 2nd ed. Sinauer Associates
Incorporated. ISBN 0-87893-282-8.
• Page, R. D. M. & Holmes, E. C. 1998. Molecular evolution: a phylogenetic approach.
Blackwell Science, Oxford. ISBN 0-86542-889-1.
• Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1992) Molecular systematics of plants. Chapman &
Hall, New York. ISBN-0-41202-231-1.
• Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1998) Molecular Systematics of Plants II: DNA
Sequencing. Kluwer Academic Publishers Boston, Dordrecht, London. ISBN-0-41211-131-4.
[edit] See also

• molecular evolution
• computational phylogenetics
• PhyloCode
[edit] References
1. ^ Edna Suárez-Díaz & Victor H. Anaya-Muñoz (2008) History, objectivity, and the
construction of molecular phylogenies. Stud. Hist. Phil. Biol. & Biomed. Sci. 39:451–468
2. ^ Ahlquist, Jon E., 1999: Charles G. Sibley: A commentary on 30 years of collaboration. The
Auk, vol. 116, no. 3 (July 1999). A PDF or DjVu version of this article can be downloaded from the
issue's table of contents page.

• NCBI - Systematics and Molecular Phylogenetics
Relevant



Retrieved from "http://en.wikipedia.org/wiki/Molecular_phylogenetics"
Categories: Phylogenetics | Molecular evolution

W000
Computational phylogenetics

Computational phylogenetics is the application of computational algorithms, methods and programs
to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the
evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been
used to explore the family tree of hominid species[1] and the relationships between specific genes shared by
many types of organisms.[2] Traditional phylogenetics relies on morphological data obtained by measuring
and quantifying the phenotypic properties of representative organisms, while the more recent field of
molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding
proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and
make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to
classify the evolutionary relationships between homologous genes represented in the genomes of divergent
species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce
the evolutionary tree that represents the historical relationships between the species being analyzed. The
historical species tree may also differ from the historical tree of an individual homologous gene shared by
those species.
Producing a phylogenetic tree requires a measure of homology among the characteristics shared by
the taxa being compared. In morphological studies, this requires explicit decisions about which physical
characteristics to measure and how to use them to encode distinct states corresponding to the input taxa. In
molecular studies, a primary problem is in producing a multiple sequence alignment (MSA) between the
genes or amino acid sequences of interest. Progressive sequence alignment methods produce a
phylogenetic tree by necessity because they incorporate new sequences into the calculated alignment in
order of genetic distance.
Contents
[hide]
• 1 Types of phylogenetic trees
• 2 Coding characters and defining homology
• 2.1 Morphological analysis
• 2.2 Molecular analysis
• 3 Distance-matrix methods
• 3.1 Neighbor-joining
• 3.2 Fitch-Margoliash method
• 3.3 Using outgroups
• 4 Maximum parsimony
• 4.1 Branch and bound
• 4.2 Sankoff-Morel-Cedergren algorithm
• 4.3 MALIGN and POY
• 5 Maximum likelihood
• 6 Bayesian inference
• 7 Model selection
• 7.1 Types of models
• 7.2 Choosing the best model
• 8 See also
• 9 References
[edit] Types of phylogenetic trees
Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted
depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies
a most recent common ancestor (MRCA), usually an imputed sequence that is not represented in the input.
Genetic distance measures can be used to plot a tree with the input sequences as leaf nodes and their
distances from the root proportional to their genetic distance from the hypothesized MRCA. Identification of a
root usually requires the inclusion in the input data of at least one "outgroup" known to be only distantly
related to the sequences of interest.
By contrast, unrooted trees plot the distances and relationships between input sequences without
making assumptions regarding their descent. An unrooted tree can always be produced from a rooted tree,
but a root cannot usually be placed on an unrooted tree without additional data on divergence rates, such as
the assumption of the molecular clock hypothesis.[3]
The set of all possible phylogenetic trees for a given group of input sequences can be conceptualized
as a discretely defined multidimensional "tree space" through which search paths can be traced by
optimization algorithms. Although counting the total number of trees for a nontrivial number of input
sequences can be complicated by variations in the definition of a tree topology, it is always true that there are
more rooted than unrooted trees for a given number of inputs and choice of parameters.[4]
[edit] Coding characters and defining homology
[edit] Morphological analysis
The basic problem in morphological phylogenetics is the assembly of a matrix representing a
mapping from each of the taxa being compared to representative measurements for each of the phenotypic
characteristics being used as a classifier. The types of phenotypic data used to construct this matrix depend
on the taxa being compared; for individual species, they may involve measurements of average body size,
lengths or sizes of particular bones or other physical features, or even behavioral manifestations. Of course,
since not every possible phenotypic characteristic could be measured and encoded for analysis, the selection
of which features to measure is a major inherent obstacle to the method. The decision of which traits to use
as a basis for the matrix necessarily represents a hypothesis about which traits of a species or higher taxon
are evolutionarily relevant.[5] Morphological studies can be confounded by examples of convergent evolution
of phenotypes.[6] A major challenge in constructing useful classes is the high likelihood of inter-taxon overlap
in the distribution of the phenotype's variation. The inclusion of extinct taxa in morphological analysis is often
difficult due to absence of or incomplete fossil records, but has been shown to have a significant effect on the
trees produced; in one study only the inclusion of extinct species of apes produced a morphologically derived
tree that was consistent with that produced from molecular data.[1]
Some phenotypic classifications, particularly those used when analyzing very diverse groups of taxa,
are discrete and unambiguous; classifying organisms as possessing or lacking a tail, for example, is
straightforward in the majority of cases, as is counting features such as eyes or vertebrae. However, the most
appropriate representation of continuously varying phenotypic measurements is a controversial problem
without a general solution. A common method is simply to sort the measurements of interest into two or more
classes, rendering continuous observed variation as discretely classifiable (e.g., all examples with humerus
bones longer than a given cutoff are scored as members of one state, and all members whose humerus
bones are shorter than the cutoff are scored as members of a second state). This results in an easily
manipulated data set but has been criticized for poor reporting of the basis for the class definitions and for
sacrificing information compared to methods that use a continuous weighted distribution of measurements.[7]
Because morphological data is extremely labor-intensive to collect, whether from literature sources
or from field observations, reuse of previously compiled data matrices is not uncommon, although this may
propagate flaws in the original matrix into multiple derivative analyses.[8]
[edit] Molecular analysis

The problem of character coding is very different in molecular analyses, as the characters in
biological sequence data are immediate and discretely defined - distinct nucleotides in DNA or RNA
sequences and distinct amino acids in protein sequences. However, defining homology can be challenging
due to the inherent difficulties of multiple sequence alignment. For a given gapped MSA, several rooted
phylogenetic trees can be constructed that vary in their interpretations of which changes are "mutations"
versus ancestral characters, and which events are insertion mutations or deletion mutations. For example,
given only a pairwise alignment with a gap region, it is impossible to determine whether one sequence bears
an insertion mutation or the other carries a deletion. The problem is magnified in MSAs with unaligned and
nonoverlapping gaps. In practice, sizable regions of a calculated alignment may be discounted in
phylogenetic tree construction to avoid integrating noisy data into the tree calculation.
[edit] Distance-matrix methods

Distance-matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic distance"
between the sequences being classified, and therefore they require an MSA as an input. Distance is often
defined as the fraction of mismatches at aligned positions, with gaps either ignored or counted as
mismatches.[3] Distance methods attempt to construct an all-to-all matrix from the sequence query set
describing the distance between each sequence pair. From this is constructed a phylogenetic tree that places
closely related sequences under the same interior node and whose branch lengths closely reproduce the
observed distances between sequences. Distance-matrix methods may produce either rooted or unrooted
trees, depending on the algorithm used to calculate them. They are frequently used as the basis for
progressive and iterative types of multiple sequence alignments. The main disadvantage of distance-matrix
methods is their inability to efficiently use information about local high-variation regions that appear across
multiple subtrees.[4]
[edit] Neighbor-joining
Neighbor-joining methods apply general data clustering techniques to sequence analysis using
genetic distance as a clustering metric. The simple neighbor-joining method produces unrooted trees, but it
does not assume a constant rate of evolution (i.e., a molecular clock) across lineages. Its relative, UPGMA
(Unweighted Pair Group Method with Arithmetic mean) produces rooted trees and requires a constant-rate
assumption - that is, it assumes an ultrametric tree in which the distances from the root to every branch tip
are equal.
[edit] Fitch-Margoliash method

The Fitch-Margoliash method uses a weighted least squares method for clustering based on genetic
distance.[9] Closely related sequences are given more weight in the tree construction process to correct for
the increased inaccuracy in measuring distances between distantly related sequences. The distances used
as input to the algorithm must be normalized to prevent large artifacts in computing relationships between
closely related and distantly related groups. The distances calculated by this method must be linear; the
linearity criterion for distances requires that the expected values of the branch lengths for two individual
branches must equal the expected value of the sum of the two branch distances - a property that applies to
biological sequences only when they have been corrected for the possibility of back mutations at individual
sites. This correction is done through the use of a substitution matrix such as that derived from the Jukes-
Cantor model of DNA evolution. The distance correction is only necessary in practice when the evolution
rates differ among branches.[4]
The least-squares criterion applied to these distances is more accurate but less efficient than the
neighbor-joining methods. An additional improvement that corrects for correlations between distances that
arise from many closely related sequences in the data set can also be applied at increased computational
cost. Finding the optimal least-squares tree with any correction factor is NP-complete,[10] so heuristic search
methods like those used in maximum-parsimony analysis are applied to the search through tree space.
[edit] Using outgroups

Independent information about the relationship between sequences or groups can be used to help
reduce the tree search space and root unrooted trees. Standard usage of distance-matrix methods involves
the inclusion of at least one outgroup sequence known to be only distantly related to the sequences of
interest in the query set.[3] This usage can be seen as a type of experimental control. If the outgroup has
been appropriately chosen, it will have a much greater genetic distance and thus a longer branch length than
any other sequence, and it will appear near the root of a rooted tree. Choosing an appropriate outgroup
requires the selection of a sequence that is moderately related to the sequences of interest; too close a
relationship defeats the purpose of the outgroup and too distant adds noise to the analysis.[3] Care should
also be taken to avoid situations in which the species from which the sequences were taken are distantly
related, but the gene encoded by the sequences is highly conserved across lineages. Horizontal gene
transfer, especially between otherwise divergent bacteria, can also confound outgroup usage.
[edit] Maximum parsimony
Maximum parsimony (MP) is a method of identifying the potential phylogenetic tree that requires the
smallest total number of evolutionary events to explain the observed sequence data. Some ways of scoring
trees also include a "cost" associated with particular types of evolutionary events and attempt to locate the
tree with the smallest total cost. This is a useful approach in cases where not every possible type of event is
equally likely - for example, when particular nucleotides or amino acids are known to be more mutable than
others.
The most naive way of identifying the most parsimonious tree is simple enumeration - considering
each possible tree in succession and searching for the tree with the smallest score. However, this is only
possible for a relatively small number of sequences or species because the problem of identifying the most
parsimonious tree is known to be NP-hard;[4] consequently a number of heuristic search methods for
optimization have been developed to locate a highly parsimonious tree, if not the most optimal in the set.
Most such methods involve a steepest descent-style minimization mechanism operating on a tree
rearrangement criterion.
[edit] Branch and bound

The branch and bound algorithm is a general method used to increase the efficiency of searches for
near-optimal solutions of NP-hard problems first applied to phylogenetics in the early 1980s.[11] Branch and
bound is particularly well suited to phylogenetic tree construction because it inherently requires dividing a
problem into a tree structure as it subdivides the problem space into smaller regions. As its name implies, it
requires as input both a branching rule (in the case of phylogenetics, the addition of the next species or
sequence to the tree) and a bound (a rule that excludes certain regions of the search space from
consideration, thereby assuming that the optimal solution cannot occupy that region). Identifying a good
bound is the most challenging aspect of the algorithm's application to phylogenetics. A simple way of defining
the bound is a maximum number of assumed evolutionary changes allowed per tree. A set of criteria known
as Zharkikh's rules[12] severely limit the search space by defining characteristics shared by all candidate
"most parsimonious" trees. The two most basic rules require the elimination of all but one redundant
sequence (for cases where multiple observations have produced identical data) and the elimination of
character sites at which two or more states do not occur in at least two species. Under ideal conditions these
rules and their associated algorithm would completely define a tree.
[edit] Sankoff-Morel-Cedergren algorithm

The Sankoff-Morel-Cedergren algorithm was among the first published methods to simultaneously
produce an MSA and a phylogenetic tree for nucleotide sequences.[13] The method uses a maximum
parsimony calculation in conjunction with a scoring function that penalizes gaps and mismatches, thereby
favoring the tree that introduces a minimal number of such events. The imputed sequences at the interior
nodes of the tree are scored and summed over all the nodes in each possible tree. The lowest-scoring tree
sum provides both an optimal tree and an optimal MSA given the scoring function. Because the method is
highly computationally intensive, an approximate method in which initial guesses for the interior alignments
are refined one node at a time. Both the full and the approximate version are in practice calculated by
dynamic programming.[4]
[edit] MALIGN and POY

More recent phylogenetic tree/MSA methods use heuristics to isolate high-scoring, but not
necessarily optimal, trees. The MALIGN method uses a maximum-parsimony technique to compute a
multiple alignment by maximizing a cladogram score, and its companion POY uses an iterative method that
couples the optimization of the phylogenetic tree with improvements in the corresponding MSA.[14] However,
the use of these methods in constructing evolutionary hypotheses has been criticized as biased due to the
deliberate construction of trees reflecting minimal evolutionary events.[15]
[edit] Maximum likelihood

The maximum likelihood method uses standard statistical techniques for inferring probability
distributions to assign probabilities to particular possible phylogenetic trees. The method requires a
substitution model to assess the probability of particular mutations; roughly, a tree that requires more
mutations at interior nodes to explain the observed phylogeny will be assessed as having a lower probability.
This is broadly similar to the maximum-parsimony method, but maximum likelihood allows additional
statistical flexibility by permitting varying rates of evolution across both lineages and sites. In fact, the method
requires that evolution at different sites and along different lineages must be statistically independent.
Maximum likelihood is thus well suited to the analysis of distantly related sequences, but because it formally
requires search of all possible combinations of tree topology and branch length, it is computationally
expensive to perform on more than a few sequences.
The "pruning" algorithm, a variant of dynamic programming, is often used to reduce the search space
by efficiently calculating the likelihood of subtrees.[4] The method calculates the likelihood for each site in a
"linear" manner, starting at a node whose only descendants are leaves (that is, the tips of the tree) and
working backwards toward the "bottom" node in nested sets. However, the trees produced by the method are
only rooted if the substitution model is irreversible, which is not generally true of biological systems. The
search for the maximum-likelihood tree also includes a branch length optimization component that is difficult
to improve upon algorithmically; general global optimization tools such as the Newton-Raphson method are
often used. Searching tree topologies defined by likelihood has not been shown to be NP-complete,[4] but
remains extremely challenging because branch-and-bound search is not yet effective for trees represented in
this way.
[edit] Bayesian inference
Bayesian inference can be used to produce phylogenetic trees in a manner closely related to the
maximum likelihood methods. Bayesian methods assume a prior probability distribution of the possible trees,
which may simply be the probability of any one tree among all the possible trees that could be generated
from the data, or may be a more sophisticated estimate derived from the assumption that divergence events
such as speciation occur as stochastic processes. The choice of prior distribution is a point of contention
among users of Bayesian-inference phylogenetics methods.[4]
Implementations of Bayesian methods generally use Markov chain Monte Carlo sampling algorithms,
although the choice of move set varies; selections used in Bayesian phylogenetics include circularly
permuting leaf nodes of a proposed tree at each step[16] and swapping descendant subtrees of a random
internal node between two related trees.[17] The use of Bayesian methods in phylogenetics has been
controversial, largely due to incomplete specification of the choice of move set, acceptance criterion, and
prior distribution in published work.[4]
[edit] Model selection

Molecular phylogenetics methods rely on a defined substitution model that encodes a hypothesis
about the relative rates of mutation at various sites along the gene or amino acid sequences being studied.
At their simplest, substitution models aim to correct for differences in the rates of transitions and
transversions in nucleotide sequences. The use of substitution models is necessitated by the fact that the
genetic distance between two sequences increases linearly only for a short time after the two sequences
diverge from each other (alternatively, the distance is linear only shortly before coalescence). The longer the
amount of time after divergence, the more likely it becomes that two mutations occur at the same nucleotide
site. Simple genetic distance calculations will thus undercount the number of mutation events that have
occurred in evolutionary history. The extent of this undercount increases with increasing time since
divergence, which can lead to the phenomenon of long branch attraction, or the misassignment of two
distantly related but convergently evolving sequences as closely related.[18] The maximum parsimony
method is particularly susceptible to this problem due to its explicit search for a tree representing a minimum
number of distinct evolutionary events.[4]
[edit] Types of models

Main article: Substitution model
All substitution models assign a set of weights to each possible change of state represented in the
sequence. The most common model types are implicitly reversible because they assign the same weight to,
for example, a G>C nucleotide mutation as to a C>G mutation. The simplest possible model, the Jukes-
Cantor model, assigns an equal probability to every possible change of state for a given nucleotide base. The
rate of change between any two distinct nucleotides will be one-third of the overall substitution rate.[4] More
advanced models distinguish between transitions and transversions. The most general possible time-
reversible model, called the GTR model, has six mutation rate parameters. An even more generalized model
known as the general 12-parameter model breaks time-reversibility, at the cost of much additional complexity
in calculating genetic distances that are consistent among multiple lineages.[4] One possible variation on this
theme adjusts the rates so that overall GC content - an important measure of DNA double helix stability -
varies over time.[19]
Models may also allow for the variation of rates with positions in the input sequence. The most
obvious example of such variation follows from the arrangement of nucleotides in protein-coding genes into
three-base codons. If the location of the open reading frame (ORF) is known, rates of mutation can be
adjusted for position of a given site within a codon, since it is known that wobble base pairing can allow for
higher mutation rates in the third nucleotide of a given codon without affecting the codon's meaning in the
genetic code.[18] A less hypothesis-driven example that does not rely on ORF identification simply assigns to
each site a rate randomly drawn from a predetermined distribution, often the gamma distribution or log-
normal distribution.[4] Finally, a more conservative estimate of rate variations known as the covarion method
allows autocorrelated variations in rates, so that the mutation rate of a given site is correlated across sites
and lineages.[20]
[edit] Choosing the best model

The selection of an appropriate model is critical for the production of good phylogenetic analyses,
both because underparameterized or overly restrictive models may produce aberrant behavior when their
underlying assumptions are violated, and because overly complex or overparameterized models are
computationally expensive and the parameters may be overfit.[18] The most common method of model
selection is the likelihood ratio test (LRT), which produces a likelihood estimate that can be interpreted as a
measure of "goodness of fit" between the model and the input data.[18] However, care must be taken in
using these results, since a more complex model with more parameters will always have a higher likelihood
than a simplified version of the same model, which can lead to the naive selection of models that are overly
complex.[4] For this reason model selection computer programs will choose the simplest model that is not
significantly worse than more complex substitution models. A significant disadvantage of the LRT is the
necessity of making a series of pairwise comparisons between models; it has been shown that the order in
which the models are compared has a major effect on the one that is eventually selected.[21]
An alternative model selection method is the Akaike information criterion (AIC), formally an estimate
of the Kullback-Leibler divergence between the true model and the model being tested. It can be interpreted
as a likelihood estimate with a correction factor to penalize overparameterized models.[18] The AIC is
calculated on an individual model rather than a pair, so it is independent of the order in which models are
assessed. A related alternative, the Bayesian information criterion (BIC), has a similar basic interpretation but
penalizes complex models more heavily.[18]
[edit] See also

• List of phylogenetics software
• Cladistics
• PHYLIP
• Phylogenetic comparative methods
• Phylogenetic tree
• Phylogenetics
• Systematics
• Evolutionary dynamics
[edit] References
1. ^ a b Strait DS, Grine FE. (2004). Inferring hominoid and early hominid phylogeny using
craniodental characters: the role of fossil taxa. J Hum Evol 47(6):399-452.
2. ^ Hodge T, Cope MJ. (2000). A myosin family tree. J Cell Sci 113: 3353-3354.
3. ^ a b c d Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold
Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
4. ^ a b c d e f g h i j k l m n Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates:
Sunderland, MA.
5. ^ Swiderski DL, Zelditch ML, Fink WL. (1998). Why morphometrics is not special: coding
quantitative data for phylogenetic analysis. 47(3):508-19.
6. ^ Gaubert P, Wozencraft WC, Cordeiro-Estrela P, Veron G. (2005). Mosaics of convergences
and noise in morphological phylogenies: what's in a viverrid-like carnivoran? Syst Biol 54(6):865-94.
7. ^ Wiens JJ. (2001). Character analysis in morphological phylogenetics: problems and
solutions. Syst Biol 50(5):689-99.
8. ^ Jenner RA. (2001). Bilaterian phylogeny and uncritical recycling of morphological data sets.
Syst Biol 50(5): 730-743.
9. ^ Fitch WM, Margoliash E. (1967). Construction of phylogenetic trees. Science 155: 279-84.
10.^ Day, WHE. (1986). Computational complexity of inferring phylogenies from dissimilarity
matrices. Bulletin of Mathematical Biology 49:461-7.
11.^ Hendy MD, Penny D. (1982). Branch and bound algorithms to determine minimal
evolutionary trees. Math Biosci 60: 133-42.
12.^ Ratner VA, Zharkikh AA, Kolchanov N, Rodin S, Solovyov S, Antonov AS. (1995).
Molecular Evolution Biomathematics Series Vol 24. Springer-Verlag: New York, NY.
13.^ Sankoff D, Morel C, Cedergren RJ. (1973). Evolution of 5S RNA and the non-randomness
of base replacement. Nature New Biology 245:232-4.
14.^ Wheeler WC, Gladstein DG. (1994). MALIGN: a multiple nucleic acid sequence alignment
program. J Heredity 85: 417-18.
15.^ Simmons MP. (2004). Independence of alignment and tree search. Mol Phylogenet Evol
31(3):874-9.
16.^ Mau B, Newton MA. (1997). Phylogenetic inference for binary data on dendrograms using
Markov chain Monte Carlo. J Comp Graph Stat 6:122-31.
17.^ Yang Z, Rannala B. (1997). bayesian phylogenetic inference using DNA sequences: a
Markov chain Monte Carlo method. Mol Biol Evol 46:409-18.
18.^ a b c d e f Sullivan, Jack; Joyce, Paul (2005). "Model Selection in Phylogenetics". Annual
Review of Ecology Evolution and Systematics 36: 445.
19.^ Galtier N, Guoy M. (1998.) Inferring pattern and process: maximum-likelihood
implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.
Mol. Biol. Evol. 15:871–79.
20.^ Fitch WM, Markowitz E. (1970). An improved method for determining codon variability in a
gene and its application to the rate of fixation of mutations in evolution. Biochemical Genetics 4:579-
593.
21.^ Pol D. (2004.) Empirical problems of the hierarchical likelihood ratio test for model
selection. Syst Biol 53:949–62.

• Charles Semple and Mike Steel (2003), Phylogenetics, Oxford University Press, ISBN
9780198509424
• Barry A. Cipra (2007), Algebraic Geometers See Ideal Approach to Biology, SIAM News,
Volume 40, Number 6
Relevant Computational phylogenetics · Molecular phylogenetics · Cladistics

fields



Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of Anagenesis · Catagenesis · Cladogenesis

speciation

Retrieved from "http://en.wikipedia.org/wiki/Computational_phylogenetics"
Categories: Computational phylogenetics

W000
Phylogenetic tree

"ptree" redirects here. For Patricia tree, see Radix tree.
Fig. 1: A speculatively rooted tree for rRNA genes
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred
evolutionary relationships among various biological species or other entities based upon similarities and
differences in their physical and/or genetic characteristics. The taxa joined together in the tree are implied to
have descended from a common ancestor. In a rooted phylogenetic tree, each node with descendants
represents the inferred most recent common ancestor of the descendants, and the edge lengths in some
trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are
generally called hypothetical taxonomic units (HTUs) as they cannot be directly observed. Trees are useful in
fields of biology such as bioinformatics,systematics and comparative phylogenetics.
Contents
[hide]
• 1 History
• 2 Formal Definition
• 3 Types
• 4 Construction
• 5 Limitations
• 6 See also
• 6.1 The "tree of life"
• 6.2 Fields of study
• 7 References
• 9.1 Images
• 9.2 General
[edit] History
The idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower to higher
forms of life (such as in the Great Chain of Being). Early representations of branching phylogenetic trees
include a "Paleontological chart" showing the geological relationships among plants and animals in the book
Elementary Geology, by Edward Hitchcock (first edition: 1840).
Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the notion
of an evolutionary "tree" in his seminal book The Origin of Species. Over a century later, evolutionary
biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept
that speciation occurs through the adaptive and random splitting of lineages. Over time, species classification
has become less static and more dynamic.
[edit] Formal Definition

In the analysis of genetic evolution, we are given a set X of k sequences, each stands for an extant
species. Let Y be a set of hypothetical sequences, where (usually, each sequence in Y could
represent an extinct species). An evolutionary tree TX,Y for X is a weighted (sometimes rooted) tree of
nodes, where each node is associated with a unique sequence in . The cost of an edge
is the edit distance between the two sequence associated with the ends of the edge. The cost c(TX,Y) of the
tree TX,Y is the total cost of all the edges in TX,Y. [1]
[edit] Types
Fig. 1: Unrooted tree of the myosin supergene family[2]

Fig. 2: A highly resolved, automatically generated Tree Of Life, based on completely sequenced
genomes[3][4].
A phylogenetic tree, showing how Eukaryota and Archaea are more closely related to each other
than to Bacteria, based on Cavalier-Smith's theory of bacterial evolution. (Cf. LUCA, Neomura.)
A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually
imputed) most recent common ancestor of all the entities at the leaves of the tree. The most common method
for rooting trees is the use of an uncontroversial outgroup — close enough to allow inference from sequence
or trait data, but far enough to be a clear outgroup.
Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about
ancestry at all. While unrooted trees can always be generated from rooted ones by simply omitting the root, a
root cannot be inferred from an unrooted tree without some means of identifying ancestry; this is normally
done by including an outgroup in the input data or introducing additional assumptions about the relative rates
of evolution on each branch, such as an application of the molecular clock hypothesis. Figure 1 depicts an
unrooted phylogenetic tree for myosin, a superfamily of proteins.[5]
Both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either
labeled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each interior node
(that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a
free tree with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have
more than two children at some nodes and an unrooted multifurcating tree may have more than three
neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while an unlabeled tree,
sometimes called a tree shape, defines a topology only. The number of possible trees for a given number of
leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating
trees, more labeled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the
most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For
labeled bifurcating trees, there are
total rooted trees and

total unrooted trees, where n represents the number of leaf nodes. Among labeled bifurcating trees,
the number of unrooted trees with n leaves is equal to the number of rooted trees with n − 1 leaves.[6]
A dendrogram is a broad term for the diagrammatic representation of a phylogenetic tree.
A cladogram is a tree formed using cladistic methods. This type of tree only represents a branching
pattern, i.e., its branch lengths do not represent time.
A phylogram is a phylogenetic tree that explicitly represents number of character changes through its
branch lengths.
A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch
lengths.
[edit] Construction
Main article: Computational phylogenetics
Phylogenetic trees among a nontrivial number of input sequences are constructed using
computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which
calculate genetic distance from multiple sequence alignments, are simplest to implement, but do not invoke
an evolutionary model. Many sequence alignment methods such as ClustalW also create trees by using the
simpler algorithms (i.e. those based on distance) of tree construction. Maximum parsimony is another simple
method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More
advanced methods use the optimality criterion of maximum likelihood, often within a Bayesian Framework,
and apply an explicit model of evolution to phylogenetic tree estimation.[6] Identifying the optimal tree using
many of these techniques is NP-hard[6], so heuristic search and optimization methods are used in
combination with tree-scoring functions to identify a reasonably good tree that fits the data.
Tree-building methods can be assessed on the basis of several criteria:[7]
• efficiency (how long does it take to compute the answer, how much memory does it need?)
• power (does it make good use of the data, or is information being wasted?)
• consistency (will it converge on the same answer repeatedly, if each time given different data
for the same model problem?)
• robustness (does it cope well with violations of the assumptions of the underlying model?)
• falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)
Tree-building techniques have also gained the attention of mathematicians. Trees can also be built
using T-theory.[8]
[edit] Limitations
Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different
species can provide evolutionary insight, they have important limitations. They do not necessarily accurately
represent the species evolutionary history. The data on which they are based is noisy; the analysis can be
confounded by horizontal gene transfer[9], hybridisation between species that were not nearest neighbors on
the tree before hybridisation takes place, convergent evolution, and conserved sequences.
Also, there are problems in basing the analysis on a single type of character, such as a single gene
or protein or only on morphological analysis, because such trees constructed from another unrelated data
source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships
among species. This is most true of genetic material that is subject to lateral gene transfer and
recombination, where different haplotype blocks can have different histories. In general, the output tree of a
phylogenetic analysis is an estimate of the character's phylogeny (i.e. a gene tree) and not the phylogeny of
the taxa (i.e. species tree) from which these characters were sampled, though ideally, both should be very
close. For this reason, serious phylogenetic studies generally use a combination of genes that come from
different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes), or genes that would be
expected to evolve under different selective regimes, so that homoplasy (false homology) would be unlikely
to result from natural selection.
When extinct species are included in a tree, they are terminal nodes, as it is unlikely that they are
direct ancestors of any extant species. Scepticism must apply when extinct species are included in trees that
are wholly or partly based on DNA sequence data, due to the fact that little useful "ancient DNA" is preserved
for longer than 100,000 years, and except in the most unusual circumstances no DNA sequences long
enough for use in phylogenetic analyses have yet been recovered from material over 1 million years old.
In some organisms, endosymbionts have an independent genetic history from the host.
Phylogenetic networks are used when bifurcating trees are not suitable, due to these complications
which suggest a more reticulate evolutionary history of the organisms sampled..
[edit] See also

[edit] The "tree of life"
• Evolutionary history of life - An overview of the major time periods of life on earth
• Life - The top level for Wikipedia articles on living species, reflecting a diversity of
classification systems.
• Three-domain system (cell types)
• Wikispecies - An external Wikimedia Foundation project to construct a "tree of life"
appropriate for use by scientists
[edit] Fields of study

• Archaeopteryx
• Cladistics
• Comparative phylogenetics
• Computational phylogenetics
• Generalized tree alignment
• Phylogenetics
[edit] References
1. ^ "On the complexity of multiple sequence alignment", J Comput Biol 1 (4): 337–348, 1994
2. ^ Hodge T, Cope M (1 October 2000). "A myosin family tree". J Cell Sci 113 Pt 19 (19): 3353–
4. PMID 10984423. http://jcs.biologists.org/cgi/content/full/113/19/3353.
3. ^ Letunic, I; Bork, P (2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic
tree display and annotation." (Pubmed). Bioinformatics 23 (1): 127–8.
doi:10.1093/bioinformatics/btl529. PMID 17050570.
4. ^ Ciccarelli, FD; Doerks, T; Von Mering, C; Creevey, CJ; Snel, B; Bork, P (2006). "Toward
automatic reconstruction of a highly resolved tree of life." (Pubmed). Science 311 (5765): 1283–7.
doi:10.1126/science.1123061. PMID 16513982.
5. ^ Maher BA (2002). "Uprooting the Tree of Life". The Scientist 16: 18. http://www.the-
scientist.com/yr2002/sep/research1_020916.html.
6. ^ a b c Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.
7. ^ Penny, D., Hendy, M. D. & M. A. Steel. 1992. Progress with methods for constructing
evolutionary trees. Trends in Ecology and Evolution 7: 73-79.
8. ^ A. Dress, K. T. Huber, and V. Moulton. 2001. Metric Spaces in Pure and Applied
Mathematics. Documenta Mathematica LSU 2001: 121-139
9. ^ Woese C (2002). "On the evolution of cells". Proc Natl Acad Sci USA 99 (13): 8742–7.
doi:10.1073/pnas.132266999. PMID 12077305.

• Schuh, R. T. and A. V. Z. Brower. 2009. Biological Systematics: principles and applications
(2nd edn.) ISBN 978-0-8014-4799-0
• MEGA, a free software to draw phylogenetic tress.
Wikimedia Commons has media related to: Phylogenetic tree
[edit] Images
• Phylogenetic Trees Based on 16s rDNA
• Poster-sized tree of life illustration
• A 3D View
• Human Y-Chromosome 2002 Phylogenetic Tree
• In 2003, the Science journal dedicated a special issue to the tree of life, including an online
version of a tree of life.
• iTOL: Interactive Tree Of Life
• Phylogenetic Tree of Artificial Organisms Evolved on Computers
• Miyamoto and Goodman's Phylogram of Eutherian Mammals
[edit] General
• Discover Life An interactive tree based on the U.S. National Science Foundation's
Assembling the Tree of Life Project
• PhyloCode
• A Multiple Alignment of 139 Myosin Sequences and a Phylogenetic Tree
• Tree of Life Web Project
• Aisee.com, detailed and comprehensive family tree of dinosaurs yet available
• SplitsTree
• Dendroscope
• Phylogenetic inferring on the T-REX server
• NCBI's Taxonomy Database[1]
• ETE: A Python Environment for Tree Exploration This is a programming library to analyze,
manipulate and visualize phylogenetic trees. Ref.
Relevant



[hide]v · d · eOrigin of life
Quasispecies model · Protobiont · Universal common descent · Last universal ancestor · RNA world
hypothesis · Iron–sulfur world theory · PAH world hypothesis · Miller–Urey experiment · Panspermia
Retrieved from "http://en.wikipedia.org/wiki/Phylogenetic_tree"
Categories: Phylogenetics | Tree of life | Trees (structure)

W000
Phylogenetic network

A phylogenetic network is any graph used to visualize evolutionary relationships between
sequences, genes, chromosomes, genomes, or species. It is employed when reticulate events such as
hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be
involved. They differ from phylogenetic trees by the explicit modeling, by means of the addition of hybrid
nodes (nodes with two parents) instead of only tree nodes (nodes with only one parent).[1] Phylogenetic
trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with
software such as SplitsTree. A standard format for representing phylogenetic networks is a variant of Newick
format which is extended to support networks as well as trees.[2]
Many kinds and subclasses of phylogenetic networks have been defined based on the biological
phenomenon they represent or which data they are built from (hybridization networks, usually built from
rooted trees, recombination networks from binary sequences, median networks from a set of splits, optimal
realizations and reticulograms from a distance matrix), or restrictions to get computationally tractable
problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling
phylogenetic networks).
Contents
[hide]
• 1 Microevolution
• 2 See also
• 3 References
• 4 Software to compute phylogenetic networks
[edit] Microevolution
Phylogenetic trees also have trouble depicting microevolutionary events, for example the
geographical distribution of muskrat or fish populations of a given species among river networks, because
there is no species boundary to prevent gene flow between populations. Therefore, a more general
phylogenetic network better depicts these situations.[3]
[edit] See also
• Phylogenetics
• Median graph
[edit] References
1. ^ Arenas, M; Miguel Arenas, Gabriel Valiente, and David Posada (2008-10-15).
"Characterization of Reticulate Networks Based on the Coalescent with Recombination". Mol Biol
Evol 25 (12): 2517–2520. doi:10.1093/molbev/msn219. PMID 18927089. PMC 2582979.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2582979.
2. ^ Cardona, G; Gabriel Cardona, Francesc Rosselló, and Gabriel Valiente (2008-12-15).
"Extended Newick: it is time for a standard representation of phylogenetic networks". BMC
Bioinformatics 9 (532): 532. doi:10.1186/1471-2105-9-532. PMID 19077301. PMC 2621367.
3. ^ Legendre, P; Makarenkov, V (Apr 2002). "Reconstruction of biogeographic and
evolutionary networks using reticulograms". Systematic biology 51 (2): 199–216.
doi:10.1080/10635150252899725. ISSN 1063-5157. PMID 12028728
• D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies,
Mol. Biol. Evol., 23(2):254-267, 2006.|
• Makarenkov, V., Kevorkov, D. and Legendre, P. (2006),Phylogenetic Network
Reconstruction Approaches, Applied Mycology and Biotechnology, International Elsevier Series, vol.
6. Bioinformatics, 61-97.
• D. H. Huson, R. Rupp and C. Scornavacca, Phylogenetic Networks, Cambridge University
Press (2011). http://www.phylogenetic-networks.org/
• ^ Arenas, M; Patricio, M; Posada, D; Valiente, G (2010) Characterization of phylogenetic
networks with NetTest. BMC Bioinformatics 11: 268
[edit] Software to compute phylogenetic networks

• Network, Free Phylogenetic Network Software. Network generates evolutionary trees and
networks from genetic, linguistic, and other data.
• Phylogeny programs, some of which compute phylogenetic networks
• List of programs for phylogenetic network reconstruction, evaluation, visualization, etc.
• SplitsTree
• Dendroscope
• Network inferring on the T-REX server
• TCS, Phylogenetic networks from DNA sequences or nucleotide distances using statistical
parsimony.
• NetTest, Characterization of phylogenetic networks.[1]

• A tutorial that reviews the terminology used for phylogenetic networks and covers both split
networks and reticulate networks, their definition and interpretation.
Relevant



W000
Long branch attraction


The introduction to this article provides insufficient context for those unfamiliar with
the subject. Please help improve the article with a good introductory style. (October 2009)
Long branch attraction (LBA) is a phenomenon in phylogenetic analyses (most commonly those
employing maximum parsimony) when rapidly evolving lineages are inferred to be closely related, regardless
of their true evolutionary relationships. For example, in DNA sequence-based analyses, the problem arises
when sequences from two (or more) lineages evolve rapidly. There are only four possible nucleotides and
when DNA substitution rates are high, the probability that two lineages will evolve the same nucleotide at the
same site increases. When this happens, parsimony erroneously interprets this homoplasy as a
synapomorphy (i.e., evolving once in the common ancestor of the two lineages).
This problem can be minimized by using methods that correct for multiple substitutions at the same
site, by breaking up long branches adding taxa related to those with the long branches or by using alternative
slower evolving traits.
[edit] References
• Bergsten, J. (2005): A review of long-branch attraction. Cladistics 21(2): 163-193. PDF
fulltext
• Felsenstein, J. (2004): Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
Relevant


Retrieved from "http://en.wikipedia.org/wiki/Long_branch_attraction"
W000
Clade

For other uses, see Clade (disambiguation).
Cladogram (family tree) of a biological group. The red and blue boxes represent clades (i.e.,
complete branches). The green box is not a clade, but rather represents an evolutionary grade, an
incomplete group, because the blue clade descends from it, but is excluded.
A clade[note 1] is a group consisting of an organism and all its descendants. In the terms of
biological systematics, a clade is a single "branch" on the "tree of life".[1] The idea that such a "natural group"
of organisms should be grouped together and given a taxonomic name is central to biological classification.
In cladistics (which takes its name from the term), clades are the only acceptable units.
The term was coined in 1958 by English biologist Julian Huxley.[1]
Contents
[hide]
• 1 Definitions
• 1.1 Clade and ancestor
• 1.2 Clade definition
• 1.3 Clades as constructs
• 1.4 Clade names
• 2 Taxonomy and systematics
• 3 See also
• 4 Notes
• 5 References
[edit] Definitions
Main article: Phylogenetic definitions
A cladogram of crocodiles, a visual representation of their relationship
[edit] Clade and ancestor

A clade is termed monophyletic, meaning it contains one ancestor which can be an organism,
population, or species and all its descendants.[note 2][2][3] The term clade refers to the grouping of the
ancestor and its living and/or deceased descendants together. The ancestor can be a theoretical or actual
species.
[edit] Clade definition
Three methods of defining clades are featured in phylogenetic nomenclature: node-, stem-, and
apomorphy-based:
• In node-based definition, clade name A refers to the least inclusive clade containing taxa (or
specimens) X, Y, etc., and their common ancestor. The ancestor is the branch point, or node.
• In stem-based definition, A refers to the most inclusive clade containing X, Y, etc., and their
common ancestor, down to where Z branches off below A. Taxa are included between the node of A
and down to (but not including) the branching point to Z; that is, the stem of A.
• In apomorphy-based definition, A refers to the clade identified by an apomorphy (a trait)
found in X, Y, etc., and their common ancestor.
In Linnaean taxonomy, clades are defined by a set of traits (apomorphies) unique to the group. This
system is basically similar to the apomorphy-based clades of phylogenetic nomenclature. The difference is
one of weight: While phylogenetic nomenclature bases the group on an ancestor with a certain trait,
Linnaean taxonomy uses the traits themselves to define the group.
[edit] Clades as constructs

In cladistics, the clade is a hypothetical construct based on experimental data. Clades are found
using multiple (sometimes hundreds) of traits from a number of species (or specimens) and analysing them
statistically to find the most likely phylogenetic tree for the group. Although similar in some ways to a
biological classification of species, the method is statistical and more open to scrutiny than traditional
methods. Although taxonomists use clades as a tool in classification where feasible, the taxonomic "tree of
life" is not the same as the cladistic. The traditional genus, family, etc. names are not necessarily clades;
though they will often be.
[edit] Clade names

In Linnaean systematics, the various groups are ordered into a series of taxonomic ranks (the
familiar order, family etc.). These ranks will by convention dictate the ending to names for some groups.
Clades do not by their nature fit this scheme, and no such restriction exists as to their names in cladistics.
There is however a convention for naming more or less inclusive groups, which are given prefixes like crown-
or pan-, see Crown group.
[edit] Taxonomy and systematics
Early phylogenetic tree by Haeckel, 1866
The idea of a "clade" did not exist in pre-Darwinian Linnaean taxonomy, which was based only on
morphological similarities between organisms – although it happens that many of the better known animal
groups in Linnaeus' original Systema Naturae (notably among the vertebrate groups) do represent clades.
With the publication of Darwin's theory of evolution in 1859, taxonomy gained a theoretical basis, and the
idea was born that groups used in a system of classification should represent branches on the evolutionary
tree of life. In the century and a half since then, taxonomists have worked to make the taxonomic system
reflect evolution. However, partly because the Tree of Life branches rather unevenly, the hierarchy of the
Linnaean system does not always lend itself well to representing clades. The result is that when it comes to
naming, cladistics and Linnaean taxonomy are not always compatible. In particular, higher level taxa in
Linnaean taxonomy often represent evolutionary grades rather than clades, resulting in groups made up of
clades where one or two sub-branches have been excluded. Typical examples include bony fishes, which
include the ancestor of tetrapods, and reptiles, ancestral to both birds and mammals.[note 3]
In phylogenetic nomenclature, clades can be nested at any level, and do not have to be slotted into a
small number of ranks in an overall hierarchy. In contrast, the Linnaean units of "order", "class" etc. must be
used when naming a new taxon. As there are only seven formal levels to the Linnaean system (species being
the lowest), only a finite number of sub- and super-units can be created. In order to be able to use the full
complexity of taxonomic trees (cladograms) in an area with which they are very familiar, some researchers
have opted to dispense with ranks all together, instead using clade names without Linnaean ranks. The
reason for preferring one system over the other is partly one of application: cladistic trees give details,
suitable for specialists; the Linnaean system gives a well ordered overview, at the expense of details of the
phylogenetic tree.
In a few instances, the Linnaean system has actually impeded our understanding of the phylogeny
and broad evolutionary patterns. The best known example is the interpretation of the strange fossils of the
Burgess Shale and the subsequent idea of a "Cambrian Explosion" [4] With the application of cladistics, and
the rejection of any significance of the concept of phyla, the confusion of the late 20th century over the
Burgess animals has been resolved. It appears there never was an "explosion" of major bauplans with
subsequent extinctions.[5] The seemingly weird critters themselves have been found to be representatives of
a group, the Lobopodia, that includes arthropods, water bears and velvet worms.[6]
In most instances the two systems are not at odds, however. The cladistic statement, that the clade
Lobopodia contains (among others) the Arthropoda, Tardigrada and Onychophora, is factually identical to the
Linnaean evolutionary statement that the group Lobopodia is ancestral to the phyla Arthropoda, Tardigrada
and Onychophora. The difference is one of semantics rather than phylogeny.
[edit] See also

• Cladistics
• Phylogeny
• Paraphyly
• Polyphyly
• Phylogenetic nomenclature
• Binomial nomenclature
• Crown group
[edit] Notes
1. ^ (from Ancient Greek κλάδος, klados, "branch")
2. ^ A semantic case has been made that the name should be "holophyletic," but this term has
not yet acquired widespread use. For more information, see holophyly
3. ^ The term "reptile" is here to be understood as traditionally defined, e.g. Romer & Parson
(1985): The Vertebrate Body. (6th ed.) Saunders, Philadelphia. There are other (cladistic) definitions
of "reptile" that exclude the first amniotes and the synapsid line, see Sauropsida.
[edit] References
1. ^ a b Dupuis, Claude (1984). "Willi Hennig's impact on taxonomic thought". Annual Review of
Ecology and Systematics 15: 1–24. ISSN 0066-4162.
2. ^ "The PhyloCode, Chapter 1". International Society for Phylogenetic Nomenclature. 2009.
http://www.ohio.edu/phylocode/art1-3.html#chapter1. Retrieved 23 January 2010.
3. ^ Envall, Mat S. (2008). "On the difference between mono-, holo-, and paraphyletic groups: a
consistent distinction of process and pattern". Biological Journal of the Linnaean Society 94: 217.
doi:10.1111/j.1095-8312.2008.00984.x.
4. ^ Budd, G.E.; Jensen, S. (2000). "A critical reappraisal of the fossil record of the bilaterian
phyla". Biological Reviews 75 (02): 253–295. doi:10.1017/S000632310000548X. PMID 10881389.
http://journals.cambridge.org/production/action/cjoGetFulltext?fulltextid=624.
5. ^ Erwin, D.H. (2007). "Disparity: Morphological Pattern And Developmental Context".
Palaeontology 50: 57. doi:10.1111/j.1475-4983.2006.00614.x.
6. ^ Whittle, R. J.; Gabbott, S. E.; Aldridge, R. J.; Theron, J. (2009). "An Ordovician Lobopodian
from the Soom Shale Lagerstätte, South Africa". Palaeontology 52: 561–567. doi:10.1111/j.1475-
4983.2009.00860.x.

Look up clade in Wiktionary, the free dictionary.
• Evolving Thoughts: Clade

• DM Hillis, D Zwickl & R Gutell. "Tree of life". An unrooted cladogram depicting around 3000
species.
• Phylogenetic systematics, an introductory slide-show on evolutionary trees University of
California, Berkeley
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Retrieved from "http://en.wikipedia.org/wiki/Clade"
W000
Evolutionary grade

Cladogram (family tree) of a biological group. The green box may represent an evolutionary grade, a
group united by anatomical and physiological traits rather than phylogeny. The red and blue boxes are
clades (i.e., complete branches)
In alpha taxonomy, a grade refers to a level of morphological and/or physiological complexity. The
term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.[1]
Contents
[hide]
• 1 Definition
• 2 Grades in systematics
• 3 Examples
• 4 References
[edit] Definition
An evolutionary grade is a group of species united by morphological and/or physiological traits, that
has given rise to another group that differs markedly from the ancestral condition, and is thus not considered
part of the ancestral group. The ancestral group will not be phylogenetically complete (i.e. will not form a
clade), so will usually represent a paraphyletic taxon.
The most commonly cited example is that of reptiles. In the early 19th century, the French naturalist
Latreille was the first to divide tetrapods into the four familiar classes of amphibians, reptiles, birds and
mammals.[2] In this system, reptiles are characterized by traits such as laying membranous or shelled eggs,
having skin covered in scales and/or scutes, and having a 'cold-blooded' metabolism. However, the
ancestors of mammals and birds also had these traits and so were reptiles in this sense, making reptiles a
grade rather than a clade.[3]
Paraphyletic taxa will often, but not always, represent evolutionary grades. In some cases
paraphyletic taxa are united simply by not being part of any other groups, and give rise to so called
wastebasket taxa which may even be polyphyletic.
[edit] Grades in systematics
The genus Australopithecus is ancestral to 'Homo, yet actively in use in palaeoanthropology.

The traditional Linnaean way of defining taxa is through the use of anatomical traits. When the actual
phylogenetic relationship is unknown, well defined groups sometimes turn out to be defined by traits that are
primitive rather than derived. In Linnaean systematics, evolutionary grades are accepted in higher taxonomic
ranks, though generally avoided at family level and below. In phylogenetic nomenclature evolutionary grades
(or any other form of paraphyly) are not accepted.[4]
Where information about phylogenetic relationships is available, organisms are preferentially
grouped into clades. Where data is lacking, or groups of uncertain relationship are to be compared, the
cladistic method is limited and grade provides a useful tool for comparing organisms. This is particularly
common in palaeontology, where fossils are often fragmentary and difficult to interpret. Thus,
palaeontological works are often using evolutionary grades as formal or informal taxa, including examples
such as Labyrinthodonts, Anapsids, Synapsids, Dinosaurs, Ammonites, Eurypterid, Lobopodes and many of
the more well known taxa of human evolution.
Evolutionary grades, being united by gross morphological traits are often eminently recognizable in
the field. While paraphyletic taxa are sought eliminated in taxonomy, such grades are sometimes kept as
formal or informal groups on basis of their usefulness for laymen and field researchers.[4] When referring to a
group of organisms, the term "grade" is usually enclosed in quotation marks to denote its status as a
paraphyletic term.
[edit] Examples
Bryophyta, mosses in the wide sense, are the physiologically primitive land plants
• Bryophytes were long considered a natural group, defined as those land plants which lacked
vascular systems. However, molecular evidence shows that the bryophytes are not monophyletic
since mosses, liverworts and hornworts are in fact separate lineages.[5] However, the three clades
have a similar degree of complexity, and the "bryophyte grade" is a useful benchmark when
analysing early plants - it contains information about the status of fossils which cannot always be
classified into extant groups.[6]
• Fish represent a grade, inasmuch as they have given rise to the land vertebrates. In fact, the
three traditional classes of fish (Agnatha, Chondrichthyes and Osteichthyes) all represent
evolutionary grades.[7]
• Amphibians in the biological sense (including the extinct Labyrinthodonts) represent a grade,
in that they are also the ancestors of the amniotes.[7]
• Reptiles are composed of the cold-blooded amniotes, this excludes birds and mammals[7]
• Dinosaurs were proposed to be the ancestors of birds as early as the 1860s.[8] Yet the term
sees both popular and scientific use, the dinosaurs representing an easily recognizable group.
• Lizards as a unit represent an evolutionary grade, defined by their retention of limbs relative
to snakes and Amphisbaenans.[9]
[edit] References
1. ^ Huxley J. 1959. Clades and grades. In Cain A.J. (ed) Function and taxonomic importance.
Systematics Association, London.
2. ^ Latreille, P.A. (1804). Nouveau Dictionnaire à Histoire Naturelle, xxiv; cited in Latreille, P.A.
(1825).Familles naturelles du règne animal, exposés succinctement et dans un ordre analytique .
3. ^ Colin Tudge (2000). The Variety of Life. Oxford University Press. ISBN 0198604262.
4. ^ a b Grant, Verne (1998), "Primary Classification and Phylogeny of the Polemoniaceae, with
Comments on Molecular Cladistics", American Journal of Botany (Botanical Society of America) 85
(6): 741, doi:10.2307/2446408, http://www.amjbot.org/cgi/content/abstract/85/6/741
5. ^ Qiu, Y.L.; Li, L.; Wang, B.; Chen, Z.; Knoop, V.; Groth-malonek, M.; Dombrovska, O.; Lee,
J.; Kent, L.; Rest, J.; Others, (2006). "The deepest divergences in land plants inferred from
phylogenomic evidence". Proceedings of the National Academy of Sciences 103 (42): 15511.
doi:10.1073/pnas.0603335103. PMID 17030812. PMC 1622854.
http://www.pnas.org/cgi/content/abstract/103/42/15511. Retrieved 2008-05-06.
6. ^ e.g. Strother, P.K.; Al-hajri, S.; Traverse, A. (1996). "New evidence for land plants from the
lower Middle Ordovician of Saudi Arabia". Geology 24 (1): 55–58. doi:10.1130/0091-
7613(1996)024<0055:NEFLPF>2.3.CO;2.
7. ^ a b c Romer, A.S. & T.S. Parsons. 1977. The Vertebrate Body. 5th ed. Saunders,
Philadelphia. (6th ed. 1985)
8. ^ Huxley, Thomas H. (1870). "Further evidence of the affinity between the dinosaurian
reptiles and birds". Quarterly Journal of the Geological Society of London 26: 12–31.
doi:10.1144/GSL.JGS.1870.026.01-02.08.
9. ^ Gibbons, J. Whitfield; Gibbons, Whit (1983). Their Blood Runs Cold: Adventures With
Reptiles and Amphibians. Alabama: University of Alabama Press. pp. 164. ISBN 978-0817301354.
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Retrieved from "http://en.wikipedia.org/wiki/Evolutionary_grade"
Categories: Taxonomy | Evolutionary biology terminology

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Ghost lineage

This article does not cite any references or sources.
A ghost lineage is a phylogenetic lineage that is inferred to exist but has no fossil record.

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W000
Maximum parsimony (phylogenetics)

(Redirected from Maximum parsimony)
This article's introduction section may not adequately summarize its contents. To
comply with Wikipedia's lead section guidelines, please consider expanding the lead to
provide an accessible overview of the article's key points. (September 2009)
Parsimony is a non-parametric statistical method commonly used in computational phylogenetics for
estimating phylogenies. Under parsimony, the preferred phylogenetic tree is the tree that requires the least
evolutionary change to explain some observed data.
Contents
[hide]
• 1 In detail
• 2 Character data
• 3 Taxon sampling
• 4 Analysis
• 5 Problems with maximum parsimony phylogeny estimation
• 6 Criticism
• 7 Alternatives
• 7.1 Maximum likelihood
• 7.2 Bayesian phylogenetic inference
• 7.3 Distance matrix methods
• 8 References
[edit] In detail
Parsimony is part of a class of character-based tree estimation methods which use a matrix of
discrete phylogenetic characters to infer one or more optimal phylogenetic trees for a set of taxa, commonly
a set of species or reproductively-isolated populations of a single species. These methods operate by
evaluating candidate phylogenetic trees according to an explicit optimality criterion; the tree with the most
favorable score is taken as the best estimate of the phylogenetic relationships of the included taxa. Maximum
parsimony is used with most kinds of phylogenetic data; until recently, it was the only widely-used character-
based tree estimation method used for morphological data.
Estimating phylogenies is not a trivial problem. A huge number of possible phylogenetic trees exist
for any reasonably sized set of taxa; for example, a mere ten species gives over two million possible
unrooted trees. These possibilities must be searched to find a tree that best fits the data according to the
optimality criterion. However, the data themselves do not lead to a simple, arithmetic solution to the problem.
Ideally, we would expect the distribution of whatever evolutionary characters (such as phenotypic traits or
alleles) to directly follow the branching pattern of evolution. Thus we could say that if two organisms possess
a shared character, they should be more closely related to each other than to a third organism that lacks this
character (provided that character was not present in the last common ancestor of all three, in which case it
would be a symplesiomorphy). We would predict that bats and monkeys are more closely related to each
other than either is to a fish, because they both possess hair—a synapomorphy. However, we cannot say that
bats and monkeys are more closely related to one another than they are to whales because they share hair,
because we believe the last common ancestor of the three had hair.
However, the well-understood phenomena of convergent evolution, parallel evolution, and
evolutionary reversals (collectively termed homoplasy) add an unpleasant wrinkle to the problem of
estimating phylogeny. For a number of reasons, two organisms can possess a trait not present in their last
common ancestor: If we naively took the presence of this trait as evidence of a relationship, we would
reconstruct an incorrect tree. Real phylogenetic data include substantial homoplasy, with different parts of the
data suggesting sometimes very different relationships. Methods used to estimate phylogenetic trees are
explicitly intended to resolve the conflict within the data by picking the phylogenetic tree that is the best fit to
all the data overall, accepting that some data simply will not fit. It is often mistakenly believed that parsimony
assumes that convergence is rare; in fact, even convergently-derived characters have some value in
maximum-parsimony-based phylogenetic analyses, and the prevalence of convergence does not
systematically affect the outcome of parsimony-based methods.[1]
Data that do not fit a tree perfectly are not simply "noise", they can contain relevant phylogenetic
signal in some parts of a tree, even if they conflict with the tree overall. In the whale example given above,
the lack of hair in whales is homoplastic: It reflects a return to the condition present in ancient ancestors of
mammals, who lacked hair. This similarity between whales and ancient mammal ancestors is in conflict with
the tree we accept, since it implies that the mammals with hair should form a group excluding whales.
However, among the whales, the reversal to hairlessness actually correctly associates the various types of
whales (including dolphins and porpoises) into the group Cetacea. Still, the determination of the best-fitting
tree—and thus which data do not fit the tree—is a complex process. Maximum parsimony is one method
developed to do this.
[edit] Character data

The input data used in a maximum parsimony analysis is in the form of "characters" for a range of
taxa. There is no generally agreed-upon definition of a phylogenetic character, but operationally a character
can be thought of as an attribute, an axis along which taxa are observed to vary. These attributes can be
physical (morphological), molecular, genetic, physiological, or behavioral. The only widespread agreement
on characters seems to be that variation used for character analysis should reflect heritable variation.
Whether it must be directly heritable, or whether indirect inheritance (e.g., learned behaviors) is acceptable,
is not entirely resolved.
Each character is divided into discrete character states, into which the variations observed are
classified. Character states are often formulated as descriptors, describing the condition of the character
substrate. For example, the character "eye color" might have the states "blue" and "brown." Characters can
have two or more states (they can have only one, but these characters lend nothing to a maximum parsimony
analysis, and are often excluded).
Coding characters for phylogenetic analysis is not an exact science, and there are numerous
complicating issues. Typically, taxa are scored with the same state if they are more similar to one another in
that particular attribute than each is to taxa scored with a different state. This is not straightforward when
character states are not clearly delineated or when they fail to capture all of the possible variation in a
character. How would one score the previously mentioned character for a taxon (or individual) with hazel
eyes? Or green? As noted above, character coding is generally based on similarity: Hazel and green eyes
might be lumped with blue because they are more similar to that color (being light), and the character could
be then recoded as "eye color: light; dark." Alternately, there can be multi-state characters, such as "eye
color: brown; hazel, blue; green."
Ambiguities in character state delineation and scoring can be a major source of confusion, dispute,
and error in phylogenetic analysis using character data. Note that, in the above example, "eyes: present;
absent" is also a possible character, which creates issues because "eye color" is not applicable if eyes are
not present. For such situations, a "?" ("unknown") is scored, although sometimes "X" or "-" (the latter usually
in sequence data) are used to distinguish cases where a character cannot be scored from a case where the
state is simply unknown. Current implementations of maximum parsimony generally treat unknown values in
the same manner: the reasons the data are unknown have no particular effect on analysis. Effectively, the
program treats a ? as if it held the state that would involve the fewest extra steps in the tree (see below),
although this is not an explicit step in the algorithm.
Genetic data are particularly amenable to character-based phylogenetic methods such as maximum
parsimony because protein and nucleotide sequences are naturally discrete: A particular position in a
nucleotide sequence can be either adenine, cytosine, guanine, or thymine / uracil, or a sequence gap; a
position (residue) in a protein sequence will be one of the basic amino acids or a sequence gap. Thus,
character scoring is rarely ambiguous, except in cases where sequencing methods fail to produce a definitive
assignment for a particular sequence position. Sequence gaps are sometimes treated as characters,
although there is no consensus on how they should be coded.
Characters can be treated as unordered or ordered. For a binary (two-state) character, this makes
little difference. For a multi-state character, unordered characters can be thought of as having an equal "cost"
(in terms of number of "evolutionary events") to change from any one state to any other; complementarily,
they do not require passing through intermediate states. Ordered characters have a particular sequence in
which the states must occur through evolution, such that going between some states requires passing
through an intermediate. This can be thought of complementarily as having different costs to pass between
different pairs of states. In the eye-color example above, it is possible to leave it unordered, which imposes
the same evolutionary "cost" to go from brown-blue, green-blue, green-hazel, etc. Alternately, it could be
ordered brown-hazel-green-blue; this would normally imply that it would cost two evolutionary events to go
from brown-green, three from brown-blue, but only one from brown-hazel. This can also be thought of as
requiring eyes to evolve through a "hazel stage" to get from brown to green, and a "green stage" to get from
hazel to blue, etc.
There is a lively debate on the utility and appropriateness of character ordering, but no consensus.
Some authorities order characters when there is a clear logical, ontogenetic, or evolutionary transition among
the states (for example, "legs: short; medium; long"). Some accept only some of these criteria. Some run an
unordered analysis, and order characters that show a clear order of transition in the resulting tree (which
practice might be accused of circular reasoning). Some authorities refuse to order characters at all,
suggesting that it biases an analysis to require evolutionary transitions to follow a particular path.
It is also possible to apply differential weighting to individual characters. This is usually done relative
to a "cost" of 1. Thus, some characters might be seen as more likely to reflect the true evolutionary
relationships among taxa, and thus they might be weighted at a value 2 or more; changes in these characters
would then count as two evolutionary "steps" rather than one when calculating tree scores (see below). There
has been much discussion in the past about character weighting. Most authorities now weight all characters
equally, although exceptions are common. For example, allele frequency data is sometimes pooled in bins
and scored as an ordered character. In these cases, the character itself is often downweighted so that small
changes in allele frequencies count less than major changes in other characters. Also, the third codon
position in a coding nucleotide sequence is particularly labile, and is sometimes downweighted, or given a
weight of 0, on the assumption that it is more likely to exhibit homoplasy. In some cases, repeated analyses
are run, with characters reweighted in inverse proportion to the degree of homoplasy discovered in the
previous analysis (termed successive weighting); this is another technique that might be considered circular
reasoning.
Character state changes can also be weighted individually. This is often done for nucleotide
sequence data; it has been empirically determined that certain base changes (A-C, A-T, G-C, G-T, and the
reverse changes) occur much less often than others. These changes are therefore often weighted more. As
shown above in the discussion of character ordering, ordered characters can be thought of as a form of
character state weighting.
Some systematists prefer to exclude characters known to be, or suspected to be, highly homoplastic
or that have a large number of unknown entries ("?"). As noted below, theoretical and simulation work has
demonstrated that this is likely to sacrifice accuracy rather than improve it. This is also the case with
characters that are variable in the terminal taxa: theoretical, congruence, and simulation studies have all
demonstrated that such polymorphic characters contain significant phylogenetic information.[ citation needed]
[edit] Taxon sampling
The time required for a parsimony analysis (or any phylogenetic analysis) is proportional to the
number of taxa (and characters) included in the analysis. Also, because more taxa require more branches to
be estimated, more uncertainty may be expected in large analyses. Because data collection costs in time and
money often scale directly with the number of taxa included, most analyses include only a fraction of the taxa
that could have been sampled. Indeed, some authors have contended that four taxa (the minimum required
to produce a meaningful unrooted tree) are all that is necessary for accurate phylogenetic analysis, and that
more characters are more valuable than more taxa in phylogenetics. This has led to a raging controversy
about taxon sampling.
Empirical, theoretical, and simulation studies have led to a number of dramatic demonstrations of the
importance of adequate taxon sampling. Most of these can be summarized by a simple observation: a
phylogenetic data matrix has dimensions of characters times taxa. Doubling the number of taxa doubles the
amount of information in a matrix just as surely as doubling the number of characters. Each taxon represents
a new sample for every character, but, more importantly, it (usually) represents a new combination of
character states. These character states can not only determine where that taxon is placed on the tree, they
can inform the entire analysis, possibly causing different relationships among the remaining taxa to be
favored by changing estimates of the pattern of character changes.
The most disturbing weakness of parsimony analysis, that of long-branch attraction (see below) is
particularly pronounced with poor taxon sampling, especially in the four-taxon case. This is a well-understood
case in which additional character sampling may not improve the quality of the estimate. As taxa are added,
they often break up long branches (especially in the case of fossils), effectively improving the estimation of
character state changes along them. Because of the richness of information added by taxon sampling, it is
even possible to produce highly accurate estimates of phylogenies with hundreds of taxa using only a few
thousand characters.[citation needed]
Although many studies have been performed, there is still much work to be done on taxon sampling
strategies. Because of advances in computer performance, and the reduced cost and increased automation
of molecular sequencing, sample sizes overall are on the rise, and studies addressing the relationships of
hundreds of taxa (or other terminal entities, such as genes) are becoming common. Of course, this is not to
say that adding characters is not also useful; the number of characters is increasing as well.
Some systematists prefer to exclude taxa based on the number of unknown character entries ("?")
they exhibit, or because they tend to "jump around" the tree in analyses (i.e., they are "wildcards"). As noted
below, theoretical and simulation work has demonstrated that this is likely to sacrifice accuracy rather than
improve it. Although these taxa may generate more most-parsimonious trees (see below), methods such as
agreement subtrees and reduced consensus can still extract information on the relationships of interest.
It has been observed that inclusion of more taxa tends to lower overall support values (bootstrap
percentages or decay indices, see below). The cause of this is clear: as additional taxa are added to a tree,
they subdivide the branches to which they attach, and thus dilute the information that supports that branch.
While support for individual branches is reduced, support for the overall relationships is actually increased.
Consider analysis that produces the following tree: (fish ,(lizard ,(whale, (cat, monkey)))). Adding a rat and a
walrus will probably reduce the support for the (whale, (cat, monkey)) clade, because the rat and the walrus
may fall within this clade, or outside of the clade, and since these five animals are all relatively closely
related, there should be more uncertainty about their relationships. Within error, it may be impossible to
determine any of these animals' relationships relative to one another. However, the rat and the walrus will
probably add character data that cements the grouping any two of these mammals exclusive of the fish or the
lizard; where the initial analysis might have been mislead, say, by the presence of fins in the fish and the
whale, the presence of the walrus, with blubber and fins like a whale but whiskers like a cat and a rat, firmly
ties the whale to the mammals.
To cope with this problem, agreement subtrees, reduced consensus, and double-decay analysis
seek to identify supported relationships (in the form of "n-taxon statements," such as the four-taxon statement
"(fish, (lizard, (cat, whale)))") rather than whole trees. If the goal of an analysis is a resolved tree, as is the
case for comparative phylogenetics, these methods cannot solve the problem. However, if the tree estimate
is so poorly supported, the results of any analysis derived from the tree will probably be too suspect to use
anyway.
[edit] Analysis
A maximum parsimony analysis runs in a very straightforward fashion. Trees are scored according to
the degree to which they imply a parsimonious distribution of the character data. The most parsimonious tree
for the dataset represents the preferred hypothesis of relationships among the taxa in the analysis.
Trees are scored (evaluated) by using a simple algorithm to determine how many "steps"
(evolutionary transitions) are required to explain the distribution of each character. A step is, in essence, a
change from one character state to another, although with ordered characters some transitions require more
than one step. Contrary to popular belief, the algorithm does not explicitly assign particular character states
to nodes (branch junctions) on a tree: the least number of steps can involve multiple, equally costly
assignments and distributions of evolutionary transitions. What is optimized is the total number of changes.
There are many more possible phylogenetic trees than can be searched exhaustively for more than
eight taxa or so. A number of algorithms are therefore used to searching among the possible trees. Many of
these involve taking an initial tree (usually the favored tree from the last iteration of the algorithm), and
perturbing it to see if the change produces a higher score.
The trees resulting from parsimony search are unrooted: They show all the possible relationships of
the included taxa, but they lack any statement on relative times of divergence. A particular branch is chosen
to root the tree by the user. This branch is then taken to be outside all the other branches of the tree, which
together form a monophyletic group. This imparts a sense of relative time to the tree. Incorrect choice of a
root can result in incorrect relationships on the tree, even if the tree is itself correct in its unrooted form.
Parsimony analysis often returns a number of equally most-parsimonious trees (MPTs). A large
number of MPTs is often seen as an analytical failure, and is widely believed to be related to the number of
missing entries ("?") in the dataset, characters showing too much homoplasy, or the presence of topologically
labile "wildcard" taxa (which may have many missing entries). Numerous methods have been proposed to
reduce the number of MPTs, including removing characters or taxa with large amounts of missing data
before analysis, removing or downweighting highly homoplastic characters (successive weighting) or
removing wildcard taxa (the phylogenetic trunk method) a posteriori and then reanalyzing the data.
Numerous theoretical and simulation studies have demonstrated that highly homoplastic characters,
characters and taxa with abundant missing data, and "wildcard" taxa contribute to the analysis. Although
excluding characters or taxa may appear to improve resolution, the resulting tree is based on less data, and
is therefore a less reliable estimate of the phylogeny (unless the characters or taxa are non informative, see
safe taxonomic reduction). Today's general consensus is that having multiple MPTs is a valid analytical
result; it simply indicates that there is insufficient data to resolve the tree completely. In many cases, there is
substantial common structure in the MPTs, and differences are slight and involve uncertainty in the
placement of a few taxa. There are a number of methods for summarizing the relationships within this set,
including consensus trees, which show common relationships among all the taxa, and pruned agreement
subtrees, which show common structure by temporarily pruning "wildcard" taxa from every tree until they all
agree. Reduced consensus takes this one step further, but showing all subtrees (and therefore all
relationships) supported by the input trees.
Even if multiple MPTs are returned, parsimony analysis still basically produces a point-estimate,
lacking confidence intervals of any sort. This has often been levelled as a criticism, since there is certainly
error in estimating the most-parsimonious tree, and the method does not inherently include any means of
establishing how sensitive its conclusions are to this error. Several methods have been used to assess
support.
Jackknifing and bootstrapping, well-known statistical resampling procedures, have been employed
with parsimony analysis. The jackknife, which involves resampling without replacement ("leave-one-out") can
be employed on characters or taxa; interpretation may become complicated in the latter case, because the
variable of interest is the tree, and comparison of trees with different taxa is not straightforward. The
bootstrap, resampling with replacement (sample x items randomly out of a sample of size x, but items can be
picked multiple times), is only used on characters, because adding duplicate taxa does not change the result
of a parsimony analysis. The bootstrap is much more commonly employed in phylogenetics (as elsewhere);
both methods involve an arbitrary but large number of repeated iterations involving perturbation of the
original data followed by analysis. The resulting MPTs from each analysis are pooled, and the results are
usually presented on a 50% Majority Rule Consensus tree, with individual branches (or nodes) labelled with
the percentage of bootstrap MPTs in which they appear. This "bootstrap percentage" (which is not a P-value,
as is sometimes claimed) is used as a measure of support. Technically, it is supposed to be a measure of
repeatability, the probability that that branch (node, clade) would be recovered if the taxa were sampled
again. Experimental tests with viral phylogenies suggest that the bootstrap percentage is not a good
estimator of repeatability for phylogenetics, but it is a reasonable estimator of accuracy.[ citation needed] In
fact, it has been shown that the bootstrap percentage, as an estimator of accuracy, is biased, and that this
bias results on average in an underestimate of confidence (such that as little as 70% support might really
indicate up to 95% confidence). However, the direction of bias cannot be ascertained in individual cases, so
assuming that high values bootstrap support indicate even higher confidence is unwarranted.
Another means of assessing support is Bremer support, or the decay index (which is technically not
an index). This is simply the difference in number of steps between the score of the MPT(s), and the score of
the most parsimonious tree that does NOT contain a particular clade (node, branch). It can be thought of as
the number of steps you have to add to lose that clade; implicitly, it is meant to suggest how great the error in
the estimate of the score of the MPT must be for the clade to no longer be supported by the analysis,
although this is not necessarily what it does. Decay index values are often fairly low (one or two steps being
typical), but they often appear to be proportional to bootstrap percentages. However, interpretation of decay
values is not straightforward, and they seem to be preferred by authors with philosophical objections to the
bootstrap (although many morphological systematists, especially paleontologists, report both). Double-decay
analysis is a decay counterpart to reduced consensus that evaluates the decay index for all possible subtree
relationships (n-taxon statements) within a tree.
[edit] Problems with maximum parsimony phylogeny estimation
An example of long branch attraction. Branches A & C have a high number of substitutions.
Maximum parsimony is a very simple approach, and is popular for this reason. However, it is not
statistically consistent. That is, it is not guaranteed to produce the true tree with high probability, given
sufficient data. Consistency, here meaning the monotonic convergence on the correct answer with the
addition of more data, is a desirable property of any statistical method. As demonstrated in 1978 by Joe
Felsenstein, maximum parsimony can be inconsistent under certain conditions. The category of situations in
which this is known to occur is called long branch attraction, and occurs, for example, where there are long
branches (a high level of substitutions) for two characters (A & C), but short branches for another two (B &
D). A and B diverged from a common ancestor, as did C and D.
Assume for simplicity that we are considering a single binary character (it can either be + or -).
Because the distance from B to D is small, in the vast majority of all cases, B and D will be the same. Here,
we will assume that they are both + (+ and - are assigned arbitrarily and swapping them is only a matter of
definition). If this is the case, there are four remaining possibilities. A and C can both be +, in which case all
taxa are the same and all the trees have the same length. A can be + and C can be -, in which case only one
character is different, and we cannot learn anything, as all trees have the same length. Similarly, A can be -
and C can be +. The only remaining possibility is that A and C are both -. In this case, however, we group A
and C together, and B and D together. As a consequence, when we have a tree of this type, the more data
we collect (i.e. the more characters we study), the more we tend towards the wrong tree.
A simple and effective method for determining whether or not long branch attraction is affecting tree
topology is the SAW method, named for Siddal and Whiting. If long branch attraction is suspected in a pair of
taxa (A and B), simply remove taxon A ("saw" off the branch) and re-run the analysis. Then remove A and
replace B, running the analysis again. If either of the taxa appear at different branch points in the absence of
the other, there is evidence of long branch attraction. Since long branches can't possibly attract one another
when only one is in the analysis, consistent taxon placement between treatments would indicate long branch
attraction is not a problem (Siddal & Whiting, 1999).
Several other methods of phylogeny estimation are available, including maximum likelihood,
Bayesian phylogeny inference, neighbour joining, and quartet methods. Of these, the first two both use a
likelihood function, and, if used properly, are theoretically immune to long-branch attraction. These methods
are both parametric, meaning that they rely on an explicit model of character evolution. It has been shown
that, for some suboptimal models, these methods can also be inconsistent.[ citation needed]
Another complication with maximum parsimony is that finding the most parsimonious tree is an NP-
Hard problem[2]. The only currently available, efficient way of obtaining a solution, given an arbitrarily large
set of taxa, is by using heuristic methods which do not guarantee that the most parsimonious tree will be
recovered. These methods employ hill-climbing algorithms to progressively approach the best tree. However,
it has been shown that there can be "tree islands" of suboptimal solutions, and the analysis can become
trapped in these local optima. Thus, complex, flexible heuristics are required to ensure that tree space has
been adequately explored. Several heuristics are available, including nearest neighbor interchange (NNI),
tree bisection / reconnection (TBR), and the phylogenetic ratchet. This problem is certainly not unique to MP;
any method that uses an optimality criterion faces the same problem, and none offer easy solutions.
[edit] Criticism
It has been asserted that a major problem, especially for paleontology, is that maximum parsimony
assumes that the only way two species can share the same nucleotide at the same position is if they are
genetically related. This asserts that phylogenetic applications of parsimony assume that all similarity is
homologous (other interpretations, such as the assertion that two organisms might NOT be related at all, are
nonsensical). This is emphatically not the case: as with any form of character-based phylogeny estimation,
parsimony is used to test the homologous nature of similarities by finding the phylogenetic tree which best
accounts for all of the similarities.
For example, birds and bats have wings, while crocodiles and humans do not. If these were the only
data available, maximum parsimony would tend to group crocodiles with humans, and birds with bats (as
would any other method of phylogenetic inference). We believe that humans are actually more closely related
to bats than to crocodiles or birds. Our belief is founded on additional data that was not considered in the
one-character example (using wings). If even a tiny fraction of these additional data, including information on
skeletal structure, soft-tissue morphology, integument, behaviour, genetics, etc., were included in the
analysis, the faint phylogenetic signal produced by the presence of wings in birds and bats would be
overwhelmed by the preponderance of data supporting the (human, bat)(bird, crocodile) tree.
It is often stated that parsimony is not relevant to phylogenetic inference because "evolution is not
parsimonious." In most cases, there is no explicit alternative proposed; if no alternative is available, any
statistical method is preferable to none at all. Additionally, it is not clear what would be meant if the statement
"evolution is parsimonious" were in fact true. This could be taken to mean that more character changes may
have occurred historically than are predicted using the parsimony criterion. Because parsimony phylogeny
estimation reconstructs the minimum number of changes necessary to explain a tree, this is quite possible.
However, it has been shown through simulation studies, testing with known in vitro viral phylogenies, and
congruence with other methods, that the accuracy of parsimony is in most cases not compromised by this.
Parsimony analysis uses the number of character changes on trees to choose the best tree, but it does not
require that exactly that many changes, and no more, produced the tree. As long as the changes that have
not been accounted for are randomly distributed over the tree (a reasonable null expectation), the result
should not be biased. In practice, the technique is robust: maximum parsimony exhibits minimal bias as a
result of choosing the tree with the fewest changes.
An analogy can be drawn with choosing among contractors based on their initial (nonbinding)
estimate of the cost of a job. The actual finished cost is very likely to be higher than the estimate. Despite
this, choosing the contractor who furnished the lowest estimate should theoretically result in the lowest final
project cost. This is because, in the absence of other data, we would assume that all of the relevant
contractors have the same risk of cost overruns. In practice, of course, unscrupulous business practices may
bias this result; in phylogenetics, too, some particular phylogenetic problems (for example, long branch
attraction, described above) may potentially bias results. In both cases, however, there is no way to tell if the
result is going to be biased, or the degree to which it will be biased, based on the estimate itself. With
parsimony too, there is no way to tell that the data are positively misleading, without comparison to other
evidence.
Along the same lines, parsimony is often characterized as implicitly adopting the philosophical
position that evolutionary change is rare, or that homoplasy (convergence and reversal) is minimal in
evolution. This is not entirely true: parsimony minimizes the number of convergences and reversals that are
assumed by the preferred tree, but this may result in a relatively large number of such homoplastic events. It
would be more appropriate to say that parsimony assumes only the minimum amount of change implied by
the data. As above, this does not require that these were the only changes that occurred; it simply does not
infer changes for which there is no evidence. The shorthand for describing this is that "parsimony minimizes
assumed homoplasies, it does not assume that homoplasy is minimal."
Parsimony is also sometimes associated with the notion that "the simplest possible explanation is the
best," a generalisation of Occam's Razor. Parsimony does prefer the solution that requires the least number
of unsubstantiated assumptions and unsupportable conclusions, the solution that goes the least theoretical
distance beyond the data. This is a very common approach to science, especially when dealing with systems
that are so complex as to defy simple models. Parsimony does not by any means necessarily produce a
"simple" assumption. Indeed, as a general rule, most character datasets are so "noisy" that no truly "simple"
solution is possible.
[edit] Alternatives
There are several other methods for inferring phylogenies based on discrete character data. Each
offers potential advantages and disadvantages. Most of these methods have particularly avid proponents and
detractors; parsimony especially has been advocated as philosophically superior (most notably by ardent
cladists).
[edit] Maximum likelihood
Main article: Maximum likelihood
Among the most popular alternative phylogenetic methods is maximum likelihood phylogenetic
inference, sometimes simply called "likelihood" or "ML." Maximum likelihood is an optimality criterion, as is
parsimony. Mechanically, maximum likelihood analysis functions much like parsimony analysis, in that trees
are scored based on a character dataset, and the tree with the best score is selected. Maximum likelihood is
a parametric statistical method, in that it employs an explicit model of character evolution. Such methods are
potentially much more powerful than non-parametric statistical methods like parsimony, but only if the model
used is a reasonable approximation of the processes that produced the data. Maximum likelihood has
probably surpassed parsimony in popularity with nucleotide sequence data, and Bayesian phylogenetic
inference, which uses the likelihood function, is becoming almost as prevalent.
Likelihood is the relative counterpart to absolute probability. If we know the number of possible
outcomes of a test (N), and we know the number of those outcomes that fit a particular criterion (n), we can
say that the probability of that criterion being met by an execution of that test is n/N. Thus, the probability of
heads in the toss of a fair coin is 50% (1/2). What if we don't know the number of possible outcomes?
Obviously, we cannot then calculate probabilities. However, if we observe that one outcome happens twice
as often as the other over an arbitrarily large number of tests, we can say that that outcome is twice as likely.
Likelihoods are proportional to the true probabilities: if an outcome is twice as likely, we can say that it is
twice as probable, even though we cannot say how probable it is.
Practically, the probability of a tree cannot be calculated directly. The probability of the data given a
tree can be calculated if you assume a specific set of probabilities of character change (a model). The critical
part of likelihood analysis is that the probability of the data given the tree is the likelihood of the tree given the
data. Thus, the tree that has the highest probability of producing the observed data is the most likely tree.
Maximum likelihood, as implemented in phylogenetics, uses a stochastic model that gives the
probability of a particular character changing at any given point on a tree. This model can have a potentially
large number of parameters, which can account for differences in the probabilities of particular states, the
probabilities of particular changes, and differences in the probabilities of change among characters.
A likelihood tree has meaningful branch lengths (i.e. it is a phylogram); these lengths are usually
interpreted as being proportional to the average probability of change for characters on that branch (thus, on
a branch of length 1, we would expect an average of one change per character, which is a lot). The state of
each character is plotted on the tree, and the probability of that distribution of character states is calculated
using the model and the branch lengths (which can be altered to maximize the probability of the data). This is
the probability of that character, given the tree. The probabilities of all of the characters is multiplied together;
they are usually negative log-transformed and added (producing the same effect), because the numbers
become very small very quickly. This sum is the probability of the data, given the tree, or the likelihood of the
tree. The tree with the highest likelihood (lowest negative log-transformed likelihood) given the data is
preferred.
In the above analogy regarding choosing a contractor, maximum likelihood would be analogous to
gathering data on the final cost of broadly comparable jobs performed by each contractor over the past year,
and selecting the contractor with the lowest average cost for those comparable jobs. This method would be
highly dependent on how comparable the jobs are, but, if they are properly chosen, it will produce a better
estimate of the actual cost of the job. Further, it would not be mislead by bias in contractor estimates,
because it is based on the final cost, not on the (potentially biased) estimates.
In practice, maximum likelihood tends to favor trees that are very similar to the most parsimonious
tree(s) for the same dataset. It has been shown to outperform parsimony in certain situations where the latter
is known to be biased, including long-branch attraction. Note, however, that the performance of likelihood is
dependent on the quality of the model employed; an incorrect model can produce a biased result. Studies
have shown that incorporating a parameter to account for differences in rate of evolution among characters is
often critical to accurate estimation of phylogenies; failure to model this or other crucial parameters may
produce incorrect or biased results. Model parameters are usually estimated from the data, and the number
(and type) of parameters is often determined using the hierarchical likelihood ratio test. The consequences of
mis-specified models are just beginning to be explored in detail.
Likelihood is generally regarded as a more desirable method than parsimony, in that it is statistically
consistent, and has a better statistical foundation, and because it allows complex modeling of evolutionary
processes. A major drawback is that ML is still quite slow relative to parsimony methods, sometimes
requiring days to run large datasets. Maximum likelihood phylogenetic inference was proposed in the mid-
Twentieth Century, but it has only been a popular method for phylogenetic inference since the 1990s, when
computational power caught up with tremendous demands of ML analysis. Newer algorithms and
implementations are bringing analysis times for large datasets into acceptable ranges. Until these methods
gain widespread acceptance, parsimony will probably be preferred for extremely large datasets, especially
when bootstrapping is used to assess confidence in the results.
One area where parsimony still holds much sway is in the analysis of morphological data. Until
recently, stochastic models of character change were not available for non-molecular data. New methods,
proposed by Paul Lewis, make essentially the same assumptions that parsimony analysis does, but do so
within a likelihood framework. These models are not, however, widely implemented, and, unless modified,
they require the modification of existing datasets (to deal with ordered characters, and the tendency to not
record autapomorphies in morphological datasets.
Maximum likelihood has been criticised as assuming neutral evolution implicitly in its adoption of a
stochastic model of evolution. This is not necessarily the case: as with parsimony, assuming a stochastic
model does not presume that all evolution is stochastic. In practice, likelihood is robust to deviations from
stochasticity. It performs well even on coding sequences that include sites believed to be under selection.
A related objection (often brought up by parsimony-only advocates) is the idea that evolution is too
complex or too poorly understood to be modeled. This objection probably rests on a misunderstanding of the
term "model." While it is customary to think of models as representing the mechanics of a process, this is not
necessarily literally the case. In fact, a model is often selected not so much for its faithful reproduction of the
phenomenon as its ability to make predictions. In practice, it is best not to try and exactly fit a model to a
process, because there is a trade-off between number of parameters in a model and its statistical power.
Stochasticity may be a reasonably good fit to evolutionary data at a broad level, even if it does not accurately
mirror the process at finer scales.
By analogy, no one claims that the human foot varies only in length and width, but differing
combinations of length and width values can be combined to fit a wide variety of feet. In some cases, a
slightly wider overall foot may be better fitted by increasing overall size rather than instep width, while a foot
with a narrower heel might be better fit by a wider instep and a smaller shoe. Adding several more
measurements would probably improve shoe fit somewhat, but would be impractical from a business
standpoint. With increasingly precise fitting, differences between feet would make selling matched pairs of
shoes impossible, and differences through time would mean that a proper fit at purchase might not be a
proper fit when worn.
Parsimony has recently been shown to be more likely to recover the true tree in the face of profound
changes in evolutionary ("model") parameters (e.g., the rate of evolutionary change) within a tree
(Kolaczkowski & Thornton 2004). This is particularly troublesome, since it is generally agreed that such
changes may be a significant feature of deep divergences. Likelihood has had substantial success
recovering known in vitro viral phylogenies, simulated phylogenies, and phylogenies confirmed by other
method. It seems likely therefore that this potential complication does not strongly bias results for more
shallow divergences. Several research groups are currently exploring ways to incorporate profound shifts in
evolutionary parameters into likelihood analysis.
[edit] Bayesian phylogenetic inference

Main article: Bayesian inference in phylogeny
Bayesian phylogenetics uses the likelihood function, and is normally implemented using the same
models of evolutionary change used in Maximum Likelihood. It is very different, however, in both theory and
application. Bayesian phylogenetic analysis uses Bayes' theorem, which relates the posterior probability of a
tree to the likelihood of data, and the prior probability of the tree and model of evolution. However, unlike
parsimony and likelihood methods, Bayesian analysis does not produce a single tree or set of equally optimal
trees. Bayesian analysis uses the likelihood of trees in a Markov chain Monte Carlo (MCMC) simulation to
sample trees in proportion to their likelihood, thereby producing a credible sample of trees.
One commonly cited drawback of Bayesian analysis is the need to explicitly set out a set of prior
probabilities for the range of potential outcomes. The idea of incorporating prior probabilities into an analysis
has been suggested as a potential source of bias. Bayesian methods involve other potential issues, such as
the evaluation of "convergence," the point at which the MCMC process stops searching for the "space" of
credible solutions and begins to build the credible sample.
[edit] Distance matrix methods

Main article: Distance matrices in phylogeny
Non-parametric distance methods were originally applied to phenetic data using a matrix of pairwise
distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch
lengths). The distance matrix can come from a number of different sources, including measured distance (for
example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as
euclidean distance) applied to discrete morphological characters, or genetic distance from sequence,
restriction fragment, or allozyme data. For phylogenetic character data, raw distance values can be
calculated by simply counting the number of pairwise differences in character states (Manhattan distance).
Several simple algorithms exist to construct a tree directly from pairwise distances, including UPGMA
and neighbor joining (NJ), but these will not necessarily produce the best tree for the data. UPGMA assumes
an ultrametric tree (a tree where all the path-lengths from the root to the tips are equal). Neighbor-joining is a
form of star decomposition, and can very quickly produce reasonable trees. It is very often used on its own,
and in fact quite frequently produces reasonable trees.
Phylogeny estimation using distance methods has produced a number of controversies. The
relationship between individual characters and the tree is lost in the process of reducing characters to
distances. Since these methods do not use character data directly, and information locked in the distribution
of character states can be lost in the pairwise comparisons. Also, some complex phylogenetic relationships
may produce biased distances. Despite these potential problems, distance methods are extremely fast, and
they often produce a reasonable estimate of phylogeny. They also have certain benefits over the methods
that use characters directly. Notably, distance methods allow use of data that may not be easily converted to
character data, such as DNA-DNA hybridization assays.
[edit] References
1. ^ Sober, E. (1983). "Parsimony in Systematics: Philosophical Issues". Annual Review of
Ecology and Systematics 14: 335–357. doi:10.1146/annurev.es.14.110183.002003. edit
2. ^ William H. E. Day, Computational complexity of inferring phylogenies from dissimilarity
matrices. Bulletin of Mathematical Biology, volume 49, number 4, pages 461-467.
• Bremer, Kåre. (1994) Branch support and tree stability. Cladistics 10:295–304.Link
• J. Felsenstein. (1978) Cases in which parsimony and compatibility methods will be positively
misleading. Syst. Zool., 27:401-410.
• Kolaczkowski, B.; Thornton, J. W. (2004), "Performance of maximum parsimony and
likelihood phylogenetics when evolution is heterogeneous", Nature 431: 980–984 .
• Siddal, M. & Whiting, M. (1999) Long-branch abstractions. Cladistics 15:9–24.
Relevant

Retrieved from "http://en.wikipedia.org/wiki/Maximum_parsimony_(phylogenetics)"
Categories: Phylogenetics | Computational phylogenetics

W000
Maximum likelihood

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has insufficient inline citations.
Please help to improve this article by introducing more precise citations where appropriate.
(September 2009)
Maximum likelihood estimation (MLE) is a popular statistical method used for fitting a statistical
model to data, and providing estimates for the model's parameters.
The method of maximum likelihood corresponds to many well-known estimation methods in
statistics. For example, one may be interested in the heights of adult female giraffes, but be unable due to
cost or time constraints, to measure the height of every single giraffe in a population. Assuming that the
heights are normally (Gaussian) distributed with some unknown mean and variance, the mean and variance
can be estimated with MLE while only knowing the heights of some sample of the overall population. MLE
would accomplish this by taking the mean and variance as parameters and finding the specific values for
these parameters that produces the distribution most likely to have produced the observed results (see
examples below).
In general, for a fixed set of data and underlying probability model, the method of maximum likelihood
selects values of the model parameters that produce the distribution most likely to have resulted in the
observed data (i.e. the parameters that maximize the likelihood function). Maximum likelihood estimation
gives a unified approach to estimation, which is well-defined in the case of the normal distribution and many
other problems. However, in some complex problems, difficulties do occur: in such problems the maximum-
likelihood estimators may be unsuitable or may not even exist.
Contents
[hide]
• 1 Principles
• 2 Properties
• 2.1 Consistency
• 2.2 Asymptotic normality
• 2.3 Functional invariance
• 2.4 Higher-order properties
• 3 Examples
• 3.1 Discrete uniform distribution
• 3.2 Discrete distribution, finite parameter space
• 3.3 Discrete distribution, continuous parameter
space
• 3.4 Continuous distribution, continuous parameter
space
• 3.5 Non-independent variables
• 4 Applications
• 5 History
• 6 See also
• 7 Notes
• 8 References
[edit] Principles
Suppose there is a sample x1, x2, …, xn of n iid observations, coming from a distribution with unknown
density ƒ0(·). It is however surmised that the function ƒ0 belongs to a certain family of distributions { ƒ(·|θ), θ
∈ Θ }, called the parametric model, so that ƒ0 = ƒ(·|θ0). The value θ0 is unknown and is referred to as the
“true value” of the parameter. It is desirable to find some estimator which would be as close to
the true value θ0 as possible. Both the observed variables xi and the parameter θ can be vectors.
To use the method of maximum likelihood, one first specifies the joint density function for all
observations. For an iid sample this joint density function will be
Now we want to look at this function at a different angle: let the observed values x1, x2, …, xn be fixed
“parameters” of this function, whereas θ will be the function’s variable and allowed to vary freely. From this
point of view this distribution function will be called the likelihood:
In practice it is often more convenient to work with the logarithm of the likelihood function, called the
log-likelihood, or its scaled version, called the average log-likelihood:
The hat over indicates that it is akin to some estimator. Indeed, estimates
the expected log-likelihood of a single observation in the model.
The method of maximum likelihood estimates θ0 by finding a value of θ that maximizes .

This method of estimation is a maximum likelihood estimator (MLE) of θ0:
A MLE estimate is the same regardless of whether we maximize the likelihood or the log-likelihood
function, since log is a monotone transformation.
For many models, a maximum likelihood estimator can be found as an explicit function of the
observed data x1, …, xn. For many other models, however, no closed-form solution to the maximization
problem is known or available, and a MLE has to be found numerically using optimization methods. For some
problems, there may be multiple estimates that maximize the likelihood. For other problems, no maximum
likelihood estimate exists (meaning that the log-likelihood function increases without attaining the supremum
value).
In the exposition above, it is assumed that the data are independent and identically distributed. The
method can be applied however to a broader setting, as long as it is possible to write the joint density
function ƒ(x1,…,xn | θ), and its parameter θ has a finite dimension which does not depend on the sample size
n. In a simpler extension, an allowance can be made for data heterogeneity, so that the joint density is equal
to ƒ1(x1|θ) · ƒ2(x2|θ) · … · ƒn(xn|θ). In the more complicated case of time series models, the independence
assumption may have to be dropped as well.
A maximum likelihood estimator coincides with the most probable Bayesian estimator given a
uniform prior distribution on the parameters.
[edit] Properties
Maximum likelihood is the extremum estimator based upon the objective function
and its sample analogue, the average log-likelihood . The expectation here is taken with
respect to the true density f(·|θ0).
For a large class of problems, the maximum likelihood estimator possesses a number of attractive
asymptotic properties:
• Consistency: the estimator converges in probability to the value being estimated.
• Asymptotic normality: as the sample size increases, the distribution of the MLE tends to the
Gaussian distribution with mean θ and covariance matrix equal to the inverse of the Fisher
information matrix. (see e.g. Myung & Navarro 2004).
• Efficiency, i.e., it achieves the Cramér–Rao lower bound when the sample size tends to
infinity. This means that no asymptotically unbiased estimator has lower asymptotic mean squared
error than the MLE.
• Second-order efficiency after correction for bias.
[edit] Consistency
Under the conditions outlined below, the maximum likelihood estimator is consistent. The
consistency means that having a sufficiently large number of observations n, it is possible to find the value of
θ0 with arbitrary precision. In mathematical terms this means that as n goes to infinity the estimator
converges in probability to its true value:
Under slightly stronger conditions, the estimator converges almost surely (or strongly) too:
To establish consistency, the following conditions are sufficient:[1]

1. Identification of the model:
In other words, different parameter values θ correspond to different distributions within the model. If
this condition did not hold, there would be some value θ1 such that θ0 and θ1 generate an identical
distribution of the observable data. Then we wouldn’t be able to distinguish between these two
parameters even with an infinite amount of data — these parameters would have been
observationally equivalent.
The identification condition is absolutely necessary for the ML estimator to be consistent. When this
condition holds, the limiting likelihood function ℓ(θ|·) has unique global maximum at θ0.
2. Compactness: the parameter space Θ of the model is compact.
The identification condition establishes that the log-likelihood has a unique global maximum.
Compactness implies that the likelihood cannot approach the maximum value arbitrarily close at
some other point (as demonstrated for example in the picture on the right).
Compactness is only a sufficient condition and not a necessary condition. Compactness can be
replaced by some other conditions, such as:
• both concavity of the log-likelihood function and compactness of some (nonempty)
upper level sets of the log-likelihood function, or
• existence of a compact neighborhood N of θ0 such that outside of N the log-
likelihood function is less than the maximum by at least some ε > 0.
3. Continuity: the function ln f(x|θ) is continuous in θ for almost all x’s:
The continuity here can be replaced with a slightly weaker condition of upper semi-continuity.
4. Dominance: there exists an integrable function d(x) such that
By the uniform law of large numbers, the dominance condition together with continuity establish the
uniform convergence in probability of the log-likelihood:
The dominance condition can be employed in the case of i.i.d. observations. In the non-i.i.d. case the
uniform convergence in probability can be checked by showing that the sequence is

stochastically equicontinuous.
If one wants to demonstrate that the ML estimator converges to θ0 almost surely, then a
stronger condition of uniform convergence almost surely has to be imposed:
[edit] Asymptotic normality

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Maximum-likelihood estimators can lack asymptotic normality and can be inconsistent if there is a
failure of one (or more) of the below regularity conditions:
Estimate on boundary. Sometimes the maximum likelihood estimate lies on the boundary of the set
of possible parameters, or (if the boundary is not, strictly speaking, allowed) the likelihood gets larger and
larger as the parameter approaches the boundary. Standard asymptotic theory needs the assumption that
the true parameter value lies away from the boundary. If we have enough data, the maximum likelihood
estimate will keep away from the boundary too. But with smaller samples, the estimate can lie on the
boundary. In such cases, the asymptotic theory clearly does not give a practically useful approximation.
Examples here would be variance-component models, where each component of variance, σ 2, must satisfy
the constraint σ2 ≥0.
Data boundary parameter-dependent. For the theory to apply in a simple way, the set of data values
which has positive probability (or positive probability density) should not depend on the unknown parameter.
A simple example where such parameter-dependence does hold is the case of estimating θ from a set of
independent identically distributed when the common distribution is uniform on the range (0,θ). For
estimation purposes the relevant range of θ is such that θ cannot be less than the largest observation.
Because the interval (0,θ) is not compact, there exists no maximum for the likelihood function: For any
estimate of theta, there exists a greater estimate that also has greater likelihood. In contrast, the interval [0,θ]
includes the end-point θ and is compact, in which case the maximum-likelihood estimator exists. However, in
this case, the maximum-likelihood estimator is biased. Asymptotically, this maximum-likelihood estimator is
not normally distributed.[2]
Nuisance parameters. For maximum likelihood estimations, a model may have a number of nuisance
parameters. For the asymptotic behaviour outlined to hold, the number of nuisance parameters should not
increase with the number of observations (the sample size). A well-known example of this case is where
observations occur as pairs, where the observations in each pair have a different (unknown) mean but
otherwise the observations are independent and Normally distributed with a common variance. Here for 2 N
observations, there are N+1 parameters. It is well-known that the maximum likelihood estimate for the
variance does not converge to the true value of the variance.
Increasing information. For the asymptotics to hold in cases where the assumption of independent
identically distributed observations does not hold, a basic requirement is that the amount of information in the
data increases indefinitely as the sample size increases. Such a requirement may not be met if either there is
too much dependence in the data (for example, if new observations are essentially identical to existing
observations), or if new independent observations are subject to an increasing observation error.
Some regularity conditions which ensure this behavior are:
1. The first and second derivatives of the log-likelihood function must be defined.
2. The Fisher information matrix must not be zero, and must be continuous as a function of the
parameter.
3. The maximum likelihood estimator is consistent.
Suppose that conditions for consistency of maximum likelihood estimator are satisfied, and [3]
1. θ0 ∈ interior(Θ);
2. f(x|θ) > 0 and is twice continuously differentiable in θ in some neighborhood N of θ0;
3. ∫ supθ∈N||∇θf(x|θ)||dx < ∞, and ∫ supθ∈N||∇θθf(x|θ)||dx < ∞;
4. I = E[∇θlnf(x|θ0) ∇θlnf(x|θ0)′] exists and is nonsingular;
5. E[ supθ∈N||∇θθlnf(x|θ)||] < ∞.
Then the maximum likelihood estimator has asymptotically normal distribution:
Proof, skipping the technicalities:

Since the log-likelihood function is differentiable, and θ0 lies in the interior of the parameter set, in the
maximum the first-order condition will be satisfied:
When the log-likelihood is twice differentiable, this expression can be expanded into a Taylor series
around the point θ = θ0:
where is some point intermediate between θ0 and . From this expression

we can derive that
Here the expression in square brackets converges in probability to H = E[−∇θθln f(x|θ0)] by the law
of large numbers. The continuous mapping theorem ensures that the inverse of this expression also
converges in probability, to H−1. The second sum, by the central limit theorem, converges in distribution to a
multivariate normal with mean zero and variance matrix equal to the Fisher information I. Thus, applying the
Slutsky’s theorem to the whole expression, we obtain that
Finally, the information equality guarantees that when the model is correctly specified, matrix H will
be equal to the Fisher information I, so that the variance expression simplifies to just I−1.
[edit] Functional invariance
The maximum likelihood estimator selects the parameter value which gives the observed data the
largest possible probability (or probability density, in the continuous case). If the parameter consists of a
number of components, then we define their separate maximum likelihood estimators, as the corresponding
component of the MLE of the complete parameter. Consistent with this, if is the MLE for θ, and
if g(θ) is any transformation of θ, then the MLE for α = g(θ) is by definition
It maximizes the so-called profile likelihood:
The MLE is also invariant with respect to certain transformations of the data. If Y = g(X) where g is
one to one and does not depend on the parameters to be estimated, then the density functions satisfy
and hence the likelihood functions for X and Y differ only by a factor that does not depend on the
model parameters.
For example, the MLE parameters of the log-normal distribution are the same as those of the normal
distribution fitted to the logarithm of the data.
[edit] Higher-order properties

The standard asymptotics tells that the maximum-likelihood estimator is √ n-consistent and
asymptotically efficient, meaning that it reaches the Cramér–Rao bound:
where I is the Fisher information matrix:
In particular, it means that the bias of the maximum-likelihood estimator is equal to zero up to the
order n−1/2. However when we consider the higher-order terms in the expansion of the distribution of this
estimator, it turns out that θmle has bias of order n−1. This bias is equal to (componentwise) [4]
where Einstein’s summation convention over the repeating indices has been adopted; I jk denotes the
j,k-th component of the inverse Fisher information matrix I−1, and
Using these formulas it is possible to estimate the second-order bias of the maximum likelihood
estimator, and correct for that bias by subtracting it:
This estimator is unbiased up to the terms of order n−1, and is called the bias-corrected maximum
likelihood estimator.
This bias-corrected estimator is second-order efficient (at least within the curved exponential family),
meaning that it has minimal mean squared error among all second-order bias-corrected estimators, up to the
terms of the order n−2. It is possible to continue this process, that is to derive the third-order bias-correction
term, and so on. However as was shown by Kano (1996), the maximum-likelihood estimator is not third-order
efficient.
[edit] Examples
[edit] Discrete uniform distribution
Main article: German tank problem
Consider a case where n tickets numbered from 1 to n are placed in a box and one is selected at
random (see uniform distribution); thus, the sample size is 1. If n is unknown, then the maximum-likelihood
estimator of n is the number m on the drawn ticket. (The likelihood is 0 for n < m, 1/n for n ≥ m,
and this is greatest when n = m. Note that the maximum likelihood estimate of n occurs at the lower extreme
of possible values {m, m + 1, ...}, rather than somewhere in the “middle” of the range of possible values,
which would result in less bias.) The expected value of the number m on the drawn ticket, and therefore the
expected value of , is (n + 1)/2. As a result, the maximum likelihood estimator for n will
systematically underestimate n by (n − 1)/2 with a sample size of 1.
[edit] Discrete distribution, finite parameter space

Suppose one wishes to determine just how biased an unfair coin is. Call the probability of tossing a
HEAD p. The goal then becomes to determine p.
Suppose the coin is tossed 80 times: i.e., the sample might be something like x1 = H, x2 = T, ...,
x80 = T, and the count of the number of HEADS "H" is observed.
The probability of tossing TAILS is 1 − p (so here p is θ above). Suppose the outcome is 49 HEADS
and 31 TAILS, and suppose the coin was taken from a box containing three coins: one which gives HEADS
with probability p = 1/3, one which gives HEADS with probability p = 1/2 and another which gives HEADS
with probability p = 2/3. The coins have lost their labels, so which one it was is unknown. Using maximum
likelihood estimation the coin that has the largest likelihood can be found, given the data that were observed.
By using the probability mass function of the binomial distribution with sample size equal to 80, number
successes equal to 49 but different values of p (the "probability of success"), the likelihood function (defined
below) takes one of three values:
The likelihood is maximized when p = 2/3, and so this the maximum likelihood estimate for p.
[edit] Discrete distribution, continuous parameter space

Now suppose that there was only one coin but its p could have been any value 0 ≤ p ≤ 1. The
likelihood function to be maximised is
and the maximisation is over all possible values 0 ≤ p ≤ 1.

Likelihood of different proportion parameter values for a binomial process with t = 3 and n = 10
One way to maximize this function is by differentiating with respect to p and setting to zero:
which has solutions p = 0, p = 1, and p = 49/80. The solution which maximizes the likelihood is
clearly p = 49/80 (since p = 0 and p = 1 result in a likelihood of zero). Thus the maximum likelihood estimator
for p is 49/80.
This result is easily generalized by substituting a letter such as t in the place of 49 to represent the
observed number of 'successes' of our Bernoulli trials, and a letter such as n in the place of 80 to represent
the number of Bernoulli trials. Exactly the same calculation yields the maximum likelihood estimator t / n for
any sequence of n Bernoulli trials resulting in t 'successes'.
[edit] Continuous distribution, continuous parameter space
For the normal distribution which has probability density function
the corresponding probability density function for a sample of n independent identically distributed
normal random variables (the likelihood) is
or more conveniently:
where is the sample mean.

This family of distributions has two parameters: θ = (μ, σ), so we maximize the likelihood,
, over both parameters simultaneously, or if possible, individually.

Since the logarithm is a continuous strictly increasing function over the range of the likelihood, the
values which maximize the likelihood will also maximize its logarithm. Since maximizing the logarithm often
requires simpler algebra, it is the logarithm which is maximized below. (Note: the log-likelihood is closely
related to information entropy and Fisher information.)
which is solved by
This is indeed the maximum of the function since it is the only turning point in μ and the second
derivative is strictly less than zero. Its expectation value is equal to the parameter μ of the given distribution,
which means that the maximum-likelihood estimator is unbiased.

Similarly we differentiate the log likelihood with respect to σ and equate to zero:
which is solved by
Inserting we obtain
To calculate its expected value, it is convenient to rewrite the expression in terms of zero-mean
random variables (statistical error) . Expressing the estimate in these variables yields
Simplifying the expression above, utilizing the facts that and , allows us
to obtain
This means that the estimator is biased. However, is consistent.

Formally we say that the maximum likelihood estimator for θ = (μ,σ2) is:
In this case the MLEs could be obtained individually. In general this may not be the case, and the
MLEs would have to be obtained simultaneously.
[edit] Non-independent variables

It may be the case that variables are correlated, that is, not independent. Two random variables X
and Y are independent only if their joint probability density function is the product of the individual probability
density functions, i.e.
Suppose one constructs an order-n Gaussian vector out of random variables , where
each variable has means given by . Furthermore, let the covariance matrix be denoted by Σ,
The joint probability density function of these n random variables is then given by:
In the two variable case, the joint probability density function is given by:
In this and other cases where a joint density function exists, the likelihood function is defined as
above, under Principles, using this density.
[edit] Applications
Maximum likelihood estimation is used for a wide range of statistical models, including:
• linear models and generalized linear models;
• exploratory and confirmatory factor analysis;
• structural equation modeling;
• many situations in the context of hypothesis testing and confidence interval formation.
• discrete choice models
These uses arise across applications in widespead set of fields, including:
• communication systems;
• psychometrics;
• econometrics;
• time-delay of arrival (TDOA) in acoustic or electromagnetic detection;
• data modeling in nuclear and particle physics;
• magnetic resonance imaging
• computational phylogenetics;
• origin/destination and path-choice modeling in transport networks.
[edit] History
Maximum-likelihood estimation was recommended, analyzed and vastly popularized by R. A. Fisher
between 1912 and 1922 (although it had been used earlier by Gauss, Laplace, Thiele, and F. Y. Edgeworth).
[5] Reviews of the development of maximum likelihood have been provided by a number of authors.[6]
Much of the theory of maximum-likelihood estimation was first developed for Bayesian statistics, and
then simplified by later authors.[7]
[edit] See also
Statistics portal
• Other estimation methods

• Restricted maximum likelihood, a variation using a likelihood function calculated from
a transformed set of data.
• Quasi-maximum likelihood estimator, a MLE estimator that is misspecified, but still
consistent.
• Maximum a posteriori (MAP) estimator, for a contrast in the way to calculate
estimators when prior knowledge is postulated.
• Method of support, a variation of the maximum likelihood technique.
• M-estimator, an approach used in robust statistics.
• Method of moments (statistics), another popular method for finding parameters of
distributions.
• Generalized method of moments are methods related to the likelihood equation in
maximum likelihood estimation.
• Minimum distance estimation
• Maximum spacing estimation, a related method that is more robust in many
situations.
• Related concepts:
• Fisher information, information matrix, its relationship to covariance matrix of ML
estimates
• Likelihood function, a description on what likelihood functions are.
• Mean squared error, a measure of how 'good' an estimator of a distributional
parameter is (be it the maximum likelihood estimator or some other estimator).
• Extremum estimator, a more general class of estimators to which MLE belongs.
• The Rao–Blackwell theorem, a result which yields a process for finding the best
possible unbiased estimator (in the sense of having minimal mean squared error). The MLE
is often a good starting place for the process.
• Sufficient statistic, a function of the data through which the MLE (if it exists and is
unique) will depend on the data.
• The BHHH algorithm is a non-linear optimization algorithm that is popular for
Maximum Likelihood estimations.
[edit] Notes
1. ^ Newey & McFadden (1994, Theorem 2.5.)
2. ^ Lehmann and Casella.
3. ^ Newey & McFadden (1994, Theorem 3.3.)
4. ^ Cox & Snell (1968, formula (20))
5. ^ Edgeworth (September 1908, December 1908)
6. ^ Savage (1976), Pratt (1976), Stigler (1978, 1986, 1999), Hald (1998, 1999), Aldrich (1997).
7. ^ Pfanzagl, Johann; with the assistance of R. Hamböker (1994). Parametric Statistical
Theory. Berlin: Walter de Gruyter. pp. 207–208. ISBN 3-11-01-3863-8.
[edit] References
• Aldrich, John (1997). "R. A. Fisher and the making of maximum likelihood 1912–1922".
Statistical Science 12 (3): 162–176. doi:10.1214/ss/1030037906. MR1617519.
• Anderson, Erling B. 1970. "Asymptotic Properties of Conditional Maximum Likelihood
Estimators". Journal of the Royal Statistical Society B 32, 283–301.
• Andersen, Erling B. 1980. Discrete Statistical Models with Social Science Applications. North
Holland, 1980.
• Debabrata Basu. Statistical Information and Likelihood : A Collection of Critical Essays by
Dr. D. Basu ; J.K. Ghosh, editor. Lecture Notes in Statistics Volume 45, Springer-Verlag, 1988.
• Cox, D. R.; Snell, E. J. (1968). "A general definition of residuals". Journal of the Royal
Statistical Society. Series B (Methodological): 248–275. JSTOR 2984505.
• Edgeworth, F.Y. (Sep 1908). "On the probable errors of frequency-constants". Journal of the
Royal Statistical Society 71 (3): 499–512. doi:10.2307/2339293. JSTOR 2339293.
• Edgeworth, F.Y. (Dec 1908). "On the probable errors of frequency-constants". Journal of the
Royal Statistical Society 71 (4): 651–678. doi:10.2307/2339378. JSTOR 2339378.
• Ferguson, Thomas S (1996). A course in large sample theory. Chapman & Hall.
ISBN 0412043718.
• Hald, Anders (1998). A history of mathematical statistics from 1750 to 1930 . New York:
Wiley. ISBN 0471179124.
• Hald, Anders (1999). "On the history of maximum likelihood in relation to inverse probability
and least squares". Statistical Science 14 (2): 214–222. JSTOR 2676741.
• Kano, Y. (1996). "Third-order efficiency implies fourth-order efficiency". Journal of the Japan
Statistical Society 26: 101–117. http://www.journalarchive.jst.go.jp/english/jnlabstract_en.php?
cdjournal=jjss1995&cdvol=26&noissue=1&startpage=101.
• Le Cam, Lucien (1990). "Maximum likelihood — an introduction". ISI Review 58 (2): 153–171.
• Le Cam, Lucien; Lo Yang, Grace (2000). Asymptotics in statistics: some basic concepts
(Second ed.). Springer. ISBN 0-387-95036-2.
• Le Cam, Lucien (1986). Asymptotic methods in statistical decision theory. Springer-Verlag.
ISBN 0387963073.
• Lehmann, E.L.; Casella, G. (1998). Theory of Point Estimation, 2nd ed. Springer. ISBN 0-
387-98502-6.
• Myung, Jay I.; Navarro, Daniel J. (2004). "Information Matrix", Department of Psychology,
Ohio State University, http://faculty.psy.ohio-state.edu/myung/personal/info_matrix.pdf
• Newey, Whitney K.; McFadden, Daniel (1994). "Chapter 35: Large sample estimation and
hypothesis testing". In Engle, Robert; McFadden, Dan. Handbook of Econometrics, Vol.4 . Elsevier
Science. pp. 2111–2245. ISBN 0444887660.
• Pratt, John W. (1976). "F. Y. Edgeworth and R. A. Fisher on the efficiency of maximum
likelihood estimation". The Annals of Statistics 4 (3): 501–514. doi:10.1214/aos/1176343457.
JSTOR 2958222.
• Savage, Leonard J. (1976). "On rereading R. A. Fisher". The Annals of Statistics 4 (3): 441–
500. doi:10.1214/aos/1176343456. JSTOR 2958221.
• Stigler, Stephen M. (1978). "Francis Ysidro Edgeworth, statistician". Journal of the Royal
Statistical Society. Series A (General) 141 (3): 287–322. doi:10.2307/2344804. JSTOR 2344804.
• Stigler, Stephen M. (1986). The history of statistics: the measurement of uncertainty before
1900. Harvard University Press. ISBN 0-674-40340-1.
• Stigler, Stephen M. (1999). Statistics on the table: the history of statistical concepts and
methods. Harvard University Press. ISBN 0-674-83601-4.
• van der Vaart, A.W. (1998). Asymptotic Statistics. ISBN 0-521-78450-6.

• Maximum Likelihood Estimation Primer (an excellent tutorial)
• Implementing MLE for your own likelihood function using R
• Tutorial on maximum likelihood estimation in Journal of Mathematical Psychology
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W000
Neighbor-joining

introducing more precise citations where appropriate. (June 2009)
In bioinformatics, neighbor-joining is a bottom-up clustering method used for the construction of
phylogenetic trees. Usually used for trees based on DNA or protein sequence data, the algorithm requires
knowledge of the distance between each pair of taxa (e.g., species or sequences) in the tree.
This genetic distance map made in 2002 is an estimate of 18 world human groups by a neighbour-
joining method based on 23 kinds of genetic information.[1]
Contents
[hide]
• 1 The algorithm
• 1.1 The Q-matrix
• 1.2 Distance of the pair members to the new node
• 1.3 Distance of the other taxa to the new node
• 1.4 The next iteration step
• 2 Advantages and disadvantages
• 3 See also
• 4 References
[edit] The algorithm

Neighbor-joining is an iterative algorithm. Each iteration consists of the following steps:
1. Based on the current distance matrix calculate the matrix Q (defined below).
2. Find the pair of taxa in Q with the lowest value. Create a node on the tree that joins these two
taxa (i.e., join the closest neighbors, as the algorithm name implies).
3. Calculate the distance of each of the taxa in the pair to this new node.
4. Calculate the distance of all taxa outside of this pair to the new node.
5. Start the algorithm again, considering the pair of joined neighbors as a single taxon and
using the distances calculated in the previous step.
[edit] The Q-matrix

Based on a distance matrix relating the r taxa, calculate Q as follows:
where d(i,j) is the distance between taxa i and j.

For example, if we have four taxa (A, B, C, D) and the following distance matrix:
A B C D
A 0 7 11 14
B 7 0 6 9
C 11 6 0 7
D 14 9 7 0
We obtain the following values for the Q matrix:
A B C D
A 0 −40 −34 −34
B −40 0 −34 −34
C −34 −34 0 −40
D −34 −34 −40 0

In the example above, two pairs of taxa have the lowest value, namely −40. We can select either of
them for the second step of the algorithm. We follow the example assuming that we joined taxa A and B
together.
[edit] Distance of the pair members to the new node

For each neighbor in the pair just joined, use the following formula to calculate the distance to the
new node. (Taxa f and g are the paired taxa and u is the newly generated node.):
and, by reflection:
In the example above, this formula would give a distance of 6 between A and the new node and a
distance of 1 between B and the new node.
[edit] Distance of the other taxa to the new node
For each taxon not considered in the previous step, we calculate the distance to the new node as
follows:
where u is the new node, k is the node for which we want to calculate the distance and f and g are
the members of the pair just joined.
Following the example, the distance between C and the new node is 5. Also, the distance between
the new node and D is 8.
[edit] The next iteration step

From the steps above, the following matrix will result (AB acting as a new taxon):
AB C D
AB 0 5 8
C 5 0 7
D 8 7 0
We can start the procedure anew taking this matrix as the original distance matrix. In our example, it
suffices to do one more step of the recursion to obtain the complete tree.
[edit] Advantages and disadvantages
Neighbor-joining is based on the minimum-evolution criterion for phylogenetic trees, i.e. the topology
that gives the least total branch length is preferred at each step of the algorithm. However, neighbor-joining
may not find the true tree topology with least total branch length because it is a greedy algorithm that
constructs the tree in a step-wise fashion. Even though it is sub-optimal in this sense, it has been extensively
tested and usually finds a tree that is quite close to the optimal tree. Nevertheless, it has been largely
superseded in phylogenetics by methods that do not rely on distance measures and offer superior accuracy
under most conditions.
The main virtue of neighbor-joining relative to these other methods is its computational efficiency.
That is, neighbor-joining is a polynomial-time algorithm. It can be used on very large data sets for which other
means of phylogenetic analysis (e.g. minimum evolution, maximum parsimony, maximum likelihood) are
computationally prohibitive. Unlike the UPGMA algorithm for phylogenetic tree reconstruction, neighbor-
joining does not assume that all lineages evolve at the same rate (molecular clock hypothesis) and produces
an unrooted tree. Rooted trees can be created by using an outgroup and the root can then effectively be
placed on the point in the tree where the edge from the outgroup connects.
Furthermore, neighbor-joining is statistically consistent under many models of evolution. Hence,
given data of sufficient length, neighbor-joining will reconstruct the true tree with high probability.
Atteson proved that if each entry in the distance matrix differs from the true distance by less than half
of the shortest branch length in the tree, then neighbor joining will construct the correct tree.
RapidNJ and NINJA are fast implementations of the neighbor joining algorithm.
[edit] See also
• UPGMA
[edit] References
1. ^ Saitou. Kyushu Museum. 2002. February 2, 2007
Notes
• Atteson K (1997). "The performance of neighbor-joining algorithms of phylogeny
reconstruction", pp. 101–110. In Jiang, T., and Lee, D., eds., Lecture Notes in Computer Science,
1276, Springer-Verlag, Berlin. COCOON '97.
• Gascuel O, Steel M (2006). "Neighbor-joining revealed". Mol Biol Evol 23 (11): 1997–2000.
doi:10.1093/molbev/msl072. PMID 16877499.
• Mihaescu R, Levy D, Pachter L (2006). "Why neighbor-joining works".
• Saitou N, Nei M (1987). "The neighbor-joining method: a new method for reconstructing
phylogenetic trees". Mol Biol Evol 4 (4): 406–425. PMID 3447015.
http://mbe.oxfordjournals.org/cgi/reprint/4/4/406.
• Studier JA, Keppler KJ (1988). "A note on the Neighbor-Joining algorithm of Saitou and Nei".
Mol Biol Evol 5 (6): 729–731. PMID 3221794. http://mbe.oxfordjournals.org/cgi/reprint/5/6/729.pdf.
• Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen (2008). "Rapid Neighbour
Joining". Proceedings of WABI 5251: 113–122. doi:10.1007/978-3-540-87361-7_10.
http://birc.au.dk/fileadmin/uploaded/rapidNJ.pdf.
• The Neighbor-Joining Method — a tutorial
• Geneious Pro NJ implementation as part of an all-in-one sequence analysis package
Relevant



Retrieved from "http://en.wikipedia.org/wiki/Neighbor-joining"
Categories: Bioinformatics algorithms | Phylogenetics | Computational phylogenetics | Data

clustering algorithms
W000
UPGMA

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a simple agglomerative or
hierarchical clustering method used in bioinformatics for the creation of phenetic phylogenetic trees
(phenograms). UPGMA assumes a constant rate of evolution (molecular clock hypothesis), and is not a well-
regarded method for inferring phylogenetic trees unless this assumption has been tested and justified for the
data set being used. UPGMA was initially designed for use in protein electrophoresis studies, but is currently
most often used to produce guide trees for more sophisticated phylogenetic reconstruction algorithms.
The algorithm examines the structure present in a pairwise distance matrix (or a similarity matrix) to
then construct a rooted tree (dendrogram).
At each step, the nearest two clusters are combined into a higher-level cluster. The distance between
any two clusters A and B is taken to be the average of all distances between pairs of objects "x" in A and "y"
in B, that is, the mean distance between elements of each cluster:
The method is generally attributed to Sokal and Michener[1]. Fionn Murtagh found a time optimal
O(n2) time algorithm to construct the UPGMA tree.[2]
[edit] See also

• Neighbor-joining
• Cluster analysis
[edit] References
1. ^ R. Sokal and C. Michener. A statistical method for evaluating systematic relationships.
University of Kansas Science Bulletin, 38:1409-1438, 1958.
2. ^ F. Murtagh. Complexities of Hierarchic Clustering Algorithms: the state of the art.
Computational Statistics Quarterly 1:101-113, 1984.

• UPGMA clustering algorithm implementation in Ruby (AI4R)
• Example calculation of UPGMA using a similarity matrix
• Example calculation of UPGMA using a distance matrix
Relevant



This bioinformatics-related article is a stub. You can help Wikipedia by expanding

it.v · d · e
Retrieved from "http://en.wikipedia.org/wiki/UPGMA"
Categories: Bioinformatics | Computational phylogenetics | Data clustering algorithms |

Phylogenetics | Bioinformatics stubs
W000
Three-taxon analysis

Three taxon-analysis (or TTS, or three-item analysis) is a cladistic based method of phylogenetic
reconstruction. Introduced by Nelson and Platnick (1991)[1] to reconstruct organisms' phylogeny, this method
can also be applied to biogeographic areas.
Contents
[hide]
• 1 Introduction
• 1.1 Character coding
• 1.2 Analysis process
• 1.3 Missing and inapplicable data
• 2 See also
• 3 References
• 4 Further readings
[edit] Introduction
TTS distinguishes itself from parsimony by two capital features, regarding character coding and the
analysis process itself.
[edit] Character coding

TTS accepts an equivalence between characters and taxa. Homologous characters are classified
and coded as rooted trees (see Phylogenetic tree) and called homology hypothesis. Hence homologous
characters belonging to the same class are considered closer to one another than to a third. For example
legs, which belongs to the class "legs", are closer to one another than another paired limb. Meanwhile
coelacanth fins are closer to tetrapod legs than teleost fins. Therefore the concept of fin, which is
plesiomorphic regarding the concept of leg, can be considered paraphyletic by TTS.
[edit] Analysis process

Every homology hypothesis is decomposed into simpler hypotheses, the minimal relation being a
character A closer to B than C. This is called a three item statement, or 3is. If this relation is verified, then A
and B belong to a class that excludes C. The parenthetical expression for this relationship is the following:
(C(AB)). On the other hand the relation (AC) does not inform on evolutionary relationships. For example the
homology hypothesis (AB(CD)) can be decomposed into two minimal relations: A(CD) and B(CD). It implies
that characters C and D are closer to one another than A or B. Along with the analysis, every homology
hypothesis will be decomposed into 3is. The 3is obtained by studying every characters will form a clique.
Another important concept in TTS is accommodation. A 3is is accommodated on a tree if the 3is’s relation is
respected by the tree. For example (A(BC)), (A(CE)) or (B(ED)) are accommodated 3is on the tree (A((BC)
(DE))). On the other hand, (E(AB)) or ((CE)B) are not.
Among every possible tree for a set of taxa (or biogeographic areas), the tree featuring the most
accommodated 3is with the clique’s 3is will be accepted. Hence the accepted tree will feature the majority of
phylogenetic information included in the homology hypothesis.
Example of accommodated and not accommodated 3is
[edit] Missing and inapplicable data

The TTS method does not request data matrix in any part of the analysis, the character coding is
done with rooted trees, therefore less constrained [2]. In parsimony analysis, a missing or inapplicable state
of character would be coded identically as a question mark (meaning that every state of character is
acceptable). The following example shows the TTS treatment of states of character for 6 taxa, the homology
hypothesis is is figured by the tree:
A: No antennae
B and C: curved antennae
D and F: dichotomized antennae
E: missing head
Since A has no antennae, 'curved antennae' or ' dichotomized antennae' are inapplicable states of
character. A will simply not be included in the homology hypothesis 'presence of antennae'. For E, one can
imagine a specimen lacking the head. Thus E will not appear on the homology hypothesis. In TTS a lacking
character is simply lacking.
A homology hypothesis for the hypothetical taxa
[edit] See also
• Cladistics
[edit] References
1. ^ Nelson and Platnick, 3-Taxon statements - a more precise use of parsimony, Cladistics,
1991
2. ^ R. Zaragüeta-Bagils & E. Bourdon, Three-item analysis: Hierarchical representation and
treatment of missing and inapplicable data, Comptes Rendus Palevol, Volume 6, Issues 6-7,
November 2007, Pages 527-534
[edit] Further readings

• I. J. Kitching, P. L. Forey, C. J. Humphries et D. M. Williams, "Cladistics. Second edition. The
theory and practice of parsimony analysis", Oxford science publications, 1998.
Relevant

Retrieved from "http://en.wikipedia.org/wiki/Three-taxon_analysis"
W000
Least squares inference in phylogeny


Least squares inference in phylogeny generates a phylogenetic tree based on an observed matrix of
pairwise genetic distances and optionally a weight matrix. The goal is to find a tree which satisfies the
distance constraints as best as possible.
Contents
[hide]
• 1 Ordinary and weighted least squares
• 2 Generalized least squares
• 3 Computational Complexity
• 5 References
[edit] Ordinary and weighted least squares

The discrepancy between the observed pairwise distances Dij and the distances Tij over a
phylogenetic tree (i.e. the sum of the branch lengths in the path from leaf i to leaf j) is measured by
S= ∑ wij(Dij − Tij)2
ij
where the weights wij depend on the least squares method used. Least squares distance tree
construction aims to find the tree (topology and branch lengths) with minimal S. This is a non-trivial problem.
It involves searching the discrete space of unrooted binary tree topologies whose size is exponential in the
number of leaves. For n leaves there are 1 • 3 • 5 • ... • (2n-3) different topologies. Enumerating them is not
feasible already for a small number of leaves. Heuristic search methods are used to find a reasonably good
topology. The evaluation of S for a given topology (which includes the computation of the branch lengths) is a
linear least squares problem. There are several ways to weight the squared errors ( Dij − Tij)2, depending on
the knowledge and assumptions about the variances of the observed distances. When nothing is known
about the errors, or if they are assumed to be independently distributed and equal for all observed distances,
then all the weights wij are set to one. This leads to an ordinary least squares estimate. In the weighted least
squares case the errors are assumed to be independent (or their correlations are not known). Given
independent errors, a particular weight should ideally be set to the inverse of the variance of the
corresponding distance estimate. Sometimes the variances may not be known, but they can be modeled as a
function of the distance estimates. In the Fitch and Margoliash method [1] for instance it is assumed that the
variances are proportional to the squared distances.
[edit] Generalized least squares

The ordinary and weighted least squares methods described above assume independent distance
estimates. If the distances are derived from genomic data their estimates covary, because evolutionary
events on internal branches (of the true tree) can push several distances up or down at the same time. The
resulting covariances can be taken into account using the method of generalized least squares, i.e.
minimizing the following quantity
∑ wij,kl(Dij − Tij)(Dkl − Tkl)
ij,kl
where wij,kl are the entries of the inverse of the covariance matrix of the distance estimates.
[edit] Computational Complexity

Finding the tree and branch lengths minimizing the least squares residual is an NP-complete problem
[2]. However, for a given tree, the optimal branch lengths can be determined in O(n2) time for ordinary least
squares, O(n3) time for weighted least squares, and O(n4) time for generalised least squares (given the
inverse of the covariance matrix).[3]

• PHYLIP, a freely distributed phylogenetic analysis package containing an implementation of
the weighted least squares method
• PAUP, a similar package available for purchase
• Darwin, a programming environment with a library of functions for statistics, numerics,
sequence and phylogenetic analysis
[edit] References
1. ^ Fitch WM, Margoliash E. (1967). Construction of phylogenetic trees. Science 155: 279-84.
2. ^ William H.E. Day, Computational complexity of inferring phylogenies from dissimilarity
matrices, Bulletin of Mathematical Biology, Volume 49, Issue 4, 1987, Pages 461-467, ISSN 0092-
8240, DOI: 10.1016/S0092-8240(87)80007-1.
3. ^ David Bryant, Peter Waddell, Rapid Evaluation of Least-Squares and Minimum-Evolution
Criteria on Phylogenetic Trees, Mol Biol Evol (1998) 15(10): 1346
Relevant



Retrieved from "http://en.wikipedia.org/wiki/Least_squares_inference_in_phylogeny"
Categories: Computational phylogenetics

W000
Bayesian inference in phylogeny


Bayesian inference in phylogeny generates a posterior distribution for a parameter, composed of a
phylogenetic tree and a model of evolution, based on the prior for that parameter and the likelihood of the
data, generated by a multiple alignment. The Bayesian approach has become more popular due to advances
in computational machinery, especially, Markov chain Monte Carlo algorithms. Bayesian inference has a
number of applications in molecular phylogenetics, for example, estimation of species phylogeny and species
divergence times.
Contents
[hide]
• 1 Basic Bayesian theory
• 2 The LOCAL algorithm of Larget and Simon
• 2.1 Assessing convergence
• 3 Metropolis-coupled MCMC (Geyer)
• 4 References
[edit] Basic Bayesian theory

Recall that for Bayesian inference:
The denominator is the marginal probability of the data, averaged over all possible
parameter values weighted by their prior distribution. Formally,
where is the parameter space for .
In the original Metropolis algorithm, given a current -value , and a new
-value , the new value is accepted with probability:
[edit] The LOCAL algorithm of Larget and Simon

The LOCAL algorithm begins by selecting an internal branch of the tree at random. The nodes at the
ends of this branch are each connected to two other branches. One of each pair is chosen at random.
Imagine taking these three selected edges and stringing them like a clothesline from left to right, where the
direction (left/right) is also selected at random. The two endpoints of the first branch selected will have a sub-
tree hanging like a piece of clothing strung to the line. The algorithm proceeds by multiplying the three
selected branches by a common random amount, akin to stretching or shrinking the clothesline. Finally the
leftmost of the two hanging sub-trees is disconnected and reattached to the clothesline at a location selected
uniformly at random. This is the candidate tree.
Suppose we began by selecting the internal branch with length (in Figure (a) (to be
added)) that separates taxa and from the rest. Suppose also that we have
(randomly) selected branches with lengths and from each side, and that we
oriented these branches as shown in Figure(b). Let , be the current length of the clothesline. We
select the new length to be , where is a uniform random variable on .

Then for the LOCAL algorithm, the acceptance probability can be computed to be:
[edit] Assessing convergence
Suppose we want to estimate a branch length of a 2-taxon tree under JC, in which n1 sites are
unvaried and n2 are variable. Assume exponential prior distribution with rate . The density is
. The probabilities of the possible site patterns are:
for unvaried sites, and
Thus the unnormalized posterior distribution is:
or, alternately,
Update branch length by choosing new value uniformly at random from a window of half-width
centered at the current value:
where is uniformly distributed between and . The acceptance

probability is:
Example: , . We will compare results for two values of ,
and . In each case, we will begin with an initial length of and update
the length times. (See Figure 3.2 (to be added) for results.)
[edit] Metropolis-coupled MCMC (Geyer)
If the target distribution has multiple peaks, separated by low valleys, the Markov chain may have
difficulty in moving from one peak to another. As a result, the chain may get stuck on one peak and the
resulting samples will not approximate the posterior density correctly. This is a serious practical concern for
phylogeny reconstruction, as multiple local peaks are known to exist in the tree space during heuristic tree
search under maximum parsimony (MP), maximum likelihood (ML), and minimum evolution (ME) criteria, and
the same can be expected for stochastic tree search using MCMC. Many strategies have been proposed to
improve mixing of Markov chains in presence of multiple local peaks in the posterior density. One of the most
successful algorithms is the Metropolis-coupled MCMC (or ).
In this algorithm, chains are run in parallel, with different stationary distributions ,
, where the first one, is the target density, while ,

are chosen to improve mixing. For example, one can choose incremental heating of the form:
so that the first chain is the cold chain with the correct target density, while chains
are heated chains. Note that raising the density π(.) to the power with has the effect of
flattening out the distribution, similar to heating a metal. In such a distribution, it is easier to traverse between
peaks (separated by valleys) than in the original distribution. After each iteration, a swap of states between
two randomly chosen chains is proposed through a Metropolis-type step. Let be the current state in
chain , . A swap between the states of chains and is accepted with probability:
At the end of the run, output from only the cold chain is used, while those from the hot chains are
discarded. Heuristically, the hot chains will visit the local peaks rather easily, and swapping states between
chains will let the cold chain occasionally jump valleys, leading to better mixing. However, if
is unstable, proposed swaps will seldom be accepted. This is the reason for using several chains which differ
only incrementally. (See Figure3.3 (to be added)).
An obvious disadvantage of the algorithm is that chains are run and only one chain is used for
inference. For this reason, is ideally suited for implementation on parallel machines, since each chain
will in general require the same amount of computation per iteration.
[edit] References
• Geyer, C.J. (1991) Markov chain Monte Carlo maximum likelihood. In Computing Science
and Statistics: Proceedings of the 23rd Symposium of the Interface (ed. E.M. Keramidas), pp. 156–
163. Interface Foundation, Fairfax Station, VA.
• Yang, Z. and B. Rannala. (1997) Bayesian phylogenetic inference using DNA sequences: A
Markov chain Monte Carlo method. Molecular Biology and Evolution, 14, 717–724.
• Larget, B. and D.L. Simon. (1999) Markov chain Monte Carlo algorithms for the Bayesian
analysis of phylogenetic trees. Molecular Biology and Evolution , 16, 750–759.
• Huelsenbeck, J.P. and F. Ronquist. (2001) MrBayes: Bayesian inference in phylogenetic
trees. Bioinformatics, 17, 754–755.
• Ronquist, F. and J.P. Huelsenbeck. (2003) MrBayes3: Bayesian phylogenetic inference
under mixed models. Bioinformatics, 19, 1572–1574.
• Rannala, B. and Z. Yang. (2003) Bayes estimation of species divergence times and ancestral
population sizes using DNA sequences from multiple loci. Genetics, 164, 1645–1656.
Relevant


Retrieved from "http://en.wikipedia.org/wiki/Bayesian_inference_in_phylogeny"
Categories: Bioinformatics | Computational phylogenetics | Markov models | Bayesian statistics

W000
PhyloCode

The International Code of Phylogenetic Nomenclature, known as the PhyloCode for short, is a
developing draft for a formal set of rules governing phylogenetic nomenclature. Its current version is
specifically designed to regulate the naming of clades, leaving the governance of species names up to the
rank-based codes (ICBN, ICZN, ICNB).
The PhyloCode is associated with the International Society for Phylogenetic Nomenclature (ISPN).[1]
Contents
[hide]
• 1 Overview
• 1.1 Phylogenetic nomenclature
• 1.2 Versions
• 1.3 Organization
• 1.3.1 Table of contents
• 2 Registration database
• 3 History
• 3.1 Influences
• 4 Future
• 5 References
• 6 Literature
[edit] Overview
The PhyloCode proposes to regulate phylogenetic nomenclature by providing rules for how to decide
which associations of names and definitions will be considered established,[2] which of those will be
considered homonyms[3] or synonyms,[4] and which one of a set of synonyms or homonyms will be
considered accepted (generally the one registered first; see below).
Additionally, the PhyloCode will only allow the naming of clades,[5] not of paraphyletic or polyphyletic
groups, and will only allow the use of specimens, species, and apomorphies as specifiers (anchors).[6]
[edit] Phylogenetic nomenclature

Main article: Phylogenetic nomenclature
Unlike previous, rank-based nomenclatural codes (ICBN, ICZN, ICNB), the PhyloCode does not
require the use of ranks, although it does optionally allow their use.[7][8] The rank-based codes define taxa
using a rank (such as genus, family, etc.) and, in many cases, a type specimen or type subtaxon. The exact
content of a taxon, other than the type, is not specified by the rank-based codes.
In contrast, under phylogenetic nomenclature, the content of taxa are delimited using a definition that
is based on phylogeny (i.e., ancestry and descent) and uses specifiers (e.g., species, specimens,
apomorphies) to indicate actual organisms. The formula of the definition indicates an ancestor. The defined
taxon, then, is that ancestor and all of its descendants. Thus, the content of a phylogenetically-defined taxon
relies on a phylogenetic hypothesis.
The following are examples of types of phylogenetic definition (capital letters indicate specifiers)[9]:
• Node-based: "the clade originating with the most recent common ancestor of A and B" or "the
least inclusive clade containing A and B"
• Branch-based: "the clade consisting of A and all organisms or species that share a more
recent common ancestor with A than with Z" or "the most inclusive clade containing A but not Z"
• Apomorphy-based: "the clade originating with the first organism or species to possess
apomorphy M as inherited by A" or "the most inclusive clade exhibiting character state M
synapomorphic with that in A"
Other types of definition are possible as well.
The following table gives examples of the differences between rank-based and phylogenetic
definitions.
Possible Phylogenetic
Name Rank Type
Definition
the least inclusive clade

containing Tyrannosaurus rex Osborn
Tyrannosaurus
Tyrannosauridae Family 1905, Gorgosaurus libratus Lambe
Osborn 1905
1914, and Albertosaurus sarcophagus
Osborn 1905
the clade originating with the

most recent common ancestor of Homo
Mammalia Class N/A sapiens Linnaeus 1758 and
Ornithorhynchus anatinus Blumenbach
1800
[edit] Versions
The draft of the PhyloCode has gone through several revisions. All older versions can be found on
the website. As of January 12, 2010, the current version is 4c.
[edit] Organization
As with other nomenclatural codes, the rules of the PhyloCode are organized as articles, which in
turn are organized as chapters. Each article may also contain notes, examples, and recommendations.
[edit] Table of contents

• Preface (including Literature Cited)
• Preamble
• Division I. Principles
• Division II. Rules
• Chapter I. Taxa (Arts. 1-3)
• Chapter II. Publication (Arts. 4-5)
• Chapter III. Names (Arts. 6-8)
• Chapter IV. Clade Names (Arts. 9-11)
• Chapter V. Selection of Established Names (Arts. 12-15)
• Chapter VI. Provisions for Hybrids (Art. 16)
• Chapter VII. Orthography (Arts. 17-18)
• Chapter VIII. Authorship of Names (Art. 19)
• Chapter IX. Citation of Authors and Registration Numbers (Art. 20)
• Chapter X. Species Names (Art. 21)
• Chapter XI. Governance (Art. 22)
• Glossary
• Tables
• Appendices
• Appendix A. Registration Procedures and Data Requirements
• Appendix B. Code of Ethics
[edit] Registration database

Once implemented, the PhyloCode will be associated with a registration database, called RegNum,
which will store all clade names and definitions that will be considered acceptable.[10] It is hoped that this will
provide a publicly-usable tool for associating clade names with definitions, which could then be associated
with sets of subtaxa or specimens through phylogenetic tree databases (such as TreeBASE).
As currently planned, however, the most important use of RegNum will be the decision of which one
of a number of synonyms or homonyms will be considered accepted: the one with the lowest registration
number, except in cases of conservation.
[edit] History
(Condensed from the PhyloCode's Preface.[11])
The PhyloCode grew out of a workshop at Harvard University in August 1998, where decisions were
made about its scope and content. Many of the workshop participants, together with several other people
who subsequently joined the project, served as an advisory group. In April 2000, a draft was made public on
the web and comments were solicited from the scientific community.
A second workshop was held at Yale University in July 2002, at which some modifications were
made in the rules and recommendations of the PhyloCode. Other revisions have been made from time to
time as well.
The First International Phylogenetic Nomenclature Meeting, which took place from July 6, 2004 to
July 9, 2004 in Paris, France, was attended by about 70 systematic and evolutionary biologists from 11
nations.[12] This was the first open, multi-day conference that focused entirely on phylogenetic
nomenclature, and it provided the venue for the inauguration of a new association, the International Society
for Phylogenetic Nomenclature (ISPN). The ISPN membership elects the Committee on Phylogenetic
Nomenclature (CPN), which has taken over the role of the advisory group that oversaw the earlier stages of
development of the PhyloCode.
The Second International Phylogenetic Nomenclature Meeting took place from June 28, 2006 to July
2, 2006 at Yale University (New Haven, Connecticut, U.S.A.).[13]
The Third International Phylogenetic Nomenclature Meeting took place from July 21, 2008 to July 22,
2008 at Dalhousie University (Halifax, Nova Scotia, Canada). (A published report is forthcoming.)
[edit] Influences
The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and
Gauthier,[14][15][16] which was foreshadowed by earlier suggestions that a taxon name could be defined by
reference to a part of a phylogenetic tree.[17]
Whenever possible, the writers of the PhyloCode used the draft BioCode,[18] which attempted to
unify the rank-based approach into a single code, as a model. Thus, the organization of the PhyloCode,
some of its terminology, and the wording of certain rules are derived from the BioCode. Other rules are
derived from one or more of the rank-based codes, particularly the botanical[19][20][21] and zoological[22]
[23] codes. However, many rules in the PhyloCode have no counterpart in the any code based on taxonomic
ranks because of fundamental differences in the definitional foundations of the alternative systems.
[edit] Future
The PhyloCode is controversial, and has inspired downright hostility from some taxonomists.[24] The
number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2011,
whether the code will be implemented and if so, how widely it will be followed. Some supporters believe that
it should only be implemented, at least at first, as a set of rules accompanying the associated registration
database, RegNum, and that acceptance by the scientific community may proceed from the popularization of
RegNum as a utility for finding clade names and definitions.
A list of published critiques of the PhyloCode can be found on the ISPN's website, as can a list of
rebuttals.
[edit] References
1. ^ "International Society for Phylogenetic Nomenclature (website)". Phylonames.org.
http://phylonames.org/. Retrieved 2010-07-07.
2. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Chapter II. Publication".
Ohiou.edu. http://www.ohiou.edu/phylocode/art4-5.html. Retrieved 2010-07-07.
3. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 13: Homonymy".
Ohiou.edu. http://www.ohiou.edu/phylocode/art13.html. Retrieved 2010-07-07.
4. ^ "International Code of Phylogenetic Nomenclature Version 4b, Article 14: Synonymy".
Ohiou.edu. http://www.ohiou.edu/phylocode/art14.html. Retrieved 2010-07-07.
5. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Rule 1.1". Ohiou.edu.
http://www.ohiou.edu/phylocode/art1-3.html#art1.1. Retrieved 2010-07-07.
6. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 11. Specifiers and
Qualifying Clauses". Ohiou.edu. http://www.ohiou.edu/phylocode/art11.html. Retrieved 2010-07-07.
7. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 3. Hierarchy and
Rank". Ohiou.edu. http://www.ohiou.edu/phylocode/art1-3.html#art3. Retrieved 2010-07-07.
8. ^ Although note that the PhyloCode does not permit a taxon's name to change when its rank
changes, while the rank-based codes require this for at least some names.
9. ^ "International Code of Phylogenetic Nomenclature, Version 4b - Article 9. General
Requirements for Establishment of Clade Names". Ohiou.edu.
http://www.ohiou.edu/phylocode/art9.html. Retrieved 2010-07-07.
10.^ http://www.ohiou.edu/phylocode/art8.html
11.^ "International Code of Phylogenetic Nomenclature, Version 4b - Preface". Ohiou.edu.
http://www.ohiou.edu/phylocode/preface.html#preface-history. Retrieved 2010-07-07.
12.^ Laurin, M.; and P. D. Cantino (2004). "First international phylogenetic nomenclature
meeting: a report". Zool. Scr. 33 (5): 475–479. doi:10.1111/j.0300-3256.2004.00176.x.
13.^ Laurin, M.; and P. D. Cantino (2007). "Second meeting of the International Society for
Phylogenetic Nomenclature: a report". Zool. Scr. 36: 109–117. doi:10.1111/j.1463-
6409.2006.00268.x.
14.^ de Queiroz, K.; and J. Gauthier (1990). "Phylogeny as a central principle in taxonomy:
Phylogenetic definitions of taxon names". Syst. Zool (Society of Systematic Biologists) 39 (4): 307–
15.^ de Queiroz, K.; and J. Gauthier (1992). "Phylogenetic taxonomy". Annu. Rev. Ecol. Syst.
23: 449–480.
16.^ de Queiroz, K.; and J. Gauthier (1994). "Toward a phylogenetic system of biological
nomenclature". Trends Ecol. Evol. 9: 27–31. doi:10.1016/0169-5347(94)90231-3.
17.^ Ghiselin, M. T. (1984). ""Definition," "character," and other equivocal terms". Syst. Zool
(Society of Systematic Biologists) 33 (1): 104–110. doi:10.2307/2413135.
18.^ Greuter, W.; D. L. Hawksworth, J. McNeill, A. Mayo, A. Minelli, P. H. A. Sneath, B. J.
Tindall, P. Trehane, and P. Tubbs (1998). "Draft BioCode (1997): the prospective international rules
for the scientific names of organisms". Taxon (International Association for Plant Taxonomy (IAPT))
47 (1): 127–150. doi:10.2307/1224030. http://jstor.org/stable/1224030.
19.^ Greuter, W.; F. R. Barrie, H. M. Burdet, W. G. Chaloner, V. Demoulin, D. L. Hawksworth, P.
M. Jørgensen, J. McNeill, D. H. Nicolson, P. C. Silva, and P. Trehane (1994). International Code of
Botanical Nomenclature (Tokyo Code). Koeltz Scientific Books, Königstein, Germany.
ISBN 1878762664.
20.^ Greuter, W.; F. R. Barrie, H. M. Burdet, V. Demoulin, T. S. Filgueiras, D. L. Hawksworth, J.
McNeill, D. H. Nicolson, P. C. Silva, J. E. Skog, P. Trehane, and N. J. Turland (2000). International
Code of Botanical Nomenclature (Saint Louis Code). Koeltz Scientific Books, Königstein, Germany.
21.^ McNeill, J.; F. R. Barrie, H. M. Burdet, V. Demoulin, D. L. Hawksworth, K. Marhold, D. H.
Nicolson, J. Prado, P. C. Silva, J. E. Skog, J. H. Wiersema, and N. J. Turland (2006). International
Code of Botanical Nomenclature (Vienna Code). Gantner, Ruggell, Liechtenstein.
ISBN 3906166481.
22.^ International Commission on Zoological Nomenclature (1985). International Code of
Zoological Nomenclature (3rd ed.). International Trust for Zoological Nomenclature.
ISBN 0853010064.
23.^ International Commission on Zoological Nomenclature (1999). International Code of
Zoological Nomenclature (4th ed.). International Trust for Zoological Nomenclature.
ISBN 0853010064.
24.^ Nixon, K.C., Carpenter, J.M. & Stevenson, D.W. (2003): The PhyloCode Is Fatally Flawed,
and the "Linnaean" System Can Easily Be Fixed. The Botanical Review no 69(1): pp111-120 article
[edit] Literature
• Anderson, J. S. (2002). "Use of well-known names in phylogenetic nomenclature: a reply to
Laurin". Syst. Biol 51 (5): 822–827. doi:10.1080/10635150290102447. PMID 12396594.
• Baum, D. A.; W. S. Alverson, and R. Nyffeler (1998). "A durian by any other name: taxonomy
and nomenclature of the core Malvales". Harvard papers in botany 3: 315–330. ISSN 1043-4534.
• Benton, M. J. (2000). "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?".
Biological Reviews 75 (4): 633–648. ISSN 0006-3231. PMID 11117201.
http://palaeo.gly.bris.ac.uk/Essays/phylocode/biolrev.html.
• Cantino, Philip D. (2000). "Phylogenetic nomenclature: addressing some concerns". Taxon
(International Association for Plant Taxonomy (IAPT)) 49 (1): 85–93. doi:10.2307/1223935.
• Cantino, Philip D. (2004). "Classifying species versus naming clades". Taxon (International
Association for Plant Taxonomy (IAPT)) 53 (3): 795–798. doi:10.2307/4135453.
• Carpenter, J. M. (2003). "Critique of pure folly". The Botanical Review 69 (1): 79–92.
doi:10.1663/0006-8101(2003)069[0079:COPF]2.0.CO;2.
• de Queiroz, K. (1992). "Phylogenetic definitions and taxonomic philosophy". Biol. Philos. 7
(3): 295–313. doi:10.1007/BF00129972.
• de Queiroz, K. (2006). "The PhyloCode and the distinction between taxonomy and
nomenclature". Syst. Biol. 55 (1): 160–162. doi:10.1080/10635150500431221. PMID 16507533.
• de Queiroz, K.; and P. D. Cantino (2001). "Phylogenetic nomenclature and the PhyloCode".
Bull. Zool. Nomencl. 58: 254–271. ISSN 0007-5167.
• de Queiroz, K.; and J. Gauthier (1990). "Phylogeny as a central principle in taxonomy:
Phylogenetic definitions of taxon names". Syst. Zool. (Society of Systematic Biologists) 39 (4): 307–
• de Queiroz, K.; and J. Gauthier. (1992). "Phylogenetic taxonomy". Annu. Rev. Ecol. Syst. 23:
449–480. ISSN 0066-4162.
• de Queiroz, K.; and J. Gauthier (1994). "Toward a phylogenetic system of biological
nomenclature". Trends Ecol. Evol. 9 (1): 27–31. doi:10.1016/0169-5347(94)90231-3.
• Dominguez, E.; and Q. D. Wheeler (1997). "Taxonomic stability is ignorance". Cladistics 13
(4): 367–372. ISSN 748-3007.
• Donoghue, M. J.; and J. A. Gauthier (2004). "Implementing the PhyloCode". Trends Ecol.
Evol. 19 (6): 281–282. doi:10.1016/j.tree.2004.04.004. PMID 16701272.
• Gauthier, J.; and K. de Queiroz (2001). "Feathered dinosaurs, flying dinosaurs, crown
dinosaurs, and the name "Aves"". In J. A. Gauthier and L. F. Gall (eds.). New perspectives on the
origin and early evolution of birds: proceedings of the International Symposium in Honor of John H.
Ostrom. New Haven, Connecticut, U.S.A.: Peabody Museum of Natural History, Yale University.
pp. 7–41 pp.
• Laurin, M. (2005). "Dites oui au PhyloCode!" (PDF fulltext). Bull. Soc. Fr. Syst. 34: 25–31.
ISSN 1240-3253. http://sfs.snv.jussieu.fr/pdf/bulletin/bulletin_34.pdf.
• Laurin, M.; and Philip D. Cantino (2004). "First International Phylogenetic Nomenclature
Meeting: a report". Zool. Scr. 33 (5): 475–479. doi:10.1111/j.0300-3256.2004.00176.x.
• Laurin, M.; K. de Queiroz, and Philip D. Cantino (2006). "Sense and stability of taxon
names". Zool. Scr. 35 (1): 113–114. doi:10.1111/j.1463-6409.2006.00219.x.
• Nordal, I.; and B. Stedje (Coordinators) (2005). "Letters to the Editor: Paraphyletic taxa
should be accepted" (PDF fulltext). Taxon 54 (1): 5–6. doi:10.2307/25065296. ISSN 0040-0262.
http://anbg.gov.au/asbs/newsletter/newsletter-pdf/04-sept-120.pdf. including proposal, but without
the 150 supporting signatories
• Rieppel, O. (2006). "The PhyloCode: a critical discussion of its theoretical foundation".
Cladistics 22 (2): 186–197. doi:10.1111/j.1096-0031.2006.00097.x. http://www.blackwell-
synergy.com/doi/abs/10.1111/j.1096-0031.2006.00097.x.
• Sereno, P. C. (1999). "Definitions in phylogenetic taxonomy: critique and rationale". Syst.
Biol. 48 (2): 329–351. doi:10.1080/106351599260328. PMID 12066711.
• Sereno, P. C. (2005). "The logical basis of phylogenetic taxonomy". Syst. Biol. 54 (4): 595–
619. doi:10.1080/106351591007453. PMID 16109704.

• The PhyloCode (current draft)
• International Society for Phylogenetic Nomenclature
• International Society for Phylogenetic Nomenclature Discussion Forum
• Literature on Phylogenetic Nomenclature
• Christine Soares, What's in a Name?, Scientific American, (November 2004).
• PhyloCode debate
• What if we decide to rename every living thing on Earth? , Discovery Magazine, (04.28.2005)
Relevant Computational phylogenetics · Molecular phylogenetics · Cladistics

fields


Retrieved from "http://en.wikipedia.org/wiki/PhyloCode"
Categories: Biological nomenclature | Nomenclature

W000
DNA barcoding

DNA barcoding is a taxonomic method that uses a short genetic marker in an organism's DNA to
identify it as belonging to a particular species. It differs from molecular phylogeny in that the main goal is not
to determine classification but to identify an unknown sample in terms of a known classification.[1] Although
barcodes are sometimes used in an effort to identify unknown species or assess whether species should be
combined or separated,[2] the utility of DNA barcoding for these purposes is subject to debate.[3]
Applications include, for example, identifying plant leaves even when flowers or fruit are not
available, identifying the diet of an animal based on stomach contents or faeces,[4] and identifying products
in commerce (for example, herbal supplements or wood).[1]
Contents
[hide]
• 1 Choice of Locus
• 1.1 Mitochondrial DNA
• 1.2 Identifying flowering plants
• 2 Vouchered specimens
• 3 Origin
• 4 Case studies
• 4.1 Identification of birds
• 4.2 Delimiting cryptic species
• 4.3 Cataloguing ancient life
• 4.4 The Moorea Biocode Project
• 5 Criticisms
• 6 DNA Barcoding Software
• 7 See also
• 8 References
[edit] Choice of Locus
A desirable locus for DNA barcoding should be standardized (so that large databases of sequences
for that locus can be developed),[5] present in most of the taxa of interest and sequencable without species-
specific PCR primers,[5] short enough to be easily sequenced with current technology,[6] and provide a large
variation between species yet a relatively small amount of variation within a species.[7]
Although several loci have been suggested, a common set of choices are:
• For animals and many other eukaryotes, the mitochrondrial CO1 gene
• For land plants, the concatenation of the rbcL and matK chloroplast genes[5]
[edit] Mitochondrial DNA

DNA barcoding is based on a relatively simple concept. Most eukaryote cells contain mitochondria,
and mitochondrial DNA (mtDNA) has a relatively fast mutation rate, which results in significant variation in
mtDNA sequences between species and, in principle, a comparatively small variance within species. A 648-
bp region of the mitochondrial cytochrome c oxidase subunit I (COI) gene was proposed as a potential
'barcode'.
However, because all mtDNA genes are maternally inherited (direct evidence for recombination in
mtDNA is available in some bivalves such as Mytilus[8] but it is suspected that it may be more
widespread[9]), any occurrences of hybridization,[10] male-killing microoroganisms,[11] cytoplasmic
incompatibility-inducing symbionts (e.g., Wolbachia[11]), horizontal gene transfer (such as via cellular
symbionts[12]), or other "reticulate" evolutionary phenomena in a lineage can lead to misleading results (i.e.,
it is possible for two different species to share mtDNA,[13] or for one species to have more than one mtDNA
sequence exhibited among different individuals).[14][15]
As of 2009, databases of CO1 sequences included at least 620,000 specimens from over 58,000
species of animals, larger than databases available for any other gene.[16]
[edit] Identifying flowering plants

Kress et al. (2005[1]) suggest that the use of the COI sequence “is not appropriate for most species
of plants because of a much slower rate of cytochrome c oxidase I gene evolution in higher plants than in
animals”. A series of experiments was then conducted to find a more suitable region of the genome for use in
the DNA barcoding of flowering plants (or the larger group of land plants).[6] One 2005 proposal was the
nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer;[1] other researchers
advocated other regions such as matK.[6]
In 2009, a collaboration of a large group of plant DNA barcode researchers proposed two chloroplast
genes, rbcL and matK, taken together, as a barcode for plants.[5] Jesse Ausubel, a DNA barcode researcher
not involved in that effort, suggested that standardizing on a sequence was the best way to produce a large
database of plant sequences, and that time would tell whether this choice would be sufficiently good at
distinguishing different plant species.[16]
[edit] Vouchered specimens

DNA sequence databases like GenBank contain many sequences that are not tied to vouchered
specimens (for example, herbarium specimens, cultured cell lines, or sometimes images). This is problematic
in the face of taxonomic issues such as whether several species should be split or combined, or whether past
identifications were sound. Therefore, best practice for DNA barcoding is to sequence vouchered specimens.
[17][18]
[edit] Origin
The use of nucleotide sequence variations to investigate evolutionary relationships is not a new
concept. Carl Woese used sequence differences in ribosomal RNA (rRNA) to discover archaea, which in turn
led to the redrawing of the evolutionary tree, and molecular markers (e.g., allozymes, rDNA, and mtDNAvage
) have been successfully used in molecular systematics for decades. DNA barcoding provides a standardised
method for this process via the use of a short DNA sequence from a particular region of the genome to
provide a 'barcode' for identifying species. In 2003, Paul D.N. Hebert from the University of Guelph, Ontario,
Canada, proposed the compilation of a public library of DNA barcodes that would be linked to named
specimens. This library would “provide a new master key for identifying species, one whose power will rise
with increased taxon coverage and with faster, cheaper sequencing”.
[edit] Case studies

[edit] Identification of birds
In an effort to find a correspondence between traditional species boundaries established by
taxonomy and those inferred by DNA barcoding, Hebert and co-workers sequenced DNA barcodes of 260 of
the 667 bird species that breed in North America (Hebert et al. 2004a[19]). They found that every single one
of the 260 species had a different COI sequence. 130 species were represented by two or more specimens;
in all of these species, COI sequences were either identical or were most similar to sequences of the same
species. COI variations between species averaged 7.93%, whereas variation within species averaged
0.43%. In four cases there were deep intraspecific divergences, indicating possible new species. Three out of
these four polytypic species are already split into two by some taxonomists. Hebert et al.'s (2004a[19]) results
reinforce these views and strengthen the case for DNA barcoding. Hebert et al. also proposed a standard
sequence threshold to define new species, this threshold, the so-called "barcoding gap", was defined as 10
times the mean intraspecific variation for the group under study.
[edit] Delimiting cryptic species

The next major study into the efficacy of DNA barcoding was focused on the neotropical skipper
butterfly, Astraptes fulgerator at the Area Conservacion de Guanacaste (ACG) in north-western Costa Rica.
This species was already known as a cryptic species complex, due to subtle morphological differences, as
well as an unusually large variety of caterpillar food plants. However, several years would have been
required for taxonomists to completely delimit species. Hebert et al. (2004b[20]) sequenced the COI gene of
484 specimens from the ACG. This sample included “at least 20 individuals reared from each species of food
plant, extremes and intermediates of adult and caterpillar color variation, and representatives” from the three
major ecosystems where Astraptes fulgerator is found. Hebert et al. (2004b[20]) concluded that Astraptes
fulgerator consists of 10 different species in north-western Costa Rica. These results, however, were
subsequently challenged by Brower (2006[21]), who pointed out numerous serious flaws in the analysis, and
concluded that the original data could support no more than the possibility of three to seven cryptic taxa
rather than ten cryptic species. This highlights that the results of DNA barcoding analyses can be dependent
upon the choice of analytical methods used by the investigators, so the process of delimiting cryptic species
using DNA barcodes can be as subjective as any other form of taxonomy.
A more recent example used DNA barcoding for the identification of cryptic species included in the
ongoing long-term database of tropical caterpillar life generated by Dan Janzen and Winnie Hallwachs in
Costa Rica at the ACG.[22] In 2006 Smith et al.[23] examined whether a COI DNA barcode could function as
a tool for identification and discovery for the 20 morphospecies of Belvosia [3] parasitoid flies (Tachinidae)
that have been reared from caterpillars in ACG. Barcoding not only discriminated among all 17 highly host-
specific morphospecies of ACG Belvosia, but it also suggested that the species count could be as high as 32
by indicating that each of the three generalist species might actually be arrays of highly host-specific cryptic
species.
In 2007 Smith et al. expanded on these results by barcoding 2,134 flies belonging to what appeared
to be the 16 most generalist of the ACG tachinid morphospecies.[24] They encountered 73 mitochondrial
lineages separated by an average of 4% sequence divergence and, as these lineages are supported by
collateral ecological information, and, where tested, by independent nuclear markers (28S and ITS1), the
authors therefore viewed these lineages as provisional species. Each of the 16 initially apparent generalist
species were categorized into one of four patterns: (i) a single generalist species, (ii) a pair of
morphologically cryptic generalist species, (iii) a complex of specialist species plus a generalist, or (iv) a
complex of specialists with no remaining generalist. In sum, there remained 9 generalist species classified
among the 73 mitochondrial lineages analyzed.
However, also in 2007, Whitworth et al. reported that flies in the related family Calliphoridae could not
be discriminated by barcoding.[14] They investigated the performance of barcoding in the fly genus
Protocalliphora, known to be infected with the endosymbiotic bacteria Wolbachia. Assignment of unknown
individuals to species was impossible for 60% of the species, and if the technique had been applied, as in the
previous study, to identify new species, it would have underestimated the species number in the genus by
75%. They attributed the failure of barcoding to the non-monophyly of many of the species at the
mitochondrial level; in one case, individuals from four different species had identical barcodes. The authors
went on to state:
The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly
results from introgressive hybridization associated with Wolbachia infection. Given that
Wolbachia is known to infect between 15 and 75% of insect species, we conclude that
identification at the species level based on mitochondrial sequence might not be possible for
many insects.[14]
Marine biologists have also considered the value of the technique in identifying cryptic and
polymorphic species and have suggested that the technique may be helpful when associations with voucher
specimens are maintained,[17] though cases of "shared barcodes" (e.g., non-unique) have been documented
in cichlid fishes and cowries[15]
[edit] Cataloguing ancient life

Lambert et al. (2005[25]) examined the possibility of using DNA barcoding to assess the past
diversity of the Earth's biota. The COI gene of a group of extinct ratite birds, the moa, were sequenced using
26 subfossil moa bones. As with Hebert's results, each species sequenced had a unique barcode and
intraspecific COI sequence variance ranged from 0 to 1.24%. To determine new species, a standard
sequence threshold of 2.7% COI sequence difference was set. This value is 10 times the average
intraspecies difference of North American birds, which is inconsistent with Hebert's recommendation that the
threshold value be based on the group under study. Using this value, the group detected six moa species. In
addition, a further standard sequence threshold of 1.24% was also used. This value resulted in 10 moa
species which corresponded with the previously known species with one exception. This exception
suggested a possible complex of species which was previously unidentified. Given the slow rate of growth
and reproduction of moa, it is probable that the interspecies variation is rather low. On the other hand, there
is no set value of molecular difference at which populations can be assumed to have irrevocably started to
undergo speciation. It is safe to say, however, that the 2.7% COI sequence difference initially used was far
too high.
[edit] The Moorea Biocode Project

The Biocode Project is a barcoding initiative to create the first comprehensive inventory of all non-
microbial life in a complex tropical ecosystem, the island of Moorea in Tahiti. Supported by a grant from the
Gordon and Betty Moore Foundation, the Moorea Biocode Project is a 3-year project that brings together
researchers from the Smithsonian Institution, UC Berkeley, France’s National Center for Scientific Research
(CNRS), and other partners. The outcome of the project is a library of genetic markers and physical
identifiers for every species of plant, animal and fungi on the island that will be provided as a publicly
available database resource for ecologists and evolutionary biologists around the world.
The software back-end to the Moore Biocode Project is Geneious Pro and two custom-developed
plugins from the New Zealand-based company, Biomatters. The Biocode LIMS and Genbank Submission
plugins have been made freely available to the public[26] and users of the free Geneious Basic software will
be able to access and view the Biocode database upon completion of the project, while a commercial copy of
Geneious Pro is required for researchers involved int data creation and analysis.
[edit] Criticisms
DNA barcoding has met with spirited reaction from scientists, especially systematists, ranging from
enthusiastic endorsement to vociferous opposition.[27] For example, many stress the fact that DNA
barcoding does not provide reliable information above the species level, while others indicate that it is
inapplicable at the species level, but may still have merit for higher-level groups.[14] Others resent what they
see as a gross oversimplification of the science of taxonomy. And, more practically, some suggest that
recently diverged species might not be distinguishable on the basis of their COI sequences.[28] Due to
various phenomena, Funk & Omland (2003[29]) found that some 23% of animal species are polyphyletic if
their mtDNA data are accurate, indicating that using an mtDNA barcode to assign a species name to an
animal will be ambiguous or erroneous some 23% of the time (see also Meyer & Paulay, 2005[30]). Studies
with insects suggest an equal or even greater error rate, due to the frequent lack of correlation between the
mitochondrial genome and the nuclear genome or the lack of a barcoding gap (e.g., Hurst and Jiggins, 2005,
[12] Whitworth et al., 2007,[14] Wiemers & Fiedler, 2007[31]). Problems with mtDNA arising from male-killing
microoroganisms and cytoplasmic incompatibility-inducing symbionts (e.g., Wolbachia)[11] are also
particularly common among insects. Given that insects represent over 75% of all known organisms,[32] this
suggests that while mtDNA barcoding may work for vertebrates, it may not be effective for the majority of
known organisms.
Moritz and Cicero (2004[33]) have questioned the efficacy of DNA barcoding by suggesting that other
avian data is inconsistent with Hebert et al.'s interpretation, namely, Johnson and Cicero's (2004[34]) finding
that 74% of sister species comparisons fall below the 2.7% threshold suggested by Hebert et al. These
criticisms are somewhat misleading considering that, of the 39 species comparisons reported by Johnson
and Cicero, only 8 actually use COI data to arrive at their conclusions. Johnson and Cicero (2004[34]) have
also claimed to have detected bird species with identical DNA barcodes, however, these 'barcodes' refer to
an unpublished 723-bp sequence of ND6 which has never been suggested as a likely candidate for DNA
barcoding.
The DNA barcoding debate resembles the phenetics debate of decades gone by. It remains to be
seen whether what is now touted as a revolution in taxonomy will eventually go the same way as phenetic
approaches, of which was claimed exactly the same decades ago, but which were all but rejected when they
failed to live up to overblown expectations.[35] Controversy surrounding DNA barcoding stems not so much
from the method itself, but rather from extravagant claims that it will supersede or radically transform
traditional taxonomy. Other critics fear a "big science" initiative like barcoding will make funding even more
scarce for already underfunded disciplines like taxonomy, but barcoders respond that they compete for
funding not with fields like taxonomy, but instead with other big science fields, such as medicine and
genomics.[36] Barcoders also maintain that they are being dragged into long-standing debates over the
definition of a species and that barcoding is less controversial when viewed primarily as a method of
identification, not classification.[1][18]
The current trend appears to be that DNA barcoding needs to be used alongside traditional
taxonomic tools and alternative forms of molecular systematics so that problem cases can be identified and
errors detected. Non-cryptic species can generally be resolved by either traditional or molecular taxonomy
without ambiguity. However, more difficult cases will only yield to a combination of approaches. And finally,
as most of the global biodiversity remains unknown, molecular barcoding can only hint at the existence of
new taxa, but not delimit or describe them (DeSalle, 2006;[37] Rubinoff, 2006[38][39]).
[edit] DNA Barcoding Software

Software for DNA barcoding requires integration of a field information management system (FIMS),
laboratory information management system (LIMS), sequence analysis tools, workflow tracking to connect
field data and laboratory data, database submission tools and pipeline automation for scaling up to eco-
system scale projects. Geneious Pro can be used for the sequence analysis components, and the two
plugins made freely available through the Moorea Biocode Project, the Biocode LIMS and Genbank
Submission plugins handle integration with the FIMS, the LIMS, workflow tracking and database submission.
[edit] See also

• DNA taxonomy
• Consortium for the Barcode of Life
• Identification (biology)
[edit] References
1. ^ a b c d e Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (June 2005). "Use of
DNA barcodes to identify flowering plants". Proc. Natl. Acad. Sci. U.S.A. 102 (23): 8369–74.
doi:10.1073/pnas.0503123102. PMID 15928076. Supporting Information
2. ^ Koch, H. 2010. Combining morphology and DNA barcoding resolves the taxonomy of
Western Malagasy Liotrigona Moure, 1961. African Invertebrates 51 (2): 413-421.[1]PDF fulltext
3. ^ Seberg O, Petersen G. (2009). "How many loci does it take to DNA barcode a crocus?".
PLoS One 4 (2): e4598. doi:10.1371/journal.pone.0004598. PMID 19240801.
4. ^ Eeva M Soininen et al. (2009). "Analysing diet of small herbivores: the efficiency of DNA
barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex
plant mixtures". Frontiers in Zoology 6: 16. doi:10.1186/1742-9994-6-16. PMID 19695081.
5. ^ a b c d CBOL Plant Working Group (August 4, 2009). "A DNA barcode for land plants".
PNAS 106 (31): 12794–12797. doi:10.1073/pnas.0905845106. PMID 19666622.
6. ^ a b c Kress WJ, Erickson DL (2008). "DNA barcodes: Genes, genomics, and
bioinformatics". PNAS 105 (8): 2761–2762. doi:10.1073/pnas.0800476105. PMID 18287050.
7. ^ Renaud Lahaye et al. (2008-02-26). "DNA barcoding the floras of biodiversity hotspots".
Proc Natl Acad Sci USA 105 (8): 2923–2928. doi:10.1073/pnas.0709936105. PMID 18258745.
8. ^ Ladoukakis ED, Zouros E (1 July 2001). "Direct evidence for homologous recombination in
mussel (Mytilus galloprovincialis) mitochondrial DNA". Mol. Biol. Evol. 18 (7): 1168–75.
PMID 11420358. http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11420358.
9. ^ Tsaousis AD, Martin DP, Ladoukakis ED, Posada D, Zouros E (April 2005). "Widespread
recombination in published animal mtDNA sequences". Mol. Biol. Evol. 22 (4): 925–33.
doi:10.1093/molbev/msi084. PMID 15647518.
10.^ Melo-Ferreira J, Boursot P, Suchentrunk F, Ferrand N, Alves PC (July 2005). "Invasion
from the cold past: extensive introgression of mountain hare ( Lepus timidus) mitochondrial DNA into
three other hare species in northern Iberia". Mol. Ecol. 14 (8): 2459–64. doi:10.1111/j.1365-
294X.2005.02599.x. PMID 15969727.
11.^ a b c Johnstone RA, Hurst GDD (1996). "Maternally inherited male-killing microorganisms
may confound interpretation of mitochondrial DNA variability". Biol. J. Linnaean Soc. 58: 453–70.
doi:10.1111/j.1095-8312.1996.tb01446.x.
12.^ a b Hurst GD, Jiggins FM (August 2005). "Problems with mitochondrial DNA as a marker in
population, phylogeographic and phylogenetic studies: the effects of inherited symbionts". Proc. Biol.
Sci. 272 (1572): 1525–34. doi:10.1098/rspb.2005.3056. PMID 16048766.
13.^ Croucher PJP, Oxford GS, Searle JB (2004). "Mitochondrial differentiation, introgression
and phylogeny of species in the Tegenaria atrica group (Araneae: Agelenidae)". Biological Journal of
the Linnean Society 81: 79–89. doi:10.1111/j.1095-8312.2004.00280.x.
14.^ a b c d e Whitworth TL, Dawson RD, Magalon H, Baudry E (July 2007). "DNA barcoding
cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae)". Proc.
Biol. Sci. 274 (1619): 1731–9. doi:10.1098/rspb.2007.0062. PMID 17472911.
15.^ a b Meier R (2008). "Ch. 7: DNA sequences in taxonomy: Opportunities and challenges". In
Wheeler, Quentin. The new taxonomy. Boca Raton: CRC Press. ISBN 0-8493-9088-5.
16.^ a b Jesse H. Ausubel (August 4, 2009). "A botanical macroscope". Proceedings of the
National Academy of Sciences 106 (31): 12569. doi:10.1073/pnas.0906757106. ISSN 00278424.
PMID 19666620.
17.^ a b Schander C, Willassen E (2005). "What can Biological Barcoding do for Marine
Biology?" (PDF). Marine Biology Research 1 (1): 79–83. doi:10.1080/17451000510018962.
http://www.bolinfonet.org/pdf/schander&willassen_2005.pdf.
18.^ a b Scott E. Miller (2007-03-20). "DNA barcoding and the renaissance of taxonomy". Proc
Natl Acad Sci U S A. 104 (12): 4775–4776. doi:10.1073/pnas.0700466104. PMID 17363473.
19.^ a b Hebert PD, Stoeckle MY, Zemlak TS, Francis CM (October 2004). "Identification of
Birds through DNA Barcodes". PLoS Biol. 2 (10): e312. doi:10.1371/journal.pbio.0020312.
PMID 15455034. Supporting Information
20.^ a b Hebert PD, Penton EH, Burns JM, Janzen DH, Hallwachs W (October 2004). "Ten
species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes
fulgerator". Proc. Natl. Acad. Sci. U.S.A. 101 (41): 14812–7. doi:10.1073/pnas.0406166101.
PMID 15465915. Supporting Information
21.^ Brower AVZ (2006). "Problems with DNA barcodes for species delimitation: 'ten species' of
Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae)". Systematics and Biodiversity 4 (2): 127–
32. doi:10.1017/S147720000500191X.
22.^ "Database homepage for ACG caterpillar (Lepidoptera) rearing databases".
http://janzen.sas.upenn.edu/caterpillars/database.lasso. Retrieved 2007-08-12.
23.^ Smith MA, Woodley NE, Janzen DH, Hallwachs W, Hebert PD (2006). "DNA barcodes
reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid
flies (Diptera: Tachinidae)". Proc. Natl. Acad. Sci. U.S.A. 103 (10): 3657–62.
doi:10.1073/pnas.0511318103. PMID 16505365.
24.^ Smith MA, Wood DM, Janzen DH, Hallwachs W, Hebert PD (2007). "DNA barcodes affirm
that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all
generalists". Proc. Natl. Acad. Sci. U.S.A. 104 (12): 4967–72. doi:10.1073/pnas.0700050104.
PMID 17360352.
25.^ Lambert DM, Baker A, Huynen L, Haddrath O, Hebert PD, Millar CD (2005). "Is a large-
scale DNA-based inventory of ancient life possible?" (PDF fulltext). J. Hered. 96 (3): 279–84.
doi:10.1093/jhered/esi035. PMID 15731217. http://jhered.oxfordjournals.org/cgi/reprint/96/3/279.pdf.
26.^ http://www.bio-itworld.com/2010/11/30/biomatters-moorea-LIMS.html
27.^ Rubinoff D, Cameron S, Will K (2006). "A genomic perspective on the shortcomings of
mitochondrial DNA for "barcoding" identification". J. Hered. 97 (6): 581–94.
doi:10.1093/jhered/esl036. PMID 17135463.
28.^ Kevin, C.R. Kerr, Mark Y. Stoeckle, Carla J. Dove, Lee A. Weigt, Charles M. Francis & Paul
D. N. Hebert. 2006. Comprehensive DNA barcode coverage of North American birds. Molecular
Ecology Notes. (OnlineEarly Articles). doi:10.1111/j.1471-8286.2006.01670.x Full text
29.^ Funk DJ, Omland KE (2003). "Species-level paraphyly and polyphyly: frequency, causes,
and consequences, with insights from animal mitochondrial DNA". Annu Rev Ecol Syst 34: 397–423.
30.^ Meyer CP, Paulay G (December 2005). "DNA barcoding: error rates based on
comprehensive sampling". PLoS Biol. 3 (12): e422. doi:10.1371/journal.pbio.0030422.
PMID 16336051.
31.^ Wiemers M, Fiedler K (2007). "Does the DNA barcoding gap exist? – a case study in blue
butterflies (Lepidoptera: Lycaenidae)". Front. Zool. 4: 8. doi:10.1186/1742-9994-4-8.
PMID 17343734. PMC 1838910. http://www.frontiersinzoology.com/content/4/1/8.
32.^ [2][dead link]
33.^ Moritz C, Cicero C (2004). "DNA Barcoding: Promise and Pitfalls" (PDF fulltext). PLoS Biol.
2 (10): 1529–31. doi:10.1371/journal.pbio.0020354. PMID 15486587. PMC 519004.
http://biology.plosjournals.org/perlserv/?request=get-pdf&file=10.1371_journal.pbio.0020354-L.pdf.
34.^ a b Johnson NK, Cicero C (May 2004). "New mitochondrial DNA data affirm the importance
of Pleistocene speciation in North American birds". Evolution 58 (5): 1122–30. PMID 15212392.
35.^ Will KW, Mishler BD, Wheeler QD (2005). "The Perils of DNA Barcoding and the Need for
Integrative Taxonomy" (PDF). Syst. Biol. 54 (5): 844–51. doi:10.1080/10635150500354878.
PMID 16243769.
http://www.erin.utoronto.ca/~w3bio/bio443/seminar_papers/perils_of_dna_barcoding.pdf.
36.^ Gregory TR (April 2005). "DNA barcoding does not compete with taxonomy" (PDF). Nature
434 (7037): 1067. doi:10.1038/4341067b. PMID 15858548.
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37.^ Desalle R (October 2006). "Species discovery versus species identification in DNA
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1739.2006.00543.x. PMID 17002772.
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• Barcode of Life Database
• International Barcode of Life
• Consortium for the Barcode of Life
• Fish Barcode of Life Initiative (FISH-BOL)
• All Birds Barcoding Initiative (ABBI)
• Polar Flora and Fauna Barcoding website (Latest outpost in the Canadian Arctic in the field)
• The Barcode of Life Blog
• DNA Barcoding Community Network
• Guidelines for non COI gene selection
Relevant



Retrieved from "http://en.wikipedia.org/wiki/DNA_barcoding"
Categories: Taxonomy | Molecular genetics | Bioinformatics | Authentication methods | Biometrics

W000
Symplesiomorphy

A cladogram showing the terminology used to describe different patterns of ancestral and derived
character states.[1]
In cladistics, a symplesiomorphy or symplesiomorphic character is a trait which is shared (a
symmorphy) between two or more taxa, but which is also shared with other taxa which have an earlier last
common ancestor with the taxa under consideration. They are therefore not an indication that the taxa be
considered more closely related to each other than to the more distant taxa, as all share the more primitive
trait. A close phylogenetic relationship, that the taxa form a certain clade to the exclusion of certain other
taxa, can only be shown by the discovery of synapomorphies: shared traits that have originated with the last
common ancestor of the taxa considered, or at least in the branch, not including the taxa to be excluded,
leading to it.
The concept of the symplesiomorphy shows the danger of grouping species together on the basis of
general morphologic or genetic similarity, without distinguishing between resemblances caused by either
primitive or derived traits. This phenetic method of analysis was common before cladistics became popular in
the 1980s.
A famous example is pharyngeal gill breathing in bony and cartilaginous fishes. The former are more
closely related to Tetrapoda (terrestrial vertebrates, which evolved out of a clade of bony fishes) that breathe
via their skin or lungs, rather than to the sharks, rays, et al.. Their kind of gill respiration is shared by the
"fishes" because it was present in their common ancestor and lost in the other living vertebrates.
[edit] See also

• Synapomorphy
[edit] References
1. ^ Page, Roderic D.M. and Holmes, Edward C. Molecular evolution: a phylogenetic approach.
Wiley-Blackwell, 1st edition, 1998.
Relevant



W000
Synapomorphy

In cladistics, a synapomorphy or synapomorphic character is a trait that is shared ("symmorphy") by
two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait.
[2] A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in
their last common ancestor. The word "synapomorphy" is derived from the Greek words σύν, syn = with, in
company with, together with; ἀπό, apo = away from; and μορφή, morphe = shape.
True synapomorphies usually uniquely characterise a given set of terminal groups, but this is not
essential to the concept. Thus, if some descendants of a last common ancestor possess a synapomorphic
trait, it is not strictly necessary that all of its descendants must possess the same trait.
[edit] Comparisons with other shared traits

A synapomorphy should not be confused with other types of shared traits:
• A synapomorphy is a shared trait found among two or more taxa and their most recent
common ancestor, whose ancestor in turn does not possess the trait. An example is the halteres, the
uniquely modified hind wings found in all families of winged Diptera. No other group of insects
possesses similar structures. However, the fact that the trait is found exclusively in Diptera, to the
exclusion of all other groups, is not essential in identifying the trait as a synapomorphy; rather, this
fact makes its determination easier.
• A symplesiomorphy is a shared trait found among two or more taxa, but which is also found
in taxa with an earlier common ancestor. An example of this is the five toes seen on the hind legs of
rats and apes. This character-state originated very early in Tetrapoda and occurs in other tetrapod
groups, e.g. in lizards. There is thus no indication that the group formed of rats and apes is a clade to
the exclusion of these other groups.
• A homoplasy is a shared trait found among different taxa but not in their common ancestor
(i.e., the same trait emerged in different taxa independently of each other). An example of this is
homeothermy in birds and mammals. This trait is a derived character-state (in relation to
poikilothermy, the character-state of the last common ancestor of both groups), which evolved
independently in these two groups (or at least in the larger clades to which these groups belong).
[edit] Cladistic analyses

Synapomorphies are used to establish phylogenies in cladistic analyses. As such they are empirical
data which can support a certain hypothesis that terminal groups form a clade (monophyletic group) together
to the exclusion of certain other groups – whereas character-states that are shared, but also shared by other
terminal groups descending from an earlier common ancestor, cannot be used to exclude these other
groups. The latter character-states can consist of symplesiomorphies ("primitive" character-states having
originated in the earlier common ancestor) or homoplasies (superficially similar but independently evolved
derived character-states).
The key problem is to identify the polarity of the transformation series to which several character-
states belong, i.e. to tell which character-state is apomorphic and which is plesiomorphic. Various criteria
were used to polarise the transformation series in earlier cladistics; however in the recent two decades
pattern criteria based on outgroup comparison have dominated the field.
The concepts of apomorphy and plesiomorphy are relative to a certain level of generality. What
counts as an apomorphy at one level of generality may well be a plesiomorphy at the other. For example, for
rats and apes, the presence of mammary glands is a symplesiomorphy, but it is a synapomorphy for
mammals in relation to tetrapods more broadly.
It is not essential to a synapomorphy that all members of a clade possess it; even if some would have
secondarily lost the trait it could still be a synapomorphy of the clade as a whole. A character state that is a
synapomorphy for a clade, but for lineages in this clade is a plesiomorphy that is altered in some lineages, is
called underlying synapomorphy. If no crown group taxa are known, it is sometimes difficult to decide which
character state is the underlying synapomorphy and which the autapomorphy that overlies it.
Clades are not defined by synapomorphies as such, though it is possible to define them by
apomorphies in general.
[edit] References
2. ^ Gould, Steven Jay (1983). Hen's Teeth and Horse's Toes. New York: Norton. p. 358.
ISBN 0393017168.
Relevant


Retrieved from "http://en.wikipedia.org/wiki/Synapomorphy"
Categories: Phylogenetics | Evolutionary biology terminology

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Autapomorphy

In cladistics, an autapomorphy is a distinctive anatomical feature, known as a derived trait, that is
unique to a given terminal group. That is, it is found only in one member of a clade, but not found in any
others or outgroup taxa, not even those most closely related to the group (which may be a species, family or
in general any clade).[2] It can therefore be considered an apomorphy in relation to a single taxon.[3] The
word "autapomorphy" is derived from the Greek words αὐτός, aut = self; ἀπό, apo = away from; and μορφή,
morphe = shape.
An autapomorphy is not present in the closest relative of the terminal group and also was not present
in their common ancestor. An example of an autapomorphy can be described in modern snakes. Snakes
have lost the two pairs of legs that characterize all of Tetrapoda, and the closest taxa to Ophidia - as well as
their common ancestors - all have two pairs of legs. Therefore, the Ophidia taxon presents an autapomorphy
with respect to its absence of legs.[3] The words autapomorphy and synapomorphy technically describe the
same derived character-state, but they differ in context: Synapomorphy describes the trait as it typifies the
taxon and contrasts it with a different condition in outgroups, while autapomorphy should be correctly used
when the component taxa are not mentioned.[4] An autapomorphy at a given taxonomic level may therefore
also be a synapomorphy at a less-inclusive level.[5]
The autapomorphic species concept is one of many methods that scientists might use to define and
distinguish species from one another. This definition assigns species on the basis of amount of divergence
associated with reproductive incompatibility, which is measured essentially by number of autapomorphies.[6]
This grouping method is often referred to as the "monophyletic species concept" or the "phylospecies"
concept and was popularized by D.E. Rosen in 1979. Within this definition, a species is seen as "the least
inclusive monophyletic group definable by at least one autapomorphy."[7] While this model of speciation is
useful in that it avoids non-monophyletic groupings, it has its criticisms as well. N.I. Platnick, for example,
believes the autapomorphic species concept to be inadequate because it allows for the possibility of
reproductive isolation and speciation while revoking the "species" status of the mother population. In other
words, if a peripheral population breaks away and becomes reproductively isolated, it would conceivably
need to develop at least one autapomorphy to be recognized as a different species. If this can happen
without the larger mother population also developing a new autapomorphy, then the mother population
cannot remain a species under the autapomorphic species concept: it would no longer have any
apomorphies not also shared by the daughter species.[8]
[edit] See also

• Homoplasy – a trait that is found in several terminal groups but evolved independently (i.e.,
was not present in their common ancestor)
• Synapomorphy – a trait that is found in some or all terminal groups of a clade, and inherited
from a common ancestor, for which it was an autapomorphy (i.e., not present in its immediate
ancestor).
• Underlying synapomorphy – a synapomorphy that has been lost again in many
members of the clade. If lost in all but one, it can be hard to distinguish from an
autapomorphy.
• Apomorphy – a synapomorphy discussed in reference to a less derived ancestral
state.
• Symplesiomorphy – an ancestral trait shared by two or more taxa.
• Plesiomorphy – a symplesiomorphy discussed in reference to a more derived state.
[edit] References
2. ^ Futuyma, Douglas J. Evolutionary Biology. Sinauer Associaties, Inc., 3rd edition. 1998.
Page 95.
3. ^ a b Appel, Ron D.; Feytmans, Ernest. Bioinformatics: a Swiss Perspective. "Chapter 3:
Introduction of Phylogenetics and its Molecular Aspects." World Scientific Publishing Company, 1st
edition. 2009.
4. ^ Carpenter, Kenneth and Currie, Philip J. Dinosaur Systematics: Approaches and
Perspectives. Cambridge University Press, 1992. Page 134.
5. ^ Forey, Peter L. History of the Coelacanth Fishes. Sprinter, 1st edition. 1997.
6. ^ Howard, Daniel J.; Berlocher, Stewart H. Endless Forms: Species and Speciation. Oxford
University Press, USA; 1st edition. 1998.
7. ^ Bull, Alan T. Microbial Diversity and Bioprospecting. ASM Press, 2004.
8. ^ Platnick, N.I. (2001). "From Cladograms to Classifications: The Road to DePhylocode. ".
The Systematics Association. http://www.systass.org/archive/events-archive/2001/platnick.pdf.
Relevant


Retrieved from "http://en.wikipedia.org/wiki/Autapomorphy"
Categories: Phylogenetics | Evolutionary biology terminology

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Monophyly

A monophyly
Comparison of phylogenetic groups, showing a monophyly (all descendants of the first reptiles), a
paraphyly (descendants of reptiles, minus birds), and a polyphyly (warm-blooded animals: mammals and
birds)
In common cladistic usage, a monophyletic group is a taxon (group of organisms) which forms a
clade, meaning that it contains all the descendants of the possibly hypothetical closest common ancestor of
the members of the group. The term is synonymous with the uncommon term holophyly. Monophyletic
groups are typically characterized by shared derived characteristics (synapomorphies).
Monophyly is contrasted with the terms paraphyly and polyphyly, which are most easily understood
from the second diagram in this article. In current usage, a paraphyletic group consists of all of the
descendants of a possibly hypothetical closest common ancestor minus one or more monophyletic groups
(most usually one). A paraphyletic group is thus 'nearly' monophyletic (consistent with the meaning of the
prefix 'para', namely 'near' or 'alongside'.) A polyphyletic group is any group other than a monophyletic group
or a paraphyletic group, which like a paraphyletic group contains only some of the descendants of their
closest common ancestor, but unlike a paraphyletic group is not characterized by the missing descendants
forming one (or more) monophyletic groups.
These definitions have taken some time to be accepted. When the cladistic school of thought
became mainstream in the 1960s, several alternative definitions were in use. Indeed, taxonomists sometimes
used terms without defining them, leading to confusion in the early literature,[1] a confusion which persists.
See also: Crown group
Contents
[hide]
• 1 Definitions
• 2 Controversy
• 3 References
• 4 See also
[edit] Definitions
On the broadest scale, definitions fall into two groups.
• The widest, and arguably[2] the semantically correct meaning of the word,[3] is any two or
more groups sharing a common ancestor.[4] This very broad definition strips the term of scientific
utility. Therefore, scientists today restrict the term to holophyletic groups only – that is, groups
consisting of all the descendants of one (usually hypothetical) common ancestor.[1] However, when
considering taxonomic groups such as genera and species, the most appropriate nature of their
common ancestor is unclear. Assuming that it would be one individual or mating pair is unrealistic for
sexually reproducing species, which are by definition interbreeding populations.[5]
• However, using a broader definition, such as a species and all its descendants, does not
really work to define a genus.[5] A satisfactory and comprehensive cladistic definition of a species or
genus is in fact impossible, and reflects the impossibility of seamlessly impressing a gradualistic
model of continual change over the 'quantum' Linnean model, where species have defined
boundaries, and intermediaries between species cannot be accommodated.[6]
[edit] Controversy
This incompatibility with the Linnaean taxonomy model led to an initial rift, not entirely healed,
between the cladistic and Linnean schools of thought. Extreme cladists challenged the validity of Linnean
taxa such as the Reptilia. Because birds, although descended from reptiles, are not themselves considered
to be reptiles, cladists demanded that the taxon Reptilia be dismantled: a request that taxonomists were
unwilling to heed. This stand-off was eventually resolved to a degree by the construction of the term
'paraphyletic' to describe closely related groups which included most but not all of the descendants of a
common ancestor.[4]
However, the coining of this term led to yet more confusion. Some scientists considered paraphyletic
groups to be monophyletic (as they shared a common ancestor), where others insisted that monophyletic
should continue to refer only to holophyletic groups.[4] Another term, polyphyletic, fell outside of the definition
of monophyly. A strict explanation of a paraphyletic group has not been published, but the consensus
appears to be that paraphyletic groups consist of a monophyletic group, minus one smaller constituent clade
– for instance "reptiles minus birds". Polyphyletic groups can be thought of as a number of unrelated clades,
for instance "warm blooded animals" = "birds plus mammals". Non-holophyletic groups are of little use for
analysis of evolutionary processes, hence the calls for their "unnaming" - even though they are useful to
scientists who are less concerned with the evolutionary past of groups.[4] Naming is also a problem for
monophyletic groups: because the number of ancestors from which to root monophyletic groups is almost
infinite, giving each clade a unique name is impossible[4] - as illustrated by the failed attempts to instigate a
system called the Phylocode. Names obfuscate the really interesting part, which is the branching order, and
are therefore of little utility to the cladist - at odds with the taxonomist, who since the time of Linnaeus has
been naming species. Intermediate, and particularly fossil, taxa can be considered to fall 'just outside' a
widely accepted taxon. For instance, Archaeopteryx appears more reptilian than bird – it has teeth and a
number of other reptilian characteristics. But it also has feathers, which have traditionally been considered as
an avian trait. It lacks a number of other traits shared by all birds, so cannot fall within the bird clade. To
reflect this phylogenetic proximity, it is termed a 'stem group bird' - i.e. it lies on a branch close to the lineage
that led to true birds, as recognised by a taxonomist. This concept closes the gap between taxonomy and
cladistics at a broader scale,[6] but is difficult to apply at a species-level resolution.
[edit] References
1. ^ a b Hennig, Willi; Davis, D. (Translator); Zangerl, R. (Translator) (1999) [1966].
Phylogenetic Systematics (Illinois Reissue ed.). Board of Trustees of the University of Illinois. pp. 72–
77. ISBN 0252068149.
2. ^ Colless, Donald H. (March 1972). "Monophyly". Systematic Zoology (Society of Systematic
Biologists) 21 (1): 126–128. doi:10.2307/2412266. http://jstor.org/stable/2412266
3. ^ Envall, Mats (2008). "On the difference between mono-, holo-, and paraphyletic groups: a
consistent distinction of process and pattern". Biological Journal of the Linnean Society 94: 217.
doi:10.1111/j.1095-8312.2008.00984.x.
4. ^ a b c d e Ashlock, Peter D. (March 1971). "Monophyly and Associated Terms". Systematic
Zoology (Society of Systematic Biologists) 20 (1): 63–69. doi:10.2307/2412223.
http://jstor.org/stable/2412223
5. ^ a b Simpson, George (1961). Principles of Animal Taxonomy. New York: Columbia
6. ^ a b Budd, G.E.; Jensen, S. (2000). "A critical reappraisal of the fossil record of the bilaterian
phyla". Biological Reviews 75 (02): 253–295. doi:10.1017/S000632310000548X. PMID 10881389.
http://journals.cambridge.org/production/action/cjoGetFulltext?fulltextid=624
[edit] See also

• Naming clades
• Holophyly
• Paraphyly
• Polyphyly

• Abbey, Darren (1994-2006). "Graphical explanation of basic phylogenetic terms". University
of California, Berkeley. http://www.ucmp.berkeley.edu/glossary/gloss1/phyly.html. Retrieved 15
January 2010.
• Carr, Steven M. (2002). "Concepts of monophyly, polyphyly & paraphyly". Memorial
University. http://www.mun.ca/biology/scarr/Taxon_types.htm. Retrieved 15 January 2010.
• Hyvönen, Jaako (2005). "Monophyly, consensus, compromise" (pdf). University of Helsinki.
http://www.helsinki.fi/~jhyvonen/ec05/05_11.11.pdf. Retrieved 15 January 2010.
Relevant



Retrieved from "http://en.wikipedia.org/wiki/Monophyly"
W000
Holophyly

Holophyletic is a term posited as a semantically correct replacement for the term monophyletic as
used by cladists (which differs from the usage of evolutionary systematists).[1] It originated amidst confusion
over the correct definition for 'monophyletic group'; many definitions were available, of varying degrees of
restrictiveness, and 'holophyletic' was posited as a term to describe the definition with scientific utility.[1] The
least scientifically useful definition for monophyletic, which is arguably the semantically correct one,
considers any organisms with a common ancestor to be a monophyletic group.[2] Since it is presumed that
one could find a common ancestor from any group of organisms if one goes far enough into the past, this
definition implicitly or explicitly constrains what is a legitimate common ancestor, for example by requiring the
common ancestor to share a derived trait (synapomorphy) which defines the group.[1]
The term holophyletic refers specifically to the definition that a group contains the common ancestor,
all organisms descended from the common ancestor, and no other organisms.
The term holophyletic has not gained widespread acceptance in the scientific community,[3] probably
because the term 'monophyletic' is so widely used with the same widely understood meaning.
[edit] References
1. ^ a b c Ashlock, P.D. (1971). "Monophyly and associated terms". Systematic Zoology 20 (1):
63–69. doi:10.2307/2412223. http://www.jstor.org/stable/2412223.
2. ^ Envall, Mats (2008). "On the difference between mono-, holo-, and paraphyletic groups: a
consistent distinction of process and pattern". Biological Journal of the Linnean Society 94: 217.
doi:10.1111/j.1095-8312.2008.00984.x.
3. ^ Google Scholar. "Holophyletic". http://scholar.google.ca/scholar?q=holophyletic.
Relevant

Retrieved from "http://en.wikipedia.org/wiki/Holophyly"
W000
Paraphyly

challenged and removed. (January 2010)
A cladogram showing a hypothetical descent from an ancestor species of the clade vertebrata.[1]
Note that cladograms do not necessarily correspond to taxonomic classifications. In this one, Reptilia are a
paraphyletic group. It can be made monophyletic by including the birds ( Aves).
Comparison of phylogenetic groups, showing a monophyly (all descendants of the first reptiles), a
paraphyly (descendants of reptiles, minus birds), and a polyphyly (warm-blooded animals: mammals and
birds)
A group of taxa is said to be paraphyletic if the group consists of all the descendants of a possibly
hypothetical closest common ancestor minus one or more monophyletic groups of descendants (typically one
such group). This term is used in both phylogenetics[note 1] and linguistics.
Contents
[hide]
• 1 Phylogenetics
• 1.1 Relation to monophyletic groups
• 1.2 Examples of paraphyletic groups
• 1.3 Cladistics generally discourages paraphyletic
groups
• 1.3.1 Uses for paraphyletic groups
• 2 Linguistics
• 3 Notes
• 4 References
• 5 Bibliography
[edit] Phylogenetics
[edit] Relation to monophyletic groups
Groups that do include all the descendants of the most recent common ancestor are said to be
monophyletic. A paraphyletic group is a monophyletic group from which one or more of the clades is
excluded to form a separate group (as in the paradigmatic example of reptiles and birds, shown in the
picture).
A group that is neither monophyletic nor paraphyletic is said to be polyphyletic (Greek πολύς [polys],
"many").
These terms were developed during the debates of the 1960s and 70s accompanying the rise of
cladistics (a clade is a term for a monophyletic group).
[edit] Examples of paraphyletic groups

Many of the older classifications contain paraphyletic groups, especially the traditional 2–6 kingdom
systems and the classic division of the vertebrates. Paraphyletic groups are often erected on the basis of
(sym)plesiomorphies (ancestral similarities) instead of (syn)apomorphies (derived similarities). Examples of
well-known paraphyletic groups includes:
• In the flowering plants, Dicotyledons, in the traditional sense, because they exclude
Monocotyledons. The former name has not been used as an ICBN classification for decades, but is
allowed as a synonym of Magnoliopsida.[note 2] The former angiosperms (Magnoliophyta), or
flowering plants, comprised both. Phylogenetic analysis, however, indicates that the monocots are a
development from a dicot ancestor. Excluding them from the dicots makes the latter a paraphyletic
group.[2]
• The order Artiodactyla (even-toed ungulates), because it excludes Cetaceans (whales,
dolphins, etc.). In the ICZN Code, the two taxa are orders of equal rank. Molecular studies, however,
have shown that the Cetacea descend from the Artiodactyl ancestors, although the precise
phylogeny within the order remains uncertain. Without the Cetacean descendants the Artiodactyls
must be paraphyletic.[3]
• The class Reptilia as traditionally defined, because it excludes birds (class Aves). In the
ICZN Code, the two taxa are classes of equal rank. Phylogenetic analysis, however, indicates that
the birds are descended from the Diapsida, which were reptiles (see the illustration above). Reptiles
would be monophyletic if they were defined to include Aves.[1]
• The Prokaryotes (single-celled life forms without cell nuclei), because the Archaea descend
from a common ancestor with the Eukaryotes. The Prokayote/Eukaryote distinction was proposed by
Edouard Chatton in 1937[4] and was generally accepted after being adopted by Roger Stanier and
C.B. van Niel in 1962. It was never adopted by any code because by that time the inappropriateness
of the ICBN code and the ICZN Code for classifying life forms that are neither plant nor animal was
also generally recognized and the ICNB code did not appear until 1975. It did recognize Prokaryotic
taxa beginning in 1980.[5] Chatton's system became known as the two-empire system but the latter
was replaced by Carl Woese's three-domain system published in 1990. The former Prokaryotes
became the Bacteria and the Archaea, while the third domain remained the Eukaryotes. Subsequent
phylogenetic analysis led to a conclusion that the Archaea and the Eukaryotes share a common
ancestor.[6]
• Agnatha, jawless fish, because of its two significant animal groups, hagfish and lampreys,
the lampreys descend from the stem of the Gnathostomes. In 1806 Duméril united the hagfish with
the lampreys under Cyclostomi, which Cope in 1889 made into Agnatha, as opposed to
Gnathostome, the jawed fish. These two taxa became classes or superclasses in the ICZN Code. In
the late 20th century phylogenetic analysis using dozens of characters (features) indicated the
lampreys came from gnathostome ancestors, but the original agnatha/gnathostome ancestor did not
have a jaw. The removal of the lampreys from the Agnatha downgraded the latter to a paraphyletic
group.[7]
• Osteichthyes, bony fish, are paraphyletic because they include Actinopterygii (ray-finned
fish) and Sarcopterygii (lungfish, etc.). However, tetrapods are descendants of the nearest common
ancestor of Actinopterygii and Sarcopterygii, and tetrapods are not in Osteichthyes, hence
Osteichthyes is paraphyletic.[8]
• Porifera are now divided into siliceous sponges and calcareous sponges, which together are
not monophyletic.[citation needed]
• Invertebrates are defined as all animals other than vertebrates, although vertebrates are
derived from this group.
• Recently Crustaceans has been defined as paraphyletic group by molecular phylogenetic
study, so Hexapods would be evolved from a subfamily of this group.[ citation needed]
[edit] Cladistics generally discourages paraphyletic groups
In most cladistics-based schools of taxonomy, the existence of paraphyletic groups (as well as
polyphyletic groups) in a classification is discouraged. Monophyletic groups (that is, clades) are considered
by these schools of thought to be the most important grouping of organisms, for the following reasons:
• Clades are simple to define: a typical clade definition is "All descendants of the nearest
common ancestor of species X and Y". On the other hand, in cladistics polyphyletic and paraphyletic
groups are always defined in terms of clades, for example "reptiles are the Sauropsid clade, minus
the Aves clade". Or "Warm-blooded animals are the Aves clade plus the Mammals clade". Because
polyphyletic and paraphyletic groups are defined in terms of clades, they are considered less
important than clades.
• For a given evolutionary tree of, say, N nodes, there are exactly N clades (one per node).
However, the number of paraphyletic groups and polyphyletic groups is exponentially larger than
that, on the order of 2N. Yet only a small fraction of the paraphyletic groups are given names or
discussed.
• Paraphyletic groups often have their origin in traditional taxonomy, based on similar
morphological characteristics. The original perception may have been that the group was entirely
descended from a single ancestor. If such a group is later discovered (for instance, due to
convergent evolution) to be paraphyletic, rather than monophyletic, then such a group loses its
original significance.
• Another possibility is that the presence of a group that is not monophyletic, indicates that the
group is positioned incorrectly.
[edit] Uses for paraphyletic groups
Others argue that paraphyletic groups are necessary for a comprehensive classification including
extinct groups, since each species, genus, and so forth necessarily originates from part of another.
Ereshefsky notes that paraphyletic taxa are the result of anagenesis.
For instance, the Prokaryote group is paraphyletic because it excludes many of its descendent
organisms (the Eukaryotes), yet the Prokaryote group is very useful because it has a clearly-defined and
significant distinction (no cell nucleus) from its excluded descendants. So, even though Prokaryotes are not a
clade, the term is still useful.
It has been suggested that paraphyletic groups be clearly marked to distinguish them from clades, for
instance with asterisks: Reptilia*. The term evolutionary grade is sometimes used for such groups.[9]
[edit] Linguistics
Main article: Tree model
The concept of paraphyly has also been applied to historical linguistics, where the methods of
cladistics have found some utility in comparing languages. For instance, the Formosan languages form a
paraphyletic group of the Austronesian languages as the term refers to the nine branches of the Austronesian
family that are not Malayo-Polynesian and restricted to the island of Taiwan.[10]
[edit] Notes
1. ^ A paraphyletic group is defined in terms of a clade; that is, the group is the same as the
equivalent clade, except that it lacks one or more of the clade's full complement. The concept of the
last common ancestor is the same, but it has been expanded to be node-based, branch-based and
apomorphy-based. Those terms are defined under Phylogenetic nomenclature.
2. ^ The history of flowering plant classification can be found under History of the classification
of flowering plants.
[edit] References
1. ^ a b Laurin, Michel; Gauthier, Jacques A. (1996). "Amniota". Tree of Life Web Project.
http://tolweb.org/amniota. Retrieved 25 January 2010.
2. ^ Simpson 2006, pp. 139–140. "It is now thought that the possession of two cotyledons is an
ancestral feature for the taxa of the flowering plants and not an apomorphy for any group within. The
'dicots' ... are paraphyletic ...."
3. ^ O'Leary, Maureen A. (2001). "The Phylogenetic Position of Cetaceans: Further Combined
Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character
Optimization". American Zoologist 41 (3): 487–506. doi:10.1093/icb/41.3.487.
4. ^ Sapp, Jan (June 2005). "The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology".
Microbiology and Molecular Biology Reviews 69 (2): 292–305. doi:10.1128/MMBR.69.2.292-
305.2005. PMID 15944457. PMC 1197417. http://mmbr.asm.org/cgi/content/full/69/2/292?
ijkey=9c01f67410bfc780c9d62495284c6efd50dc4f46#THE_TALE_OF_EDOUARD_CHATTON.
5. ^ Stackebrabdt, E.; Tindell, B.; Ludwig, W.; Goodfellow, M. (1999). "Prokaryotic Diversity and
Systematics". In Lengeler, Joseph W.; Drews, Gerhart; Schlegel, Hans Günter. Biology of the
prokaryotes. Stuttgart: Georg Thieme Verlag. p. 679
6. ^ Berg, Linda (2008). Introductory Botany: Plants, People, and the Environment (2nd ed.).
Belmont CA: Thomson Corporation. p. 360. ISBN 0030754534.
7. ^ Janvier, Philippe (2002) [1996]. Early Vertebrates. Oxford Monographs in Geology. Oxford:
Oxford University Press. p. 44. ISBN 0198540477.
8. ^ A Tree of Life
9. ^ Dawkins, Richard (2004). "Mammal-like Reptiles". The Ancestor's Tale, A Pilgrimage to the
Dawn of Life. Boston: Houghton Mifflin Company. ISBN 0-618-00583-8.
10.^ Greenhill, Simon J. and Russell D. Gray. (2009.) "Austronesian Language and
Phylogenies: Myths and Misconceptions About Bayesian Computational Methods," in Austronesian
Historical Linguistics and Culture History: a Festschrift for Robert Blust , edited by Alexander Adelaar
and Andrew Pawley. Canberra: Pacific Linguistics, Research School of Pacific and Asian Studies,
The Australian National University.
[edit] Bibliography
• Simpson, Michael George (2006). Plant systematics. Burlington; San Diego; London:
Elsevier Academic Press. ISBN 0126444609.
• Colin Tudge (2000). The Variety of Life. Oxford University Press. ISBN 0198604262.

Look up paraphyletic in Wiktionary, the free dictionary.
• Funk, D. J.; Omland, K. E. (2003). "Species-level paraphyly and polyphyly: Frequency, cause
and consequences, with insights from animal mitochondrial DNA". Annual Review of Ecology,
Evolution and Systematics 34: 397–423. doi:10.1146/annurev.ecolsys.34.011802.132421.
http://www.umbc.edu/biosci/Faculty/OmlandLabWebpage/NewPages/papers/FunkOmlandARev.pdf.
Relevant



Retrieved from "http://en.wikipedia.org/wiki/Paraphyly"
W000
Polyphyly

The group of "warm-blooded animals" is polyphyletic.
Comparison: monophyly = yellow, polyphyly = red, paraphyly = aqua
A polyphyletic (Greek for "of many races") group is one whose members' last common ancestor is
not a member of the group.
For example, the group consisting of warm-blooded animals is polyphyletic, because it contains both
mammals and birds, but the most recent common ancestor of mammals and birds was cold-blooded. Warm-
bloodedness evolved separately in the ancestors of mammals and the ancestors of birds, so it is not a true
phylogenetic grouping.
Scientific classification aims to group species together such that every group is descended from a
single common ancestor and therefore it is frequently a goal to eliminate groups that are found to be
polyphyletic. This is often the stimulus for major revisions of the classification schemes. A polyphyletic group
can be "fixed" either by excluding clades or by adding the common ancestor.
Opinions differ as to whether valid groups need to contain all the descendants of a common
ancestor. Groups that do so are called monophyletic, and according to cladistics it should be the aim of
classification to ensure that all groups have this property. However, many other taxonomists would argue that
there is a valid place for groups that are paraphyletic, i.e. contains its most recent common ancestor but does
not contain all the descendants of that ancestor.
Contents
[hide]
• 1 Cladistics generally discourages polyphyletic groups
• 2 See also
• 3 References
[edit] Cladistics generally discourages polyphyletic groups
In most cladistics-based schools of taxonomy, the existence of polyphyletic groups (as well as
paraphyletic groups) in a classification is discouraged. Monophyletic groups (that is, clades) are considered
by these schools of thought to be the most important grouping of organisms, for the following reasons:
• Clades are simple to define: a typical clade definition is "All descendants of the nearest
common ancestor of species X and Y". On the other hand, polyphyletic and paraphyletic groups are
always defined in terms of clades, for example "reptiles are the Sauropsid clade, minus the Aves
clade". Or "Warm-blooded animals are the Aves clade plus the Mammals clade". Because
polyphyletic and paraphyletic groups are defined in terms of clades plus or minus other clades, they
are considered less important than monophyletic (single, whole) clades.
• For a given evolutionary tree of, say, N nodes, there are exactly N clades (one per node).
However, the number of paraphyletic groups and polyphyletic groups is exponentially larger than
that, on the order of 2N. Yet only a small fraction of the paraphyletic groups are given names or
discussed.
• Polyphyletic groups often have their origin in traditional taxonomy, based on similar
morphological characteristics. The original perception may have been that the group was entirely
descended from a single ancestor. If such a group is later discovered (for instance, due to
convergent evolution) to be polyphyletic, rather than monophyletic, then such a group loses its
original significance.
[edit] See also
• Phylogeny
• Monophyly and clade
• Paraphyly
[edit] References
• Colin Tudge (2000). The Variety of Life. Oxford University Press. ISBN 0198604262.

• Funk, D. J., and Omland, K. E. (2003). Species-level paraphyly and polyphyly: Frequncy,
cause and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst.
34: 397–423.
Relevant

Retrieved from "http://en.wikipedia.org/wiki/Polyphyly"
W000
Canalisation (genetics)

Norms of reaction for two genotypes. Genotype B shows a strongly bimodal distribution indicating
differentiation into distinct phenotypes. Each phenotype is buffered against environmental variation - it is
canalised.
Canalisation (canalization in American English) is a measure of the ability of a population to produce
the same phenotype regardless of variability of its environment or genotype. In other words, it means
robustness. The term canalisation was coined by C. H. Waddington.[1] He used this word rather than
robustness to take into account that biological systems are not robust in the quite the same way as, for
example, engineered systems. Biological robustness or canalisation comes about when developmental
pathways are shaped by evolution. Waddington introduced the epigenetic landscape, in which the state of an
organism rolls "downhill" during development. In this metaphor, a canalised trait is illustrated as a valley
enclosed by high ridges, safely guiding the phenotype to its "fate". Waddington claimed that canals form in
the epigenetic landscape during evolution, and that this heuristic is useful for understanding the unique
qualities of biological robustness.[2]
Contents
[hide]
• 1 Genetic assimilation
• 2 Congruence hypothesis
• 3 Evolutionary capacitance
• 4 See also
• 5 References
[edit] Genetic assimilation

Waddington used the concept of canalisation to explain his experiments on genetic assimilation.[3] In
these experiments, he exposed Drosophila pupae to heat shock. This environmental disturbance caused
some flies to develop a crossveinless phenotype. He then selected for crossveinless. Eventually, the
crossveinless phenotype appeared even without heat shock. Through this process of genetic assimilation, an
environmental induced phenotype had become inherited. Waddington explained this as the formation of a
new canal in the epigenetic landscape.
It is, however, possible to explain this observation of genetic assimilation using only quantitative
genetics and a threshold model, with no reference to the concept of canalisation.[4][5][6][7] However,
theoretical models that incorporate a complex genotype-phenotype map have found evidence for the
evolution of phenotypic robustness[8] contributing to genetic assimilation,[9] even when selection is only for
developmental stability and not for a particular phenotype, and so the quantitative genetics models do not
apply. These studies suggest that the canalisation heuristic may still be useful, beyond the more simple
concept of robustness.
[edit] Congruence hypothesis

Neither canalisation nor robustness are simple quantities to quantify: it is always necessary to specify
which trait is canalised/robust to which perturbations. For example, perturbations can come either from the
environment or from mutations. It has been suggested that different perturbations have congruent effects on
development taking place on an epigenetic landscape.[10][11][12][13][14] This could, however, depend on
the molecular mechanism responsible for robustness, and be different in different cases.[15]
[edit] Evolutionary capacitance

The canalisation metaphor suggests that phenotypes are very robust to small perturbations, for
which development does not exit the canal, and rapidly returns back down, with little effect on the final
outcome of development. But perturbations whose magnitude exceeds a certain threshold will break out of
the canal, moving the developmental process into uncharted territory. Strong robustness up to a limit, with
little robustness beyond, is a pattern that could increase evolvability in a fluctuating environment.[16] Genetic
canalization could allow for evolutionary capacitance, where genetic diversity outside the canal accumulates
in a population over time, sheltered from natural selection because it does not normally affect phenotypes.
This hidden diversity could then be unleashed by extreme changes in the environment or by molecular
switches, releasing previously cryptic genetic variation that can then contribute to a rapid burst of evolution.
[edit] See also

• Developmental noise
• Evolutionary developmental biology
• Evolutionary capacitance
• Evolvability
• Gene regulatory network
• Phenotypic plasticity
• Systems biology
[edit] References
1. ^ Waddington CH (1942). "Canalization of development and the inheritance of acquired
characters". Nature 150: 563–565. doi:10.1038/150563a0.
2. ^ Waddington CH (1957). The strategy of the genes. George Allen & Unwin.
3. ^ Waddington CH (1953). "Genetic assimilation of an acquired character". Evolution 7 (2):
4. ^ Stern C (1958). "Selection for subthreshold differences and the origin of pseudoexogenous
adaptations". American Naturalist 92: 313–316. doi:10.1086/282040.
5. ^ Bateman KG (1959). "The genetic assimilation of the dumpy phenocopy". American
Naturalist 56: 341–351.
6. ^ Scharloo W (1991). "Canalization – genetic and developmental aspects". Annual Reviews
in Ecology and Systematics 22: 65–93. doi:10.1146/annurev.es.22.110191.000433.
7. ^ Falconer DS, Mackay TFC (1996). Introduction to Quantitative Genetics. pp. 309–310.
8. ^ Siegal ML, Bergman A (2002). "Waddington’s canalization revisited: developmental stability
and evolution". Proceedings of the National Academy of Sciences of the United States of America 99
(16): 10528–10532. doi:10.1073/pnas.102303999. PMID 12082173.
9. ^ Masel J (2004). "Genetic assimilation can occur in the absence of selection for the
assimilating phenotype, suggesting a role for the canalization heuristic". Journal of Evolutionary
Biology 17 (5): 1106–1110. doi:10.1111/j.1420-9101.2004.00739.x. PMID 15312082.
10.^ Meiklejohn CD, Hartl DL (2002). "A single mode of canalization". Trends in Ecology &
Evolution 17: e9035.
11.^ Ancel LW, Fontana W (2000). "Plasticity, evolvability, and modularity in RNA". Journal of
Experimental Zoology 288 (3): 242–283. doi:10.1002/1097-010X(20001015)288:3<242::AID-
JEZ5>3.0.CO;2-O. PMID 11069142.
12.^ Szöllősi GJ, Derényi I (2009). "Congruent Evolution of Genetic and Environmental
Robustness in Micro-RNA". Molecular Biology & Evolution 26 (4): 867–874.
doi:10.1093/molbev/msp008. PMID 19168567.
13.^ Wagner GP, Booth G Bagheri-Chaichian H (1997). "A population genetic theory of
canalization". Evolution 51 (2): 329–347. doi:10.2307/2411105. http://jstor.org/stable/2411105.
14.^ Lehner B; Lehner, Ben (2010). "Genes Confer Similar Robustness to Environmental,
Stochastic, and Genetic Perturbations in Yeast". PLoS ONE 5 (2): 468–473.
15.^ Masel J Siegal ML (2009). "Robustness: mechanisms and consequences". Trends in
Genetics 25 (9): 395–403. doi:10.1016/j.tig.2009.07.005. PMID 19717203.
16.^ Eshel,I. Matessi, C. (1998). "Canalization, genetic assimilation and preadaptation: A
quantitative genetic model". Genetics 4: 2119–2133.


phenotype
Non-genetic
Developmental

Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of

Retrieved from "http://en.wikipedia.org/wiki/Canalisation_(genetics)"
Categories: Developmental biology | Genetics | Population genetics

W000
Genotype-phenotype distinction

The genotype–phenotype distinction is drawn in genetics. "Genotype" is an organism's full hereditary
information, even if not expressed. "Phenotype" is an organism's actual observed properties, such as
morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and
their evolution.
The genotype represents its exact genetic makeup — the particular set of genes it possesses. Two
organisms whose genes differ at even one locus (position in their genome) are said to have different
genotypes. The transmission of genes from parents to offspring is under the control of precise molecular
mechanisms. The discovery of these mechanisms and their manifestations began with Mendel and
comprises the field of genetics.
It is the organism's physical properties that directly determine its chances of survival and
reproductive output, while the inheritance of physical properties occurs only as a secondary consequence of
the inheritance of genes. Therefore, to properly understand the theory of evolution via natural selection, one
must understand the genotype–phenotype distinction.
The mapping of a set of genotypes to a set of phenotypes is sometimes referred to as the genotype–
phenotype map.
Similar genotypic changes may result in similar phenotypic alterations, even across a wide range of
species.
An organism's genotype is a major (the largest by far for morphology) influencing factor in the
development of its phenotype, but it is not the only one. Even two organisms with identical genotypes
normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical)
twins. Identical twins share the same genotype, since their genomes are identical; but they never have the
same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their
mothers and close friends can always tell them apart, even though others might not be able to see the subtle
differences. Further, identical twins can be distinguished by their fingerprints, which are never completely
identical.
The concept of phenotypic plasticity describes the degree to which an organism's phenotype is
determined by its genotype. A high level of plasticity means that environmental factors have a strong
influence on the particular phenotype that develops. If there is little plasticity, the phenotype of an organism
can be reliably predicted from knowledge of the genotype, regardless of environmental peculiarities during
development. An example of high plasticity can be observed in larval newts1: when these larvae sense the
presence of predators such as dragonflies, they develop larger heads and tails relative to their body size and
display darker pigmentation. Larvae with these traits have a higher chance of survival when exposed to the
predators, but grow more slowly than other phenotypes.
In contrast to phenotypic plasticity, the concept of genetic canalization addresses the extent to which
an organism's phenotype allows conclusions about its genotype. A phenotype is said to be canalized if
mutations (changes in the genome) do not noticeably affect the physical properties of the organism. This
means that a canalized phenotype may form from a large variety of different genotypes, in which case it is
not possible to exactly predict the genotype from knowledge of the phenotype (i.e. the genotype-phenotype
map is not invertible). If canalization is not present, small changes in the genome have an immediate effect
on the phenotype that develops.
The terms "genotype" and "phenotype" were created by Wilhelm Johannsen in 1911.



phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Genotype-phenotype_distinction"
Categories: Genetics
W000
Norms of reaction

In ecology and genetics, a norm of reaction describes the pattern of phenotypic expression of a
single genotype across a range of environments. One use of norms of reaction is in describing how different
species—especially related species—respond to varying environments. But differing genotypes within a single
species will also often show differing norms of reaction relative to a particular phenotypic trait and
environment variable. For every genotype, phenotypic trait, and environmental variable, a different norm of
reaction can exist; in other words, an enormous complexity can exist in the interrelationships between
genetic and environmental factors in determining traits.
Contents
[hide]
• 1 A monoclonal example
• 2 Misunderstanding genetic/environmental interactions
• 3 Bibliography
• 4 See also
[edit] A monoclonal example
Different peaks in Gaussian distributions

Approximately linear norms at opposite slopes
Scientifically analyzing norms of reaction in natural populations can be very difficult, simply because
natural populations of sexually reproductive organisms usually do not have cleanly separated or superficially
identifiable genetic distinctions. However, seed crops produced by humans are often engineered to contain
specific genes, and in some cases seed stocks consist of clones. Accordingly, distinct seed lines present
ideal examples of differentiated norms of reaction. In fact, agricultural companies market seeds for use in
particular environments based on exactly this.
Suppose the seed line A contains an allele a, and a seed line B of the same crop species contains an
allele b, for the same gene. With these controlled genetic groups, we might cultivate each variety (genotype)
in a range of environments. This range might be either natural or controlled variations in environment. For
example, an individual plant might receive either more or less water during its growth cycle, or the average
temperature the plants are exposed to might vary across a range.
A simplification of the norm of reaction might state that seed line A is good for "high water conditions"
while a seed line B is good for "low water conditions". But the full complexity of the norm of reaction is a
function, for each genotype, relating environmental factor to phenotypic trait. By controlling for or measuring
actual environments across which monoclonal seeds are cultivated, one can concretely observe norms of
reaction. Normal distributions, for example, are common. Of course, the distributions need not be bell-curves.
[edit] Misunderstanding genetic/environmental interactions

Popular non-scientific or lay-scientific audiences frequently misunderstand or simply fail to recognize
the existence of norms of reaction. A widespread conception is that each genotype gives a certain range of
possible phenotypic expressions. In popular conception, something which is "more genetic" gives a narrower
range, while something which is "less genetic (more environmental)" gives a wider range of phenotypic
possibilities. This limited conceptual framework is especially prevalent in discussions of human traits such as
IQ, Sexual orientation, altruism, or schizophrenia (see Nature versus nurture).
Popular conception of genotype/phenotype interaction
TRAIT SCALE
<--6----------5----------4----------3----------2----------1----------0-->
^ (Genotype A) ^ ^ (Genotype B) ^
| | | |
Environ <------> Other Environ <------> Other
extreme extreme extreme extreme
The problem with this common simplified image is not that it does not represent a possible norm of
reaction. Rather, by reducing the picture from two dimensions to just one, it focuses only on discrete, non-
overlapping phenotypic expressions, and hides the more common pattern local minima and maxima in
phenotypic expression, with overlapping ranges of phenotypic expression between genotypes.
[edit] Bibliography
• Not in Our Genes: Biology, Ideology and Human Nature , Richard Lewontin, Steven Rose and
Leon J. Kamin (1984) ISBN 0-394-72888-2
• The Dialectical Biologist, Richard Lewontin and Richard Levins), Harvard University Press
(1985) ISBN 0-674-20283-X
• Biology as Ideology: The Doctrine of DNA, Richard Lewontin (1991) ISBN 0-06-097519-9
• The Triple Helix: Gene, Organism, and Environment , Richard Lewontin, Harvard University
Press (2000) ISBN 0-674-00159-1
• The Evolutionary Theory of Sex: Variation of Sexes and Reaction Norm
[edit] See also

• Nature versus nurture
• Differential Susceptibility
• Genetic determinism
• Wider reaction norm of females
• Phenotypic plasticity


phenotype
Non-genetic
Developmental

Retrieved from "http://en.wikipedia.org/wiki/Norms_of_reaction"
Categories: Ecology
W000
Gene–environment interaction
(Redirected from Gene-environment interaction)
Gene–environment interaction (or genotype–environment interaction or GxE) is the phenotypic effect
of interactions between genes and the environment.
Gene–environment interaction is exploited by plant and animal breeders to benefit agriculture. For
example, plants can be bred to have tolerance for specific environments, such as high or low water
availability. The way that trait expression varies across a range of environments for a given genotype is
called its norm of reaction.
In genetic epidemiology it is frequently observed that diseases cluster in families, but family
members may not inherit disease as such. Often, they inherit sensitivity to the effects of various
environmental risk factors. Individuals may be differently affected by exposure to the same environment in
medically significant ways. For example, sunlight exposure has a much stronger influence on skin cancer risk
in fair-skinned humans than in individuals with an inherited tendency to darker skin.[1]
Nature versus Nurture debates assume that variation in a given trait is primarily due to either genetic
variability or exposure to environmental experiences. The current scientific view is that neither genetics nor
environment are solely responsible for producing individual variation, and that virtually all traits show gene–
environment interaction. Evidence of statistical interaction between genetic and environmental risk factors is
often used as evidence for the existence of an underlying mechanistic interaction.
Contents
[hide]
• 1 Examples
• 2 Medical significance
• 3 Timing of environmental effects
• 4 See also
• 5 References
[edit] Examples
In some combinations of environments and genotypic ranges, heritability can be 100% even while
group differences are completely environmental. For heritability to be 100%, random variation in expression
must not occur.
1. A classic example of gene–environment interaction is Tryon's artificial selection experiment
on maze-running ability in rats.[2][3] Tryon produced a remarkable difference in maze running ability
in two selected lines after seven generations of selecting "bright" and "dull" lines by breeding the best
and worst maze running rats with others of similar abilities. The difference between these lines was
clearly genetic since offspring of the two lines, raised under identical typical lab conditions,
performed too differently. This difference disappeared in a single generation, if those rats were raised
in an enriched environment with more objects to explore and more social interaction.[4] This result
shows that maze running ability is the product of a gene-by-environment interaction; the genetic
effect is only seen under some environmental conditions.
2. Seven genetically distinct yarrow plants were collected and three cuttings taken from each
plant. One cutting of each genotype was planted at low, medium, and high elevations, respectively.
When the plants matured, no one genotype grew best at all altitudes, and at each altitude the seven
genotypes fared differently. For example, one genotype grew the tallest at the medium elevation but
attained only middling height at the other two elevations. The best growers at low and high elevation
grew poorly at medium elevation. The medium altitude produced the worst overall results, but still
yielded one tall and two medium-tall samples. Altitude had an effect on each genotype, but not to the
same degree nor in the same way.[5]
3. Phenylketonuria (PKU) is a human genetic condition caused by mutations to a gene coding
for a particular liver enzyme. In the absence of this enzyme, an amino acid known as phenylalanine
does not get converted into the next amino acid in a biochemical pathway, and therefore too much
phenylalanine passes into the blood and other tissues. This disturbs brain development leading to
mental retardation and other problems. PKU affects approximately 1 out of every 15,000 infants in
the U.S. However, most affected infants do not grow up impaired because of a standard screening
program used in the U.S. and other industrialized societies. Newborns found to have high levels of
phenylalanine in their blood can be put on a special, phenylalanine-free diet. If they are put on this
diet right away and stay on it, these children avoid the severe effects of PKU.[6]
4. A functional polymorphism in the monoamine oxidase A (MAOA) gene promoter can
moderate the association between early life trauma and increased risk for violence and antisocial
behavior. Low MAOA activity is a significant risk factor for aggressive and antisocial behavior in
adults who report victimization as children. Persons who were abused as children but have a
genotype conferring high levels of MAOA expression are less likely to develop symptoms of
antisocial behavior.[7] These findings must be interpreted with caution, however, because gene
association studies on complex traits are notorious for being very difficult to confirm.[8]
[edit] Medical significance
• Doctors are interested in knowing whether disease can be prevented by reducing exposure
to environmental risks. Gene–environment interaction means that some people carry genetic factors
that confer susceptibility or resistance to a certain disorder in a particular environment. It has been
argued that there may be significant public health benefits in using genetic information to stratify the
allocation of environmental interventions that prevent disease,[9] although this viewpoint is not
universally held.[10]
• Pharmacogenetics is the study of genetic variation that causes people to respond differently
to drugs. The clinical importance of pharmacogenetics comes from the possibility that drug treatment
can be made safer and more effective when the patient's genotype is known. Pharmacogenetic
studies can be considered studies of gene–environment interaction, with drug treatment as the
environmental variable.
[edit] Timing of environmental effects

The popular description of an animal being "born that way" does not necessarily discriminate genetic
from environmental effects. In viviparous animals, such as humans, environmental influences may act during
either pre- or post-natal development; similarly environmental influences may act before and after hatching to
affect development in oviparous animals. Environmental influences in utero may be as strong and lasting as
genetic or post-natal environmental influence. There is increasing study of environmental influences affecting
genetic factors directly but nonheritably; see the Epigenetics article for a detailed discussion.
[edit] See also
• Diathesis–stress model
• Epigenetic Theory
• Evolutionary developmental psychology
• Differential Susceptibility
• Biopsychosocial model
• Gene-environment correlation
[edit] References
1. ^ Green A; Trichopoulos D (2002). Skin cancer. In Textbook of Cancer Epidemiology (eds
Adami, H., Hunter, D. & Trichopoulos, D.) pp. 281–300 . Oxford: Oxford University Press.
2. ^ Tryon RC (1942). Individual differences. In F. A. Moss (Ed.), Comparative psychology (Rev.
ed.). NY: Prentice-Hall.
3. ^ Tryon RC (1940). "Genetic differences in maze-learning ability in rats". Yearbook of the
National Society for the Study of Education 39: 111–119.
4. ^ Cooper RM & Zubek JP (1958). "Effects of enriched and restricted early environments on
the learning ability of bright and dull rats". Canadian Journal of Psychology 12 (3): 159–164.
PMID 13573245.
5. ^ Clausen J, Keck D, Hiesey WM (1948). Experimental studies on the nature of species. III.
Environmental responses of climatic races of Achillea, Carnegie Inst Washington Publ 581 . pp. 1–
129.
6. ^ AAAS publication on Behavioral Genetics
7. ^ Caspi A, et al. (2002). "Role of genotype in the cycle of violence in maltreated children".
8. ^ Munafò M, et al. (2009). "Gene x Environment Interactions at the Serotonin Transporter
Locus". Biol Psychiatry 65: 211–219. doi:10.1016/j.biopsych.2008.06.009.
9. ^ Khoury MJ, Davis R, Gwinn M, Lindegren ML & Yoon P (2005). "Do we need genomic
research for the prevention of common diseases with environmental causes?". Am J Epidemiol 161
(9): 799–805. doi:10.1093/aje/kwi113. PMID 15840611.
10.^ Willet W (2002). "Balancing lifestyle and genomic research for disease prevention".
Science 269: 695–698.


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Gene%E2%80%93environment_interaction"
Categories: Psychological theories | Genetics

W000
Heritability

This article's tone or style may not be appropriate for Wikipedia. Specific concerns
may be found on the talk page. See Wikipedia's guide to writing better articles for
suggestions. (November 2010)
Heritability is the proportion of phenotypic variation in a population that is genetically inherited among
individuals. Phenotypic variation among individuals may be due to genetic and/or environmental factors.
Heritability analyses estimate the relative contributions of differences in genetic and non-genetic factors to
the total phenotypic variance in a population. Often measured empirically, heritability is an important notion in
quantitative genetics, particularly in selective breeding, but less so in the general theory of population
genetics.
Heritability measures the fraction of phenotype variability that can be attributed to genetic variability,
and not the fraction by which the phenotype is caused by genetics. For example, if both genes and
environment have the potential to influence intelligence, but if a given sample of individuals shows very little
genetic variation and a great deal of environmental variation, then the contribution of genetic variability to
phenotype variability in that sample will be lower than if the sample showed greater genetic variability.
Heritability is specific to a particular population in a particular environment, but the extent of the
dependence on environment is also a function of the genes involved. Individuals with the same genotype can
exhibit different phenotypes through a mechanism called phenotypic plasticity, which makes their heritability
difficult to measure in some cases. Recent insights in molecular biology have identified changes in
transcriptional activity of individual genes associated with environmental changes. However, there are a large
number of genes whose transcription is not affected by the environment.[1]
Rather than ask "is the resulting bread 70% ingredients?" one must ask "is the difference between
this bread and my last one due mostly to ingredients or method?"
Contents
[hide]
• 1 Overview
• 2 Definition
• 3 Estimating heritability
• 4 Estimation methods
• 5 Regression/correlation methods of estimation
• 5.1 Selection experiments
• 5.2 Comparison of close relatives
• 5.2.1 Parent-offspring regression
• 5.2.2 Full-sib comparison
• 5.2.3 Half-sib comparison
• 5.2.4 Twin studies
• 5.3 Large, complex pedigrees
• 6 Analysis of variance methods of estimation
• 6.1 Basic model
• 6.1.1 Intraclass correlations
• 6.1.2 The ANOVA
• 6.2 Model with additive and dominance terms
• 6.3 Larger models
• 7 Response to Selection
• 8 Controversies
[edit] Overview
An example of low heritability: a population with genotypes coding for only one hair colour
Rather than look at all the traits of an organism, heritability focuses on the differences between
multiple organisms for a single trait. Because heritability is concerned with variance, it is necessarily a
description of a certain population - not an individual.
A population of Asians would contain individuals with genetics that code only for black hair. In this
case, heritability is of course 0, since there is no variance in hair colour to analyse. But suppose some
individuals dyed their hair and increased the population's variance in hair colours. Although now there are
some differences in hair colour, theoretically heritability would still be 0 (i.e. 0% of the variance is due to
differences in genetics).
A crowd with variance in hair colour.

Oppositely, assume there is a population of mixed races where (1) hair dye is forbidden, and (2) the
hair colours of this population truly have nothing to do with environmental factors (like amount of sunlight).
Now there is again variance in hair colour, but this time heritability is 1 (i.e. 100% of the variance is due to
differences in genetics).
In practice, heritability is not that simple; environment and genetics interact.
[edit] Definition
Figure 1. Relationship of phenotypic values to additive and dominance effects using a completely
dominant locus.
Consider a statistical model for describing some particular phenotype:[2]
Phenotype (P) = Genotype (G) + Environment (E).
Considering variances (Var), this becomes:
Var(P) = Var(G) + Var(E) + 2 Cov(G,E).
In planned experiments, we can often take Cov(G,E) = 0. Heritability is then defined as:
.
The parameter H2 is the broad-sense heritability and reflects all possible genetic contributions to a
population's phenotypic variance. Included are effects due to allelic variation (additive variance), dominance
variation, epistatic (multi-genic) interactions, and maternal and paternal effects, where individuals are directly
affected by their parents' phenotype (such as with milk production in mammals).
These additional terms can be included in genetic models. For example, the simplest genetic model
involves a single locus with two alleles that affect some quantitative phenotype, as shown by + in Figure 1.
We can calculate the linear regression of phenotype on the number of B alleles (0, 1, or 2), which is shown
as the Linear Effect line. For any genotype, BiBj, the expected phenotype can then be written as the sum of
the overall mean, a linear effect, and a dominance deviation:
Pij = μ + αi + αj + dij = Population mean + Additive Effect (aij = αi + αj) + Dominance Deviation
(dij).
The additive genetic variance is the weighted average of the squares of the additive effects:
where f(bb)abb + f(Bb)aBb + f(BB)aBB = 0.
There is a similar relationship for variance of dominance deviations:
where f(bb)dbb + f(Bb)dBb + f(BB)dBB = 0.
Narrow-sense heritability is defined as
and quantifies only the portion of the phenotypic variation that is additive (allelic) by nature (note
upper case H2 for broad sense, lower case h2 for narrow sense). When interested in improving livestock via
artificial selection, for example, knowing the narrow-sense heritability of the trait of interest will allow
predicting how much the mean of the trait will increase in the next generation as a function of how much the
mean of the selected parents differs from the mean of the population from which the selected parents were
chosen. The observed response to selection leads to an estimate of the narrow-sense heritability (called
realized heritability).
[edit] Estimating heritability
Estimating heritability is not a simple process, since only P can be observed or measured directly.
Measuring the genetic and environmental variance requires various sophisticated statistical methods. These
methods give better estimates when using data from closely related individuals - such as brothers, sisters,
parents and offspring, rather than from more distantly related ones. The standard error for heritability
estimates is generally very poor unless the dataset is large.
In non-human populations it is often possible to collect information in a controlled way. For example,
among farm animals it is easy to arrange for a bull to produce offspring from a large number of cows. Due to
ethical concerns, such a degree of experimental control is impossible when gathering human data.
As a result, studies of human heritability sometimes contrast identical twins who have been
separated early in life and raised in different environments (see for example Fig. 2). Such individuals have
identical genotypes and can be used to separate the effects of genotype and environment.
Twin studies entail problems of their own, such as: independently raised twins shared a common
prenatal environment; they may have undergone intrauterine competition; the mother may be more physically
stressed (less nutrients); and twins reared apart are difficult to find, and may reflect certain types of
environments.
Heritability estimates are always relative to the genetic and environmental factors in the population,
and are not absolute measurements of the contribution of genetic and environmental factors to a phenotype.
Heritability estimates reflect the amount of variation in genotypic effects compared to variation in
environmental effects.
Heritability can be made larger by diversifying the genetic background, e.g., by using only very
outbred individuals (which increases the Variance(G)) and/or by minimizing environmental effects (which
decreases the Variance(E)). Smaller heritability, on the other hand, can be generated by using inbred
individuals (which decreases the Variance(G)) or individuals reared in very diverse environments (which
increases the Variance(E)). Due to such effects, different populations of a species might have different
heritabilities even for the same trait.
In observational studies G and E may be correlated, giving rise to gene environment correlation.
Depending on the methods used to estimate heritability, correlations between genetic factors and shared or
non-shared environments may or may not be included in the total heritability estimate.[3]
Because of the contextual nature of measured heritabilities, paradoxes often arise. For example, the
heritability of a trait could be near 100% in one study and close to zero in another. In one study, e.g., a group
of unrelated army recruits may be given identical training and nutrition and then their muscular strength may
be measured.
The variation in strength observed after the (identical) training will translate into a high heritability
estimate. In another study, whose purpose might be to assess the efficacy of various workout regimes or
nutritional programs, study subjects may be first chosen to match each other as closely as possible in prior
physical characteristics before some of them are put onto Program A and others onto Program B, and this
will lead to a low heritability estimate.
Heritability estimates are often misinterpreted. Heritability refers to the proportion of variation
between individuals in a population that is influenced by genetic factors. Heritability describes the population,
not individuals within that population. For example, It is incorrect to say that since the heritability of a
personality trait is about .6, that means that 60% of your personality is inherited from your parents and 40%
comes from the environment.
The heritability estimate changes according to the genetic and environmental variability present in
the population. In studies of genetically identical inbred animals, all traits have zero heritability. Heritability
estimates can be much higher in outbred (genetically variable) populations under very homogeneous
environments.
A highly genetically loaded trait (such as eye color) still assumes environmental input within normal
limits (a certain range of temperature, oxygen in the atmosphere, etc.). A more useful distinction than "nature
vs. nurture" is "obligate vs. facultative" -- under typical environmental ranges, what traits are more "obligate"
(e.g., the nose—everyone has a nose) or more "facultative" (sensitive to environmental variations, such as
specific language learned during infancy). Another useful distinction is between traits that are likely to be
adaptations (such as the nose) vs. those that are byproducts of adaptations (such the white color of bones),
or are due to random variation (non-adaptive variation in, say, nose shape or size).
[edit] Estimation methods

There are essentially two schools of thought regarding estimation of heritability.
One school of thought was developed by Sewall Wright at The University of Chicago, and further
popularized by C. C. Li (University of Chicago) and J. L. Lush (Iowa State University). It is based on the
analysis of correlations and, by extension, regression. Path Analysis was developed by Sewall Wright as a
way of estimating heritability.
The second was originally developed by R. A. Fisher and expanded at The University of Edinburgh,
Iowa State University, and North Carolina State University, as well as other schools. It is based on the
analysis of variance of breeding studies, using the intraclass correlation of relatives. Various methods of
estimating components of variance (and, hence, heritability) from ANOVA are used in these analyses.
[edit] Regression/correlation methods of estimation
The first school of estimation uses regression and correlation to estimate heritability.
[edit] Selection experiments
Figure 3. Strength of selection (S) and response to selection (R) in an artificial selection experiment,
h2=R/S.
Calculating the strength of selection, S (the difference in mean trait between the population as a
whole and the selected parents of the next generation, also called the selection differential [4]) and response
to selection R (the difference in offspring and whole parental generation mean trait) in an artificial selection
experiment will allow calculation of realized heritability as the response to selection relative to the strength of
selection, h2=R/S as in Fig. 3.
[edit] Comparison of close relatives
In the comparison of relatives, we find that in general,
where r can be thought of as the coefficient of relatedness, b is the coefficient of

regression and t the coefficient of correlation.
[edit] Parent-offspring regression
Figure 4. Sir Francis Galton's (1889) data showing the relationship between offspring height (928
individuals) as a function of mean parent height (205 sets of parents).
Heritability may be estimated by comparing parent and offspring traits (as In Fig. 4). The slope of the
line (0.57) approximates the heritability of the trait when offspring values are regressed against the average
trait in the parents. If only one parent's value is used then heritability is twice the slope. (note that this is the
source of the term "regression", since the offspring values always tend to regress to the mean value for the
population, i.e., the slope is always less than one).
[edit] Full-sib comparison

Full-sib designs compare phenotypic traits of siblings that share a mother and a father with other
sibling groups. The estimate of the sibling phenotypic correlation is an index on familiality which is equal to
half the additive genetic variance plus the common environment variance when there is only additive gene
action.
[edit] Half-sib comparison

Half-sib designs compare phenotypic traits of siblings that share one parent with other sibling groups.
[edit] Twin studies
Figure 5. Twin concordances for seven psychological traits (sample size shown inside bars).
Heritability for traits in humans is most frequently estimated by comparing resemblances between
twins (Fig. 2 & 5). Identical twins (MZ twins), on average, are twice as genetically similar as fraternal twins
(DZ twins) and so heritability is approximately twice the difference in correlation between MZ and DZ twins,
i.e. Falconer's formula H2=2(r(MZ)-r(DZ)).
The effect of shared environment, c2, contributes to similarity between siblings due to the
commonality of the environment they are raised in. Shared environment is approximated by the DZ
correlation minus half heritability, which is the degree to which DZ twins share the same genes, c2=DZ-1/2h2.
Unique environmental variance, e2, reflects the degree to which identical twins raised together are dissimilar,
e2=1-r(MZ).
The methodology of the classical twin study has been criticized, but some of these criticisms do not
take into account the methodological innovations and refinements described above.
[edit] Large, complex pedigrees

This section is empty. You can help by adding to it.
[edit] Analysis of variance methods of estimation

The second set of methods of estimation of heritability involves ANOVA and estimation of variance
components.
[edit] Basic model

We use the basic discussion of Kempthorne (1957 [1969]). Considering only the most basic of
genetic models, we can look at the quantitative contribution of a single locus with genotype Gi as
yi = μ + gi + e
where
gi is the effect of genotype Gi
and e is the environmental effect.
Consider an experiment with a group of sires and their progeny from random dams. Since the
progeny get half of their genes from the father and half from their (random) mother, the progeny equation is
[edit] Intraclass correlations

Consider the experiment above. We have two groups of progeny we can compare. The first is
comparing the various progeny for an individual sire (called within sire group). The variance will include terms
for genetic variance (since they did not all get the same genotype) and environmental variance. This is
thought of as an error term.
The second group of progeny are comparisons of means of half sibs with each other (called among
sire group). In addition to the error term as in the within sire groups, we have an addition term due to the
differences among different means of half sibs. The intraclass correlation is
,
since environmental effects are independent of each other.
[edit] The ANOVA
In an experiment with n sires and r progeny per sire, we can calculate the following ANOVA, using Vg
as the genetic variance and Ve as the environmental variance:
Table 1: ANOVA for Sire experiment

Source d.f. Mean Square Expected Mean Square
Among sire groups n−1 S
Within sire groups n(r − 1) W
The term is the intraclass correlation among half sibs. We can easily calculate
. The Expected Mean Square is calculated from the relationship

of the individuals (progeny within a sire are all half-sibs, for example), and an understanding of intraclass
correlations.
[edit] Model with additive and dominance terms
For a model with additive and dominance terms, but not others, the equation for a single locus is
yij = μ + αi + αj + dij + e,
where
αi is the additive effect of the ith allele, αj is the additive effect of the jth allele, dij is the dominance
deviation for the ijth genotype, and e is the environment.
Experiments can be run with a similar setup to the one given in Table 1. Using different relationship
groups, we can evaluate different intraclass correlations. Using Va as the additive genetic variance and Vd as
the dominance deviation variance, intraclass correlations become linear functions of these parameters. In
general,
Intraclass correlation = rVa + θVd,
where r and θ are found as

r = P[ alleles drawn at random from the relationship pair are identical by descent], and
θ = P[ genotypes drawn at random from the relationship pair are identical by descent].
Some common relationships and their coefficients are given in Table 2.
Table 2: Coefficients for calculating variance components
Relationship r θ
Identical Twins 1 1
Parent-Offspring 0
Half Siblings 0
Full Siblings
First Cousins 0
Double First Cousins
[edit] Larger models

When a large, complex pedigree is available for estimating heritability, the most efficient use of the
data is in a restricted maximum likelihood (REML) model. The raw data will usually have three or more
datapoints for each individual: a code for the sire, a code for the dam and one or several trait values.
Different trait values may be for different traits or for different timepoints of measurement.
The currently popular methodology relies on high degrees of certainty over the identities of the sire
and dam; it is not common to treat the sire identity probabilistically. This is not usually a problem, since the
methodology is rarely applied to wild populations (although it has been used for several wild ungulate and
bird populations), and sires are invariably known with a very high degree of certainty in breeding
programmes. There are also algorithms that account for uncertain paternity.
The pedigrees can be viewed using programs such as Pedigree Viewer [1], and analysed with
programs such as ASReml, VCE [2], WOMBAT [3] or BLUPF90 family's programs [4]
[edit] Response to Selection

In selective breeding of plants and animals, the expected response to selection can be estimated by
the following equation:[5]
R = h2S
In this equation, the Response to Selection (R) is defined as the realized average difference between
the parent generation and the next generation. The Selection Differential (S) is defined as the average
difference between the parent generation and the selected parents.
For example, imagine that a plant breeder is involved in a selective breeding project with the aim of
increasing the number of kernels per ear of corn. For the sake of argument, let us assume that the average
ear of corn in the parent generation has 100 kernels. Let us also assume that the selected parents produce
corn with an average of 120 kernels per ear. If h 2 equals 0.5, then the next generation will produce corn with
an average of 0.5(120-100) = 10 additional kernels per ear. Therefore, the total number of kernels per ear of
corn will equal, on average, 110.
[edit] Controversies
Some authors like Steven Rose[6] and Jay Joseph[7] have dismissed heritability estimates as
useless. A 2008 paper in Nature Reviews Genetics stated however: "Despite continuous misunderstandings
and controversies over its use and application, heritability remains key to the response to selection in
evolutionary biology and agriculture, and to the prediction of disease risk in medicine. Recent reports of
substantial heritability for gene expression and new estimation methods using marker data highlight the
relevance of heritability in the genomics era."[8]
[edit] See also

• Heredity
[edit] References
[edit] Notes
1. ^ http://jhered.oxfordjournals.org/content/98/4/382.full
2. ^ The presentation here roughly follows Kempthorne (1957)
3. ^ Cattell RB (1960). "The multiple abstract variance analysis equations and solutions: for
nature–nurture research on continuous variables". Psychol Rev 67: 353–372. doi:10.1037/h0043487.
PMID 13691636.
4. ^ Kempthorne (1957), page 507; or Falconer (1960), page 191, for example.
5. ^ Plomin, R., DeFries, J. C., & McClearn, G. E. (1990). Behavioral genetics. New York:
Freeman.
6. ^ Rose SP (June 2006). "Commentary: heritability estimates--long past their sell-by date". Int
J Epidemiol 35 (3): 525–7. doi:10.1093/ije/dyl064. PMID 16645027.
7. ^ Joseph, J. (2004), The Gene Illusion, Algora. (2003 United Kingdom Edition by PCCS
Books) (Chapter 5 contains a critique of the heritability concept)
8. ^ Visscher, P. M.; Hill, W. G.; Wray, N. R. (2008). "Heritability in the genomics era — concepts
and misconceptions". Nature Reviews Genetics 9: 255. doi:10.1038/nrg2322. edit
[edit] Books
• Kempthorne, O (1957 [1969]) An Introduction to Genetic Statistics. John Wiley. Reprinted,
1969 by Iowa State University Press.
• Falconer, D. S. & Mackay TFC (1996). Introduction to Quantitative Genetics. Fourth edition.
Addison Wesley Longman, Harlow, Essex, UK the footnotes above refer the 1st ed. from 1960

• Gillespie, G. H. (1997). Population Genetics: A Concise Guide . Johns Hopkins University
Press.
• Lynch, M. & Walsh, B. 1997. Genetics and Analysis of Quantitative Traits. Sinauer
Associates. ISBN 0-87893-481-2.
• Maher, B. (2008). "Personal genomes: the case of the missing heritability". Nature 456: 18-
21. doi:10.1038/456018a. edit

• Stanford Encyclopedia of Philosophy entry on Heredity and Heritability
• Quantitative Genetics Resources website, including the two volume book by Lynch and
Walsh. Free access
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Quantitative genetics

introducing more precise citations where appropriate. (July 2010)
Genetics
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Quantitative genetics is the study of continuous traits (such as height or weight) and their underlying
mechanisms. It is effectively an extension of simple Mendelian inheritance in that the combined effect of the
many underlying genes results in a continuous distribution of phenotypic values.
Contents
[hide]
• 1 History
• 2 Traits
• 3 Basic principles
• 3.1 Resemblance between relatives
• 3.2 Correlated traits
• 4 See also
• 5 References
[edit] History
The field was founded, in evolutionary terms, by the originators of the modern synthesis, R.A. Fisher,
Sewall Wright and J. B. S. Haldane, and aimed to predict the response to selection given data on the
phenotype and relationships of individuals.
Analysis of Quantitative Trait Loci, or QTL, is a more recent addition to the study of quantitative
genetics. A QTL is a region in the genome that affects the trait or traits of interest. Quantitative trait loci
approaches require accurate phenotypic, pedigree and genotypic data from a large number of individuals.
[edit] Traits
Quantitative genetics is not limited to continuous traits, but to all traits that are determined by many
genes. This includes:
• Continuous traits are quantitative traits with a continuous phenotypic range. They are often
polygenic, and may also be influenced significantly by environmental effects.
• Meristic traits or other ordinal numbers are expressed in whole numbers, such as number of
offspring, or number of bristles on a fruit fly. These traits can be either treated as approximately
discontinuous traits or as threshold traits.
• Some qualitative traits can be treated as if they have an underlying quantitative basis,
expressed as a threshold trait (or multiple thresholds). Some human diseases (such as,
schizophrenia) have been studied in this manner.
[edit] Basic principles
This section's factual accuracy is disputed. Please see the relevant discussion on
the talk page. (March 2008)
improve this article if you can. The talk page may contain suggestions. (November 2010)
The phenotypic value (P) of an individual is the combined effect of the genotypic value (G) and the
environmental deviation (E):
P=G+E
The genotypic value is the combined effect of all the genetic effects, including nuclear genes,
mitochondrial genes and interactions between the genes. It is worthwhile to note that the mathematics is
related to the genetics: for which the brief following revision may be useful. In disomic (diploid) organisms, a
nucleus gene is represented twice in the gene-set ("genotype"), one contribution being provided by each
parent during sexual reproduction. Each "gene" is located at a particular place (a "locus" - the Latin word for
place; plural "loci") on corresponding chromosomes (homologues), one from each parent. Any gene may
have several functional forms in the species as a whole, and each of these may lead to outwardly different
"effects" (= an average result in the phenotype considered over a large sample of gene-backgrounds and
environments). These functional forms are "alleles" (or "allelomorphs", the original term). If both alleles at a
gene have the same phenotypic effect (are the "same"), the gene is said to be "homozygous": if each allele at
a gene is different in effect, the gene is "heterozygous". The average phenotypic outcome may also depend
upon how alleles interact with their own homologous partner in the disomic genotype ("dominance"), and on
how these alleles interact with those of other genes at other loci which also affect this phenotypic trait
("epistasis"). Notice that we have combined classical genetics ideas with those of statistics in this exposition.
Terms such as "gene", "homologue", "allele", "homozygous" and "heterozygous" are genetical: but "effect" is
statistical, and refers to the average observed over an infinity of backgrounds, both genetical and
environmental. Thus, we have very sneakily defined the "genetic value" (or "genotypic" value) as the infinity
mean of all the phenotypes it can ever produce in time and space! Before molecular genetics, there simply
was no other way to do it! And after molecular genetics, this is still the most utilitarian way to tackle the idea
of genetic value! Also notice that we have openly used fundamentals of reproductive biology behind the
genetics. The founder of Quantitative Genetics - Sir Ronald Fisher - perceived all of this when he proposed
the first mathematics of this branch of Genetics [Fisher R.A. (1930). The Genetical theory of Natural
Selection. Oxford Clarendon Press.]. He sought to define a single statistical summary of all the variance
arising from phenotypic change during the course of genetical assortment and segregation, which he called
the "genetic" variance. His residual genotypic variance (which he called simply the "residual") represented
that part of assortment which did not lead to phenotypic change, although the genes themselves had in fact
been subject to meiosis and syngamy, of course. [A simplified exposition of this can be found in Falconer and
Mackay (1966) - see References.] These partitions subsequently became the familiar subdivisions of the
"additive" (A) and "dominance" (D) variances, respectively. These later names are utterly misleading and
very unfortunate, and have led to much confusion as to what they mean genetically. [It would have been
better for posterity had they been named "Assortative" (A), and "Stable" (S).] A more gene-focused
partitioning was invented by Mather and Jinks in 1971, but they also were statisticians rather than geneticists,
had their own rather opqaque symbolism, and became somewhat overwhelmed by the Fisherian approach.
Added to all of this was the problem that Fisher's underlying reproduction model (mating system) was
unrealistically simplistic: whilst it facilitated solving the equations, it didn't describe many real-life scenarios.
Fortunately, Wright (in the 1950s) did provide the means to overcome complex mating systems, but its own
complexity minimised its popular adoption. Early in this millennium [Heredity (2003) 91: 85-89], a
comprehensive linking together of all of these approaches reconciled their various meanings and
relationships (as well as correcting an error), and suggested that new partitions reflecting real homozygosis
[a] and heterozygosis [d] should replace the present "additive" [A] and "dominance" [D] subdivisions. This
paper revealed, by the way, that the Additive Genetical variance consists of all the homozygote variance,
plus part of the dominance variance, and a frequency-weighted covariance between homozygote and
heterozygote gene effects. The so-called Dominance variance contains only the remainder of the overall
dominance variance of the gene in question, being therefore very misleading indeed! It should be
understood, however, that either method of partitioning still accounts for all of the genotypic variance in the
model being used: it's the way it has been divided up which is being debated. At least the Environmental
variance is much more straight-forward. This can be subdivided into a pure environmental component (E)
and an interaction component (I) describing the gene-environment interaction. The overall "single gene"
model can be written as:
P = a + d + E + I.
Expansion of the model to multiple genes (loci) is still not resolved satisfactorily, and until that is
solved it is not possible to account for epistasis. The problem is being tackled currently. The contribution of
those components cannot be determined in a single individual, but they can be estimated for whole
populations by estimating the variances for those components, denoted as:
VP = V a + V d + V E + V I
The heritability of a trait is the proportion of the total (i.e. phenotypic) variance (V P) that is explained
by the total genotypic variance (VG). This is known also as the "broad sense" heritability (H2). If only Additive
genetic variance (VA) is used in the numerator, the heritability is "narrow sense" (h 2). Unfortunately, this is
often simply called "heritability", with little reflection about its true meaning. The broadsense heritability
indicates the genotypic determination of the phenotype: while the latter estimates the degree of assortative
disequlibrium in the trait. Fisher proposed that this narrow-sense heritability might be appropriate in
considering the results of natural selection, focusing as it does on disequilibrium: and it has been used also
for predicting the results of artificial selection. This latter usage seems to be inappropriate, however, as
breeders are interested in steering attributes towards new phenotypes (that is in utilising all the gene effects),
rather than simply exploiting disequilibrium. But old dogmas die hard!
[edit] Resemblance between relatives

Central in estimating the variances for the various components is the principle of relatedness. A child
has a father and a mother. Consequently, the child and father share 50% of their alleles, as do the child and
the mother. However, the mother and father normally do not share alleles as a result of shared ancestors.
Similarly, two full siblings share also on average 50% of the alleles with each other, while half siblings share
only 25% of their alleles. This variation in relatedness can be used to estimate which proportion of the total
phenotypic variance (VP) is explained by the above-mentioned components.
[edit] Correlated traits

Although some genes have only an effect on a single trait, many genes have an effect on various
traits. Because of this, a change in a single gene will have an effect on all those traits. This is calculated
using covariances, and the phenotypic covariance (CovP) between two traits can be partitioned in the same
way as the variances described above. The genetic correlation is calculated by dividing the covariance
between the additive genetic effects of two traits by the square root of the product of the variances for the
additive genetic effects of the two traits:
[edit] See also
• Diallel cross
• Ewens's sampling formula
• Experimental evolution
• Genetic distance
• Heritability
• Population genetics, built on some of the same principles as quantitative genetics
• Selective breeding
[edit] References
• Falconer, D. S. & Mackay TFC (1996). Introduction to Quantitative Genetics. Fourth edition.
Addison Wesley Longman, Harlow, Essex, UK.
• Roff DA (1997). Evolutionary Quantitative Genetics. Chapman & Hall, New York.
• Lynch M & Walsh B (1998). Genetics and Analysis of Quantitative Traits. Sinauer,
Sunderland, MA.
• Gordon I.L. (2003). Refinements to the partitioning of the inbred genotypic variance. Heredity
91: 85-89.
• Fisher R.A. (1930). The Genetical Theory of Natural Selection. Clarendon Press, Oxford, UK.
• Mather K. & Jinks J.L. (1971). Biometrical Genetics. Chapman & Hall, London.
• Wright S. (1951). The genetical structure of populations. Annals of Eugenics 15: 323-354.

• Quantitative Genetics Resources by Michael Lynch and Bruce Walsh, including the two
volumes of their textbook, Genetics and Analysis of Quantitative Traits and Evolution and Selection
of Quantitative Traits.
• Resources by Nick Barton et al. from the textbook, Evolution


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Dominance (genetics)
(Redirected from Dominance relationship)
For other uses, see Dominance.
This article's citation style may be unclear. The references used may be made
clearer with a different or consistent style of citation, footnoting, or external linking. (October
2009)
Dominance in genetics is a relationship between two variant forms (alleles) of a single gene, in which
one allele masks the expression of the other in influencing some trait. In the simplest case, if a gene exists in
two allelic forms (A & B), three combinations of alleles (genotypes) are possible: AA, AB, and BB. If AB
individuals (heterozygotes) show the same form of the trait (phenotype) as AA individuals (homozygotes),
and BB homozygotes show an alternative phenotype, allele A is said to dominate or be dominant to allele B,
and B is said to be recessive to A.
By convention, dominant alleles are written in uppercase letters, and recessive alleles in lowercase
letters. In this example, allele B is replaced by a. Then, A is dominant to a (and a is recessive to A), the AA
and Aa genotypes have the same phenotype, and the aa genotype has a different phenotype.
Contents
[hide]
• 1 Background: diploid, chromosomes, genes, loci, & alleles
• 1.1 Diploid / haploid
• 1.2 Chromosomes, genes, and alleles
• 1.3 Homozygous, heterozygous
• 1.4 Which trait is dominant?
• 2 Nomenclature
• 3 Relationship to other genetic concepts
• 3.1 Multiple alleles
• 3.2 Incomplete and semi-dominance
• 3.3 Co-dominance
• 3.4 Autosomal versus sex-linked dominance
• 3.5 Epistasis
• 4 Molecular mechanisms
• 5 Dominant and recessive genetic diseases in humans
• 6 History
• 7 See also
• 8 References
[edit] Background: diploid, chromosomes, genes, loci, & alleles
[edit] Diploid / haploid
Most familiar plants, like peas, and familiar animals, like fruit flies and humans, have paired
chromosomes, and are described as diploid. One chromosome of each pair is contributed by each parent,
one by the female parent in her ova, and one by the male parent in his sperm, which are joined at fertilization.
The ova and sperm cells have only one copy of each chromosome and are described as (haploid).
Production of haploid gametes occurs through a cell division process called meiosis.
[edit] Chromosomes, genes, and alleles

Each chromosome of a matching pair is structurally similar to the other, and each member of a
homologous pair has the same genetic material arranged in the same order and physical locations (loci, sing.
locus). The genetic material in each chromosome comprises a series of discrete genes that influence various
traits. Thus, each gene also has a corresponding homologue, which may exist in different forms: the variant
forms are called alleles. The alleles at the same locus on the two homologous chromosomes may be
identical or different.
In popular usage, "gene" and "allele" are often used interchangeably. This produces
misunderstandings. Properly, 'gene' refers to a hereditary unit, ordinarily at a fixed position on a
chromosome, that influences a particular trait. Genes are now understood to comprise DNA. 'Allele' refers to
any of the many particular forms of a gene that any be present in an individual. E.g., it is inaccurate to say
"This pea plant has a pair of wrinkled genes", and it is more accurate to say, "This plant has two 'w' alleles for
the 'Seed Shape' gene, and will produce wrinkled peas."
[edit] Homozygous, heterozygous
If two alleles of a given gene are identical, the organism is called a homozygote and is homozygous
with respect to that gene; if instead the two alleles are different, the organism is a heterozygote and is
heterozygous. The genetic makeup of an organism, either at a single locus or over all its genes collectively,
is called the genotype. The genotype of an organism directly or indirectly affects its molecular, physical,
behavioral, and other traits, which individually or collectively are called the phenotype. At heterozygous gene
loci, the two alleles interact to produce the phenotype. The simplest form of allele interaction is the one
described by Mendel, now called Mendelian, in which the appearance/phenotype caused by one allele is
apparent, called dominant, and the appearance/phenotype caused by the other allele is not apparent, called
recessive.
In the simplest case, the phenotypic effect of one allele completely masks the other in heterozygous
combination; that is, the phenotype produced by the two alleles in heterozygous combination is identical to
that produced by one of the two homozygous genotypes. The allele that masks the other is said to be
dominant to the latter, and the alternative allele is said to be recessive to the former.[1]
[edit] Which trait is dominant?

Dominant and recessive alleles do not necessarily produce 'stronger' and 'weaker' phenotypes,
respectively. Rather, the terms simply refer to their interaction in producing the phenotype of the
heterozygote. If there are two alternative phenotypes, by definition the phenotype exhibited by the
heterozygote is called "dominant" and the "hidden" phenotype is called "recessive." The key concept of
dominance is that the heterozygote is phenotypically identical to one of the two homozygotes. That trait
corresponding to the dominant allele may then be called the 'dominant' trait.
It is critical to understand that dominance is a genotypic relationship between alleles, as manifested
in the phenotype. It is unrelated to the nature of the phenotype itself, e.g., whether it is regarded as 'normal or
abnormal,' 'standard or nonstandard,' 'healthy or diseased,' 'stronger or weaker,' or 'more or less' extreme. It
is also important to distinguish between the 'round' gene locus, the 'round' allele at that locus, and the 'round'
phenotype it produces. It is inaccurate to say that 'the round gene dominates the wrinkled gene' or that 'round
peas dominate wrinkled peas.'
[edit] Nomenclature
In genetics, the common convention is that dominant alleles are written as capital letters and
recessive alleles as lower-case letters. In the pea example, once the dominance relationships of the two
alleles are known, it is possible to designate the dominant allele that produces a round shape by a capital-
letter symbol R, and the alternative recessive allele that produces a wrinkled shape by a lower-case symbol r.
The homozygous dominant, heterozygous, and homozygous recessive genotypes are then written RR, Rr,
and rr, respectively. It would also possible to designate the two alleles as W and w, and three genotypes
WW, Ww, and ww, the first two of which produced round peas and the third wrinkled peas. Note that the
choice or "R" or "W" as the symbol for the dominant allele does not pre-judge whether the allele causing the
'round' or 'wrinkled' phenotype when homozygous is the dominant one.
Another system of notation designates the gene involved in seed shape as the " Shp" gene, which
exists in two allelic forms, ShpR and Shpw, the dominance relationships of the two being indicated by the
case of the superscripts. This system is the standard system in Drosophila genetics.
[edit] Relationship to other genetic concepts

The concept of dominance is involved with a number of other genetic concepts.
[edit] Multiple alleles
Although any individual has at most two different alleles, most genes exist in a large number of allelic
forms in the population as a whole. In some cases, the alleles have different effects on the phenotype, and
their dominance interactions with each other can be described as a series. For example, the best known
human blood groups, the ABO system,[2] comprises three sets of alleles at the I locus, IA, IB, and IO. The first
two are dominant to the latter: that is, the AA and AO genotypes produce indistinguishable blood group
phenotypes, called "Type A", as do BB and BO, which produce "Type B" blood. In another example, coat
color in siamese cats[3] and related breeds is determined by a series of alleles at the albino gene locus (c)
that produce different levels of pigment and hence different levels of color dilution. Four of these are c+, cb,
cs, and ca (standard, Burmese, siamese, and albino, respectively), where the first allele is completely
dominant to the last three, and the last is completely recessive to the first three.
[edit] Incomplete and semi-dominance

Complete dominance occurs when the phenotype of the heterozygote is completely indistinguishable
from that of the dominant homozygote. This is frequently not the case. Incomplete dominance occurs when
the phenotype of the heterozygous genotype is an intermediate of the phenotypes of the homozygous
genotypes. For example, the snapdragon flower color is either homozygous for red or white. When the red
homozygous flower is paired with the white homozygous flower, the result yields a pink snapdragon flower.
The pink snapdragon is the result of incomplete dominance.
[edit] Co-dominance
Main article: Codominance
Co-dominance occurs when the contributions of both alleles are visible in the phenotype. In the ABO
example, the IA and IB alleles are co-dominant in producing the AB blood group phenotype, in which both A-
and B-type antigens are made. Another example occurs at the locus for the Beta-globin component of
hemoglobin, where the three molecular phenotypes of HbA/HbA, HbA/HbS, and HbS/HbS are all equally
detectable by protein electrophoresis. (The medical condition produced by the heterozygous genotype is
called an incomplete dominant, see above). For most gene loci at the molecular level, both alleles are
expressed co-dominantly, because both are transcribed into RNA.
Co-dominance and incomplete or semi-dominance are not the same phenomenon. For example, pink
flowers might be the product of two alleles that produce red and white pigments that become mixed (co-
dominance on the pigment level, no dominance on the color level), or the result of one allele that produces
the usual amount of red pigment and another non-functional allele that produces no pigment, so as to
produce a dilute, intermediate pink color (no dominance at either level).
[edit] Autosomal versus sex-linked dominance

In humans and other mammal species, sex is determined by two sex chromosomes called the X
chromosome and the Y chromosome. Human females are typically XX, males are typically XY. The
remaining pairs of chromosome are found in both sexes and are called autosomes; genetic traits due to loci
on these chromosomes are described as autosomal, and may be dominant or recessive. Genetic traits on the
X and Y chromosomes are called sex linked, because they tend to be characteristic of one sex or the other.
In practice, the term almost always refers to X-linked traits. Females have two copies of every gene locus
found on the X chromosome, just as for the autosomes, and the same dominance relationships apply. Males
however have only one copy of each X-chromosome gene locus, and are described as hemizygous for these
genes. The Y chromosome is much smaller than the X, and contains a much smaller set of genes that
influence 'maleness', such as the SRY gene for testis determining factor. Dominance rules for sex-linked
gene loci are determined by their behavior in the female: because the male has only one allele, that allele is
always expressed regardless of whether it is dominant or recessive.
[edit] Epistasis
Epistasis ["epi + stasis = to sit on top"] is an interaction between genotypes at two different gene loci,
which sometimes resembles a dominance interaction at a single locus. Epistasis modifies the characteristic
9:3:3:1 ratio expected for two non-epistatic genes. Most genetic systems involve complex epistatic
interactions among multiple gene loci. For two loci, 14 classes of epistatic interactions are recognized. As an
example of recessive epistasis, one gene locus may determine whether a flower pigment is yellow (AA or Aa)
or green (aa), while another locus determines whether the pigment is produced (BB or Bb) or not (bb). In a bb
plant, the flowers will be white, irrespective of the genotype of the other locus as AA, Aa, or aa. The b allele is
not dominant to the A allele: the B locus shows recessive epistasis to the A locus, because the B locus when
homozygous for the recessive allele (bb) suppresses phenotypic expression of the A locus. In a cross
between two AaBb plants, this produces a characteristic 9:3:4 ratio, in this case of yellow : green : white
flowers.
In dominant epistasis, one gene locus may determine yellow and green pigment as in the previous
example: AA and Aa are yellow, and aa are green. A second locus determines whether a pigment precursor
is produced (dd) or not (DD or Dd). Here, in a D- plant, the flowers will be colorless irrespective of the
genotype at the A locus, because of the epistatic effect of the dominant D allele. Thus, in a cross between
two AaDd plants, 3/4 of the plants will be colorless, and the yellow and green phenotypes are expressed only
in dd plants. This produces a characteristic 12:3:1 ratio of white : yellow : green plants.
Supplementary epistasis occurs when two loci affect the same phenotype. For example, if pigment
color is produced by CC or Cc but not cc, and by DD or Dd but not dd, then pigment is produced only in C-D-
genotypes, and not in any genotype combination with cc or dd. That is, both loci must have at least one
dominant allele to produce the phenotype. This produces a characteristic ratio 9:7 ratio of unpigmented to
pigmented plants.[4]
[edit] Molecular mechanisms

The molecular basis of dominance was unknown to Mendel. It is now understood that a gene locus
includes a long series (hundreds to thousands) of bases or nucleotides of deoxyribonucleic acid (DNA) at a
particular point on a chromosome. The central dogma of molecular biology states that "DNA makes RNA
makes protein", that is, that DNA is transcribed to make an RNA copy, and RNA is translated to make a
protein. In this process, different alleles at a locus may or may not be transcribed, and if transcribed may be
translated to slightly different forms of the same protein (called isoforms). Proteins often function as enzymes
that catalyze chemical reactions in the cell, which directly or indirectly produce phenotypes. In any diploid
organism, the DNA sequences of the two alleles present at any gene locus may be identical (homozygous) or
different (heterozygous). Even if the gene locus is heterozygous at the level of the DNA sequence, the
proteins made by each allele may be identical. In the absence of any difference between the protein
products, neither allele can be said to be dominant (see co-dominance , below). Even if the two protein
products are slightly different (allozymes), it is likely that they produce the same phenotype with respect to
enzyme action, and again neither allele can be said to be dominant.
Dominance typically occurs when one of the two alleles is non-functional at the molecular level, that
is, it is not transcribed or else does not produce a protein product. This can be the result of a mutation that
alters the DNA sequence of the allele. An organism homozygous for the non-functional allele will generally
show a distinctive phenotype, due to the absence of the protein product. For example, in humans and other
organisms, the unpigmented skin of the albino phenotype [2] results when an individual is homozygous for an
allele that prevents synthesis of the skin pigment protein melanin. It is important to understand that it is not
the lack of function that allows the allele to be described as recessive: this is the interaction with the
alternative allele in the heterozygote. Three general types of interaction are possible:
1. In the typical case, the single functional allele makes sufficient protein to produce a
phenotype identical to that of the homozygote: this is called haplosufficiency. For example, suppose
the standard amount of enzyme produced in the functional homozygote is 100%, with the two
functional alleles contributing 50% each. The single functional allele in the heterozygote produces
50% of the standard amount of enzyme, which is sufficient to produce the standard phenotype. If the
heterozygote and the functional-allele homozygote have identical phenotypes, the functional allele is
dominant to the non-functional allele. This occurs at the albino gene locus: the heterozygote
produces sufficient enzyme to convert the pigment precursor to melanin, and the individual has
standard pigmentation.
2. Alternatively, a single functional allele in the heterozygote may produce insufficient gene
product for proper function, and the phenotype resembles that of the homozygote for the non-
functional allele. This haploinsufficiency is much less common: usually the deficiency of gene product
results in incomplete dominance (below).
3. The intermediate interaction occurs where the heterozygous genotype produces a phenotype
intermediate between the two homozygotes. Depending on which of the two homozygotes the
heterozygote most resembles, one allele is said to show incomplete dominance over the other. For
example, in humans the Hb gene locus is responsible for the Beta-chain protein (HBB) that is one of
the two globin proteins that make up the blood pigment hemoglobin[3]. Many people are
homozygous for an allele called HbA; some persons carry an alternative allele called HbS, either as
homozygotes or heterozygotes. The hemoglobin molecules of HbS/HbS homozygotes undergo a
change in shape that distorts the morphology of the red blood cells, and causes a severe, life-
threatening form of anemia called sickle-cell anemia. Persons heterozygous HbA/HbS for this allele
have a much less severe form of anemia called sickle-cell trait. Because the disease phenotype of
HbA/HbS heterozygotes is more similar to but not identical to the HbA/HbA homozygote, the HbA
allele is said to be incompletely dominant to the HbS allele.
In some cases, dominance of a non-standard allele results when that allele produces a defective
protein that interferes with the proper function of the protein produced by the standard allele. The presence of
the defective protein "dominates" the standard protein, and the disease phenotype of the heterozygote more
closely resembles that of the homozygote for two variant alleles. This phenomenon occurs in a number of
trinucleotide repeat diseases: for an example and more details see Huntington Disease[4].
[edit] Dominant and recessive genetic diseases in humans

In humans, many genetic traits or diseases are classified simply as "dominant" or "recessive."
Especially with respect to so-called recessive diseases, this can oversimplify the underlying molecular basis
and lead to misunderstanding of the nature of dominance. For example, the genetic disease phenylketonuria
(PKU)[5] results from any of a large number (>60) of alleles at the gene locus for the enzyme phenylalanine
hydroxylase (PAH)[6]. Many of these alleles produce little or no PAH, as a result of which the substrate
phenylalanine and its metabolic byproducts accumulate in the central nervous system and can cause severe
mental retardation if untreated.
The genotypes and phenotypic consequences of interactions among three alleles are shown in the
following table:[5]
Genotype PAH activity [phe] conc PKU ?
AA 100% 60 uM No
AB 30% 120 uM No
CC 5% 200 ~ 300 uM Hyperphenylalanemia
BB 0.3% 600 ~ 2400 uM Yes

In unaffected persons homozygous for a standard functional allele (AA), PAH activity is standard
(100%), and the concentration of phenylalanine in the blood [phe] is about 60 uM. In untreated persons
homozygous for one of the PKU alleles (BB), PAH activity is close to zero, [phe] ten to forty times standard,
and the individual manifests PKU.
In the AB heterozygote, PAH activity is only 30% (not 50%) of standard, blood [phe] is elevated two-
fold, and the person does not manifest PKU. Thus, the A allele is dominant to the B allele with respect to
PKU, but the B allele is incompletely dominant to the A allele with respect to its molecular effect,
determination of PAH activity level (0.3% < 30% << 100%). Finally, the A allele is an incomplete dominant to
B with respect to [phe], as 60 uM < 120 uM << 600 uM. Note once more that it is irrelevant to the question of
dominance that the recessive allele produces a more extreme [phe] phenotype.
For a third allele C, a CC homozygote produces a very small amount of PAH enzyme, which results
in a somewhat elevated level of [phe] in the blood, a condition called hyperphenylalanemia, which does not
result in mental retardation.
That is, the dominance relationships of any two alleles may vary according to which aspect of the
phenotype is under consideration. It is typically more useful to talk about the phenotypic consequences of the
allelic interactions involved in any genotype, rather than to try to force them into dominant and recessive
categories.
[edit] History
The concept of dominance was first described by the "Father of Genetics," Gregor Mendel, in the
1860s. Mendel observed that, for a variety of traits of garden peas having to do with the appearance of
seeds, seed pods, and plant appearance, there occurred two discrete phenotypes: round vs wrinkled, or
yellow vs green seeds, red vs white flowers, tall vs short plants, and so on. When bred separately, the plants
always produced the same phenotypes, generation after generation. However, when lines with different
phenotypes were crossed (interbred), one and only one of the parental phenotypes showed up in the
offspring: green, or round, or red, or tall, and so on. However, when these hybrid plants were crossed, the
offspring plants showed the two original phenotypes, in a characteristic 3:1 ratio, with the more common type
having the phenotype of the parental hybrid plants. Mendel reasoned that each of the parents in the first
cross were homozygotes for different alleles (AA and aa), that each contributed one allele to the offspring,
such that all of these hybrids were heterozygotes (Aa), and that one of the two alleles in the hybrid cross
dominated expression of the other: A masked a. The final cross between two heterozygotes (Aa X Aa) would
produce AA, Aa, and aa offspring in a 1:2:1 genotype ratio with the first three classes showing the "A"
phenotype, and the last showing the "a" phenotype, thereby producing the 3:1 phenotype ratio.
Mendel did not use the terms gene, allele, phenotype, genotype, homozygote, and heterozygote, all
of which were introduced afterward. He did introduce the notation of capital and lowercase letters for
dominant and recessive alleles, respectively, still in use today.
[edit] See also

• Mitochondrial DNA
• Sex linkage
• Evolution of dominance
[edit] References
1. ^ RC King et al. 2006 A Dictionary of Genetics, 7th ed, p. 129: 'dominance [refers] to alleles
that fully manifest their phenotype when present in the heterozygous ... state.'
2. ^ http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=110300
3. ^ http://www.vgl.ucdavis.edu/service/cat/coatcolor.html
4. ^ [1]
5. ^ http://www.mun.ca/biology/scarr/2250_One_Gene_One_Enzyme.html
• On-line notes for Biology 2250 – Principles of Genetics (Memorial University of
Newfoundland) [7]
• Phenylketonuria [8]
• Sickle-Cell Anemia [9]
• ABO blood groups [10]
• Tri-nucleotide repeat: Huntington disease [11]
• Albinism [12]

• Online Mendelian Inheritance in Man (OMIM)
• Autosomal dominance of Huntington's Disease from the Huntington's Disease Outreach
Project for Education at Stanford
Retrieved from "http://en.wikipedia.org/wiki/Dominance_(genetics)"
Categories: Classical genetics

W000
Epistasis

For the condition known colloquially as a nosebleed, see Epistaxis. For the main action of a classical
drama, see Epitasis. For the method of depositing a monocrystalline film on a monocrystalline substrate, see
Epitaxis or Epitaxy.
See also: Quantitative Trait Locus
Epistasis is the phenomenon where the effects of one gene are modified by one or several other
genes, which are sometimes called modifier genes. The gene whose phenotype is expressed is said to be
epistatic, while the phenotype altered or suppressed is said to be hypostatic. Epistasis can be contrasted with
dominance, which is an interaction between alleles at the same gene locus. Epistasis is often studied in
relation to Quantitative Trait Loci (QTL) and polygenic inheritance.
In general, the fitness increment of any one allele depends in a complicated way on many other
alleles; but, because of the way that the science of population genetics was developed, evolutionary
scientists tend to think of epistasis as the exception to the rule. In the first models of natural selection devised
in the early 20th century, each gene was considered to make its own characteristic contribution to fitness,
against an average background of other genes. Some introductory college courses still teach population
genetics this way.
Epistasis and genetic interaction refer to different aspects of the same phenomenon. The term
epistasis is widely used in population genetics and refers especially to the statistical properties of the
phenomenon, and does not necessarily imply biochemical interaction between gene products. However, in
general epistasis is used to denote the departure from 'independence' of the effects of different genetic loci.
Confusion often arises due to the varied interpretation of 'independence' between different branches of
biology. For further discussion of the definitions of epistasis, and the history of these definitions, see [1].
Examples of tightly linked genes having epistatic effects on fitness are found in supergenes and the
human major histocompatibility complex genes. The effect can occur directly at the genomic level, where one
gene could code for a protein preventing transcription of the other gene. Alternatively, the effect can occur at
the phenotypic level. For example, the gene causing albinism would hide the gene controlling color of a
person's hair. In another example, a gene coding for a widow's peak would be hidden by a gene causing
baldness. Fitness epistasis (where the affected trait is fitness) is one cause of linkage disequilibrium.
Studying genetic interactions can reveal gene function, the nature of the mutations, functional
redundancy, and protein interactions. Because protein complexes are responsible for most biological
functions, genetic interactions are a powerful tool.
Contents
[hide]
• 1 Classification by fitness or trait value
• 2 Epistasis and sex
• 3 Functional or mechanistic classification
• 4 See also
• 5 References
[edit] Classification by fitness or trait value

Diagram illustrating different relationships between numbers of mutations and fitness. Synergistic
epistasis is the blue line - each mutation has a disproportionately large effect on the organism's fitness.
Antagonistic epistasis is the red line. See Evolution of Sex
Two-locus epistatic interactions can be either synergistic (enhancing the effectiveness) or
antagonistic (reducing the activity).[2][3] In the example of a haploid organism with genotypes (at two loci)
AB, Ab, aB or ab, we can think of the following trait values where higher values suggest greater expression of
the characteristic (the exact values are simply given as examples):
AB Ab aB ab
No epistasis (additive across loci) 2 1 1 0
Synergistic epistasis 3 1 1 0
Antagonistic epistasis 1 1 1 0
Hence, we can classify thus:
Trait values Type of epistasis
AB = Ab + aB − ab No epistasis, additive inheritance
AB > Ab + aB − ab Synergistic epistasis
AB < Ab + aB − ab Antagonistic epistasis

Understanding whether the majority of genetic interactions are synergistic or antagonistic will help
solve such problems as the evolution of sex.
[edit] Epistasis and sex

Negative epistasis and sex are thought to be intimately correlated. Experimentally, this idea has been
tested in using digital simulations of asexual and sexual populations. Over time, sexual populations move
towards more negative epistasis, or the lowering of fitness by two interacting alleles. It is thought that
negative epistasis allows individuals carrying the interacting deleterious mutations to be removed from the
populations efficiently. This removes those alleles from the population, resulting in an overall more fit
population. This hypothesis was proposed by Alexey Kondrashov, and is sometimes known as the
deterministic mutation hypothesis[4] and has also been tested using artificial gene networks.[2]
However, the evidence for this hypothesis has not always been straightforward and the model
proposed by Kondrashov has been criticized for assuming mutation parameters far from real world
observations. For example, see MacCarthy and Bergman [5]. In addition, in those tests which used artificial
gene networks, negative epistasis is only found in more densely connected networks[2], whereas empirical
evidence indicates that natural gene networks are sparsely connected[6], and theory shows that selection for
robustness will favor more sparsely connected and minimally complex networks.[6]
[edit] Functional or mechanistic classification

• Genetic suppression - the double mutant has a less severe phenotype than either single
mutant. [This term can also apply to a case where the double mutant has a phenotype intermediate
between those of the single mutants, in which case the more severe single mutant phenotype is
"suppressed" by the other mutation or genetic condition. For example, in a diploid organism, a
hypomorphic (or partial loss-of-function) mutant phenotype can be suppressed by knocking out one
copy of a gene that acts oppositely in the same pathway. In this case, the second gene is described
as a "dominant suppressor" of the hypomorphic mutant; "dominant" because the effect is seen when
one wild-type copy of the suppressor gene is present. For most genes, the phenotype of the
heterozygous suppressor mutation by itself would be wild type (because most genes are not haplo-
insufficient), so that the double mutant (suppressed) phenotype is intermediate between those of the
single mutants.]
• Genetic enhancement - the double mutant has a more severe phenotype than one predicted
by the additive effects of the single mutants.
• Synthetic lethality or unlinked non-complementation - two mutations fail to complement and
yet do not map to the same locus.
• Intragenic complementation, allelic complementation, or interallelic complementation - two
mutations map to the same locus, yet the two alleles complement in the heteroallelic diploid. Causes
of intragenic complementation include:
• homology effects such as transvection, where, for example, an enhancer from one
allele acts in trans to activate transcription from the promoter of the second allele.
• trans-splicing of two mutant RNA molecules to produce a functional RNA.
• At the protein level, another possibility involves proteins that normally function as
dimers. In a heteroallelic diploid, two different abnormal proteins could form a functional
dimer if each can compensate for the lack of function in the other.
[edit] See also

• Co-adaptation
• Epistasis and functional genomics
• Mutation
• Quantitative trait locus
[edit] References
1. ^ Cordell, Heather J. (2002). "Epistasis: what it means, what it doesn't mean, and statistical
methods to detect it in humans". Human Molecular Genetics 11 (20): 2463–8.
doi:10.1093/hmg/11.20.2463. PMID 12351582.
2. ^ a b c Azevedo R, Lohaus R, Srinivasan S, Dang K, Burch C (2006). "Sexual reproduction
selects for robustness and negative epistasis in artificial gene networks". Nature 440 (7080): 87–90.
doi:10.1038/nature04488. PMID 16511495.
3. ^ Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ (2004). "Evidence for
positive epistasis in HIV-1". Science 306 (5701): 1547–50. doi:10.1126/science.1101786.
PMID 15567861.
4. ^ A. S. Kondrashov (1988). "Deleterious mutations and the evolution of sexual reproduction".
Nature 336 (6198): 435–440. doi:10.1038/336435a0. PMID 3057385.
5. ^ MacCarthy T, Bergman A. (July 2007). "Coevolution of robustness, epistasis, and
recombination favors asexual reproduction". Proc Natl Acad Sci U S A 104 (31): 12801–6.
doi:10.1073/pnas.0705455104. PMID 17646644.
6. ^ a b Leclerc R. (August 2008). "Survival of the sparsest: robust gene networks are
parsimonious". Mol Syst Biol. 4 (213).

• Science Aid: Epistasis High school (GCSE, Alevel) resource.
• GeneticInteractions.org
• Epistasis.org


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Epistasis"
Categories: Classical genetics

W000
Quantitative trait locus

(Redirected from Polygenic inheritance)
See also: Epistasis
Inheritance of quantitative traits or polygenic inheritance refers to the inheritance of a phenotypic
characteristic that varies in degree and can be attributed to the interactions between two or more genes and
their environment. Though not necessarily genes themselves, quantitative trait loci (QTLs) are stretches of
DNA that are closely linked to the genes that underlie the trait in question. QTLs can be molecularly identified
(for example, with AFLP) to help map regions of the genome that contain genes involved in specifying a
quantitative trait. This can be an early step in identifying and sequencing these genes.
Contents
[hide]
• 1 Quantitative traits
• 1.1 Multifactorial traits in general
• 1.2 Heritable disease and multifactorial inheritance
• 1.3 A cursory look at some examples
• 1.4 Is it multifactorially heritable?
• 2 Quantitative trait locus
• 3 QTL mapping
• 4 Analysis of variance
• 5 Interval mapping
• 6 Composite interval mapping (CIM)
• 7 Family-pedigree based mapping in plants
• 8 See also
• 9 References
[edit] Quantitative traits

Polygenic inheritance, also known as quantitative or multifactorial inheritance refers to inheritance of
a phenotypic characteristic (trait) that is attributable to two or more genes, or the interaction with the
environment, or both. Unlike monogenic traits, polygenic traits do not follow patterns of Mendelian
inheritance (separated traits). Instead, their phenotypes typically vary along a continuous gradient depicted
by a bell curve.[1]
An example of a polygenic trait is human skin color. Many genes factor into determining a person's
natural skin color, so modifying only one of those genes changes the color only slightly. Many disorders with
genetic components are polygenic, including autism, cancer, diabetes and numerous others. Most
phenotypic characteristics are the result of the interaction of multiple genes.
Examples of disease processes generally considered to be results of multifactorial etiology:
Congenital malformation
• Cleft palate[2][3]
• Congenital dislocation of the hip[4]
• Congenital heart defects
• Neural tube defects
• Pyloric stenosis
• Talipes
Adult onset diseases
• Diabetes Mellitus[3]
• Cancer[3]
• Epilepsy
• Glaucoma
• Hypertension
• Ischaemic heart disease
• Manic depression
• Schizophrenia
Multifactorially inherited diseases are said to constitute the majority of genetic disorders affecting
humans which will result in hospitalization or special care of some kind[5][6].
[edit] Multifactorial traits in general

Generally, multifactorial traits outside of illness contribute to what we see as continuous
characteristics in organisms, such as height[5], skin color, and body mass[7]. All of these phenotypes are
complicated by a great deal of interplay between genes and environment[5]. The continuous distribution of
traits such as height and skin colour described above reflects the action of genes that do not quite show
typical patterns of dominance and recessiveness. Instead the contributions of each involved locus are
thought to be additive. Writers have distinguished this kind of inheritance as polygenic, or quantitative
inheritance[8].
Thus, due to the nature of polygenic traits, inheritance will not follow the same pattern as a simple
monohybrid or dihybrid cross[6]. Polygenic inheritance can be explained as Mendelian inheritance at many
loci[5], resulting in a trait which is normally-distributed. If n is the number of involved loci, then the coefficients
of the binomial expansion of (a + b)2n will give the frequency of distribution of all n allele combinations. For a
sufficiently high n, this binomial distribution will begin to resemble a normal distribution. From this viewpoint,
a disease state will become apparent at one of the tails of the distribution, past some threshold value.
Disease states of increasing severity will be expected the further one goes past the threshold and away from
the mean[8].
[edit] Heritable disease and multifactorial inheritance
A mutation resulting in a disease state is often recessive, so both alleles must be mutant in order for
the disease to be expressed phenotypically. A disease or syndrome may also be the result of the expression
of mutant alleles at more than one locus. When more than one gene is involved with or without the presence
of environmental triggers, we say that the disease is the result of multifactorial inheritance.
The more genes involved in the cross, the more the distribution of the genotypes will resemble a
normal, or Gaussian distribution[5]. This shows that multifactorial inheritance is polygenic, and genetic
frequencies can be predicted by way of a polyhybrid Mendelian cross. Phenotypic frequencies are a different
matter, especially if they are complicated by environmental factors.
The paradigm of polygenic inheritance as being used to define multifactorial disease has
encountered much disagreement. Turnpenny (2004) discusses how simple polygenic inheritance cannot
explain some diseases such as the onset of Type I diabetes mellitus, and that in cases such as these, not all
genes are thought to make an equal contribution[8].
The assumption of polygenic inheritance is that all involved loci make an equal contribution to the
symptoms of the disease. This should result in a normal curve distribution of genotypes. When it does not,
then idea of polygenetic inheritance cannot be supported for that illness.
[edit] A cursory look at some examples

Examples of such diseases are not new to medicine. The above examples are well-known examples
of diseases having both genetic and environmental components. Other examples involve atopic diseases
such as eczema or dermatitis[5]; also spina bifida (open spine) and anencephaly (open skull) are other
examples[2]
While schizophrenia is widely believed to be multifactorially genetic by biopsychiatrists, no
characteristic genetic markers have been determined with any certainty.
[edit] Is it multifactorially heritable?

It is difficult to ascertain if any particular disease is multifactorially genetic. If a pedigree chart is taken
of the patient's family and relations, and it is shown that the brothers and sisters of the patient have the
disease, then there is a strong chance that the disease is genetic and that the patient will also be a genetic
carrier. But this is not quite enough. It also needs to be proven that the pattern of inheritance is non-
Mendelian. This would require studying dozens, even hundreds of different family pedigrees before a
conclusion of multifactorial inheritance is drawn. This often takes several years.
If multifactorial inheritance is indeed the case, then the chance of the patient contracting the disease
is reduced if only cousins and more distant relatives have the disease[2]. It must be stated that while
multifactorially-inherited disease tends to run in families, inheritance will not follow the same pattern as a
simple monohybrid or dihybrid cross[6].
If a genetic cause is suspected and little else is known about the illness, then it remains to be seen
exactly how many genes are involved in the phenotypic expression of the disease. Once that is determined,
the question must be answered: if two people have the required genes, why some people still don't express
the disease. Generally, what makes the two individuals different are likely to be environmental factors. Due to
the involved nature of genetic investigations needed to determine such inheritance patterns, this is not
usually the first avenue of investigation one would choose to determine etiology.
[edit] Quantitative trait locus
A QTL for osteoporosis on the human chromosome 20

Typically, QTLs underlie continuous traits (those traits that vary continuously, e.g. height) as
opposed to discrete traits (traits that have two or several character values, e.g. red hair in humans, a
recessive trait, or smooth vs. wrinkled peas used by Mendel in his experiments).
Moreover, a single phenotypic trait is usually determined by many genes. Consequently, many QTLs
are associated with a single trait.
A quantitative trait locus (QTL) is a region of DNA that is associated with a particular phenotypic trait
- these QTLs are often found on different chromosomes. Knowing the number of QTLs that explains variation
in the phenotypic trait tells us about the genetic architecture of a trait. It may tell us that plant height is
controlled by many genes of small effect, or by a few genes of large effect.
Another use of QTLs is to identify candidate genes underlying a trait. Once a region of DNA is
identified as contributing to a phenotype, it can be sequenced. The DNA sequence of any genes in this
region can then be compared to a database of DNA for genes whose function is already known.
In a recent development, classical QTL analyses are combined with gene expression profiling i.e. by
DNA microarrays. Such expression QTLs (eQTLs) describe cis- and trans-controlling elements for the
expression of often disease-associated genes. Observed epistatic effects have been found beneficial to
identify the gene responsible by a cross-validation of genes within the interacting loci with metabolic
pathway- and scientific literature databases.
[edit] QTL mapping
Example of a genome-wide scan for QTL of osteoporosis

QTL mapping is the statistical study of the alleles that occur in a locus and the phenotypes (physical
forms or traits) that they produce. Because most traits of interest are governed by more than one gene,
defining and studying the entire locus of genes related to a trait gives hope of understanding what effect the
genotype of an individual might have in the real world.
Statistical analysis is required to demonstrate that different genes interact with one another and to
determine whether they produce a significant effect on the phenotype. QTLs identify a particular region of the
genome as containing a gene that is associated with the trait being assayed or measured. They are shown
as intervals across a chromosome, where the probability of association is plotted for each marker used in the
mapping experiment.
The QTL techniques were developed in the late 1980s and can be performed on inbred strains of any
species.
To begin, a set of genetic markers must be developed for the species in question. A marker is an
identifiable region of variable DNA. Biologists are interested in understanding the genetic basis of
phenotypes (physical traits). The aim is to find a marker that is significantly more likely to co-occur with the
trait than expected by chance, that is, a marker that has a statistical association with the trait. Ideally, they
would be able to find the specific gene or genes in question, but this is a long and difficult undertaking.
Instead, they can more readily find regions of DNA that are very close to the genes in question. When a QTL
is found, it is often not the actual gene underlying the phenotypic trait, but rather a region of DNA that is
closely linked with the gene.
For organisms whose genomes are known, one might now try to exclude genes in the identified
region whose function is known with some certainty not to be connected with the trait in question. If the
genome is not available, it may be an option to sequence the identified region and determine the putative
functions of genes by their similarity to genes with known function, usually in other genomes. This can be
done using BLAST, an online tool that allows users to enter a primary sequence and search for similar
sequences within the BLAST database of genes from various organisms.
Another interest of statistical geneticists using QTL mapping is to determine the complexity of the
genetic architecture underlying a phenotypic trait. For example, they may be interested in knowing whether a
phenotype is shaped by many independent loci, or by a few loci, and do those loci interact. This can provide
information on how the phenotype may be evolving.
[edit] Analysis of variance
The simplest method for QTL mapping is analysis of variance (ANOVA, sometimes called "marker
regression") at the marker loci. In this method, in a backcross, one may calculate a t-statistic to compare the
averages of the two marker genotype groups. For other types of crosses (such as the intercross), where
there are more than two possible genotypes, one uses a more general form of ANOVA, which provides a so-
called F-statistic. The ANOVA approach for QTL mapping has three important weaknesses. First, we do not
receive separate estimates of QTL location and QTL effect. QTL location is indicated only by looking at which
markers give the greatest differences between genotype group averages, and the apparent QTL effect at a
marker will be smaller than the true QTL effect as a result of recombination between the marker and the QTL.
Second, we must discard individuals whose genotypes are missing at the marker. Third, when the markers
are widely spaced, the QTL may be quite far from all markers, and so the power for QTL detection will
decrease.
[edit] Interval mapping

Lander and Botstein developed interval mapping, which overcomes the three disadvantages of
analysis of variance at marker loci. Interval mapping is currently the most popular approach for QTL mapping
in experimental crosses. The method makes use of a genetic map of the typed markers, and, like analysis of
variance, assumes the presence of a single QTL. Each location in the genome is posited, one at a time, as
the location of the putative QTL....
[edit] Composite interval mapping (CIM)
In this method, one performs interval mapping using a subset of marker loci as covariates. These
markers serve as proxies for other QTLs to increase the resolution of interval mapping, by accounting for
linked QTLs and reducing the residual variation. The key problem with CIM concerns the choice of suitable
marker loci to serve as covariates; once these have been chosen, CIM turns the model selection problem into
a single-dimensional scan. The choice of marker covariates has not been solved, however. Not surprisingly,
the appropriate markers are those closest to the true QTLs, and so if one could find these, the QTL mapping
problem would be complete anyway.
[edit] Family-pedigree based mapping in plants

Plant geneticists are attempting to incorporate some of the methods pioneered in human genetics.[9]
Using family-pedigree based approach has been discussed (Bink et al. 2008). Family-based linkage and
association has been successfully implemented (Rosyara et al. 2009)[10]
[edit] See also

• Epistasis
• Dominance (genetics)
• Expression quantitative trait loci (eQTL)
• Association Mapping
• Nested Association Mapping
[edit] References
1. ^ Ricki Lewis (2003), Multifactorial Traits, McGraw-Hill Higher Education,
http://highered.mcgraw-hill.com/sites/007246268x/student_view0/chapter7/
2. ^ a b c "Medical Genetics: Multifactorial Inheritance". Children's Hospital of the King's
Daughters. 31 December 2005. http://www.chkd.org/HealthLibrary/Content.aspx?pageid=P02134.
3. ^ a b c "Multifactorial Inheritance". Pregnancy and Newborn Health Education Centre . The
March of Dimes. http://www.marchofdimes.com/pnhec/4439_4138.asp. Retrieved 2007-01-06.
4. ^ Emery's Elements of Medical Genetics
5. ^ a b c d e f Tissot, Robert. "Human Genetics for 1st Year Students: Multifactorial Inheritance".
http://www.uic.edu/classes/bms/bms655/lesson11.html. Retrieved 2007-01-06.
6. ^ a b c "Multifactorial Inheritance". Clinical Genetics: A Self-Study Guide for Health Care
Providers. University of South Dakota School of Medicine. Archived from the original on 2006-12-30.
http://web.archive.org/web/20061230084542/http://www.usd.edu/med/som/genetics/curriculum/1GM
ULTI5.htm. Retrieved 2007-01-06.
7. ^ "Definition of Multifactorial inheritance". MedicineNet.com MedTerms Dictionary.
MedicineNet.com. http://www.medterms.com/script/main/art.asp?articlekey=4453. Retrieved 2007-
01-06.
8. ^ a b c Turnpenny, Peter (2004). "Emery's Elements of Medical Genetics, 12th Edition,
Chapter 9" (PDF). Elsevier. http://www.fleshandbones.com/readingroom/viewchapter.cfm?ID=1041.
9. ^ Jannink, J; Bink, Mc; Jansen, Rc (Aug 2001). "Using complex plant pedigrees to map
valuable genes". Trends in plant science 6 (8): 337–42. doi:10.1016/S1360-1385(01)02017-9.
ISSN 1360-1385. PMID 11495765.
10.^ Rosyara, U. R.; Maxson-stein, K.L.; Glover, K.D.; Stein, J.M.; Gonzalez-hernandez, J.L.
(2007). "Family-based mapping of FHB resistance QTLs in hexaploid wheat". Proceedings of
National Fusarium head blight forum
</ref> Bink MCAM, Boer MP, ter Braak CJF, Jansen J, Voorrips RE, van de Weg WE: Bayesian
analysis of complex traits in pedigreed plant populations. Euphytica 2008 , 161:85-96.</ref>

• Precision Mapping of Quantitative Trait Loci
• QTL Cartographer
• Complex Trait Consortium
• A Statistical Framework for Quantitative Trait Mapping
• WebQTL
• GridQTL
• QTL discussion forum
• A list of computer programs for genetic analysis including QTL analysis

biology · Heredity
Retrieved from "http://en.wikipedia.org/wiki/Quantitative_trait_locus"
Categories: Classical genetics | Genetics | Statistical genetics

W000
Pleiotropy

This article is about genetic pleiotropy. For drug pleiotropy, see Pleiotropy (drugs).
This article includes a list of references, but its sources remain unclear because it
has insufficient inline citations.
Please help to improve this article by introducing more precise citations where appropriate.
(April 2009)
Pleiotropy occurs when a single gene influences multiple phenotypic traits. Consequently, a mutation
in a pleiotropic gene may have an effect on some or all traits simultaneously. This can become a problem
when selection on one trait favors one specific version of the gene (allele), while the selection on the other
trait favors another allele.
Contents
[hide]
• 1 Etymology
• 2 Mechanism
• 3 Antagonistic pleiotropy
• 4 See also
• 5 References
[edit] Etymology
The term pleiotropy comes from the Greek πλείων pleion, meaning "more", and τρέπειν trepein,
meaning "to turn, to convert". A common mistake is to use "pleiotrophic" instead of "pleiotropic"[ citation
needed].
[edit] Mechanism
Pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. The underlying
mechanism is that the gene codes for a product that is, for example, used by various cells, or has a signaling
function on various targets.
A classic example of pleiotropy is the human disease PKU (phenylketonuria). This disease can
cause mental retardation and reduced hair and skin pigmentation, and can be caused by any of a large
number of mutations in a single gene that codes for the enzyme (phenylalanine hydroxylase), which converts
the amino acid phenylalanine to tyrosine, another amino acid. Depending on the mutation involved, this
results in reduced or zero conversion of phenylalanine to tyrosine, and phenylalanine concentrations
increase to toxic levels, causing damage at several locations in the body. PKU is totally benign if a diet free
from phenylalanine is maintained.
[edit] Antagonistic pleiotropy

Antagonistic pleiotropy refers to the expression of a gene resulting in multiple competing effects,
some beneficial but others detrimental to the organism.
This is central to a theory of aging first developed by G. C. Williams in 1957.[1] Williams suggested
that some genes responsible for increased fitness in the younger, fertile organism contribute to decreased
fitness later in life. An example is the p53 gene, which suppresses cancer, but also suppresses stem cells,
which replenish worn-out tissue[2].
Whether or not pleiotropy is antagonistic may depend upon the environment; for instance, a bacterial
gene that enhances glucose utilization efficiency at the expense of the ability to use other energy sources
(such as lactose) has positive effects when there is plenty of glucose, but can be lethal if lactose is the only
available food source.
[edit] See also

• Epistasis
• Metabolic network
• Metabolic supermice
• Enhancer (genetics)
[edit] References
1. ^ Williams, G.C. (1957) Pleiotropy, natural selection, and the evolution of senescence.
Evolution 11: 398–411
2. ^ Rodier F, Campisi J, Bhaumik D (2007). "Two faces of p53: aging and tumor suppression".
Nucleic Acids Res 35 (22): 7475. doi:10.1093/nar/gkm744. PMID 17942417.


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Pleiotropy"
W000
Phenotypic plasticity

Changes in an environmental variable (e.g. temperature) cause different genes to be expressed in
organisms
Phenotypic plasticity is the ability of an organism to change its phenotype in response to changes in
the environment.[1] Such plasticity in some cases expresses as several highly morphologically distinct
results; in other cases, a continuous norm of reaction describes the functional interrelationship of a range of
environments to a range of phenotypes. The term was originally conceived in the context of development, but
is now more broadly applied to include changes that occur during the adult life of an organism, such as
behaviour.
Organisms may differ in the degree of phenotypic plasticity they display when exposed to the same
environmental change. Hence, phenotypic plasticity can evolve and be adaptive if fitness is increased by
changing phenotype.[2] In general, sustained directional selection is predicted to increase plasticity in that
same direction.[3]
Some responses will be similar in all organisms, for example in organisms that do not
thermoregulate, as temperatures change lipids in the cell membrane must be altered by creating more
double bonds (when temperatures decrease) or removing them (when temperatures increase).[4]
Generally phenotypic plasticity is more important for immobile organisms (e.g. plants) than mobile
organisms (e.g. animals). This is because immobile organisms must adapt to their environment or they will
die, whereas mobile organisms are able to move away from a detrimental environment.[5] Examples of
phenotypic plasticity in plants include the allocation of more resources to the roots in soils that contain low
concentrations of nutrients and the alteration of leaf size and thickness.[6] The transport proteins present in
roots are also changed depending on the concentration of the nutrient and the salinity of the soil.[7] Some
plants, Mesembryanthemum crystallinum for example, are able to alter their photosynthetic pathways to use
less water when they become water- or salt-stressed.[8] Nevertheless, some mobile organisms also have
significant phenotypic plasticity, for example Acyrthosiphon pisum of the [Aphid] family exhibits the ability to
interchange between asexual and sexual reproduction, as well as growing wings between generations when
plants become too populated.[9]
In epidemiology, there exists a theory that rising incidences of coronary heart disease and type II
diabetes in human populations undergoing industrialization is due to a mismatch between a metabolic
phenotype determined in development and the nutritional environment to which an individual is subsequently
exposed. This is known as the 'thrifty phenotype' hypothesis.[10]
Contents
[hide]
• 1 See also
• 2 References
[edit] See also

• Acclimation
• Evolutionary physiology
• Beneficial acclimation hypothesis
[edit] References
1. ^ Price TD, Qvarnström A, Irwin DE (July 2003). "The role of phenotypic plasticity in driving
genetic evolution". Proc. Biol. Sci. 270 (1523): 1433–40. doi:10.1098/rspb.2003.2372.
PMID 12965006. PMC 1691402. http://journals.royalsociety.org/openurl.asp?
genre=article&issn=0962-8452&volume=270&issue=1523&spage=1433.
2. ^ De Jong G (April 2005). "Evolution of phenotypic plasticity: patterns of plasticity and the
emergence of ecotypes". New Phytol. 166 (1): 101–117. doi:10.1111/j.1469-8137.2005.01322.x.
PMID 15760355.
3. ^ Garland T,Jr Kelly SA (2006). "Phenotypic plasticity and experimental evolution". Journal of
Experimental Biology 2096: 2234–2261.
4. ^ Jane Larkindale and Bingru Huang Changes of lipid composition and saturation level in
leaves and roots for heat-stressed and heat-acclimated creeping bentgrass ( Agrostis stolonifera)
Environmental and Experimental Botany Volume 51, Issue 1, February 2004, Pages 57-67 [1]
5. ^ http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.es.17.110186.003315 Annual
Review of Ecology and Systematics Vol. 17:667-693 (Volume publication date November 1986)
[doi:10.1146/annurev.es.17.110186.003315]
6. ^ Sultan SE (December 2000). "Phenotypic plasticity for plant development, function and life
history". Trends Plant Sci. 5 (12): 537–542. doi:10.1016/S1360-1385(00)01797-0. PMID 11120476.
7. ^ Differential regulation of the HAK5 genes encoding the high-affinity K+ transporters of
Thellungiella halophila and Arabidopsis thaliana Environmental and Experimental Botany Volume 65,
Issues 2-3, March 2009, Pages 263-269 Fernando Alemána, Manuel Nieves-Cordonesa, Vicente
Martínez et al [2]
8. ^ http://pcp.oxfordjournals.org/cgi/content/abstract/38/3/236 Plant and Cell Physiology, 1997,
Vol. 38, No. 3 236-242 Induction of CAM in Mesembryanthemum crystallinum Abolishes the Stomatal
Response to Blue Light and Light-Dependent Zeaxanthin Formation in Guard Cell Chloroplasts. Gary
Tallman, Jianxin Zhu, Bruce T. Mawson et al
9. ^ http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000313 PLoS
Biology, Jan 19 2010, "Genome Sequence of the Pea Aphid Acyrthosiphon pisum". The International
Aphid Genomics Consortium
10.^ http://bmb.oxfordjournals.org/cgi/content/abstract/60/1/5 British Medical Bulletin 60:5-20
(2001) The thrifty phenotype hypothesis and David J P Barker

• Special issue of the Journal of Experimental Biology concerning phenotypic plasticity
• Massimo Pigliucci’s Evolutionary Ecology Lab web page
• Developmental Plasticity and Evolution - review of the book from American Scientist
• Isidro T. Savillo's Impermanence of Sexual Phenotypes from Biologybrowser (Thomson
Reuters)

• Mary Jane West-Eberhard (2003). Developmental Plasticity and Evolution. Oxford University
Press. ISBN 0195122348.


phenotype
Non-genetic
Developmental

Processes of
Population genetic
Evolutionary
developmental
concepts

Modes of

W000
Fitness landscape

It has been suggested that evolutionary landscape be merged into this article or
section. (Discuss)
In evolutionary biology, fitness landscapes or adaptive landscapes are used to visualize the
relationship between genotypes (or phenotypes) and reproductive success. It is assumed that every
genotype has a well-defined replication rate (often referred to as fitness). This fitness is the "height" of the
landscape. Genotypes which are very similar are said to be "close" to each other, while those that are very
different are "far" from each other.
The two concepts of height and distance are sufficient to form the concept of a "landscape". The set
of all possible genotypes, their degree of similarity, and their related fitness values is then called a fitness
landscape.
In evolutionary optimization problems, fitness landscapes are evaluations of a fitness function for all
candidate solutions (see below). The idea of studying evolution by visualizing the distribution of fitness
values as a kind of landscape was first introduced by Sewall Wright in 1932[1].
Contents
[hide]
• 1 Fitness landscapes in biology
• 2 Fitness landscapes in evolutionary optimization
• 3 See also
• 4 References
[edit] Fitness landscapes in biology

Fitness landscapes are often conceived of as ranges of mountains. There exist local peaks (points
from which all paths are downhill, i.e. to lower fitness) and valleys (regions from which most paths lead
uphill). A fitness landscape with many local peaks surrounded by deep valleys is called rugged. If all
genotypes have the same replication rate, on the other hand, a fitness landscape is said to be flat. The
shapes of fitness landscapes are also closely related to epistasis, as demonstrated by Stuart Kauffman's NK-
Landscape model.
An evolving population typically climbs uphill in the fitness landscape, by a series of small genetic
changes, until a local optimum is reached (Fig. 1). There it remains, unless a rare mutation opens a path to a
new, higher fitness peak. Note, however, that at high mutation rates this picture is somewhat simplistic. A
population may not be able to climb a very sharp peak if the mutation rate is too high, or it may drift away
from a peak it had already found; consequently, reducing the fitness of the system. The process of drifting
away from a peak is often referred to as Muller's ratchet.
The apparent lack of wheeled animals is an example of a fitness peak which is presently inaccessible
due to a surrounding valley.
In general, the higher the connectivity the more rugged the system becomes. Thus, a simply
connected system only has one peak and if part of the system is changed then there will be little, if any, effect
on any other part of the system. A high connectivity implies that the variables or sub-systems interact far
more and the system may have to settle for a level of ‘fitness’ lower than it might be able to attain. The
system would then have to change its approach to overcoming whatever problems that confront it, thus,
changing the ‘terrain’ and enabling it to continue.
[edit] Fitness landscapes in evolutionary optimization

Apart from the field of evolutionary biology, the concept of a fitness landscape has also gained
importance in evolutionary optimization methods such as genetic algorithms or evolutionary strategies. In
evolutionary optimization, one tries to solve real-world problems (e.g., engineering or logistics problems) by
imitating the dynamics of biological evolution. For example, a delivery truck with a number of destination
addresses can take a large variety of different routes, but only very few will result in a short driving time.
In order to use evolutionary optimization, one has to define for every possible solution s to the
problem of interest (i.e., every possible route in the case of the delivery truck) how 'good' it is. This is done by
introducing a scalar-valued function f(s) (scalar valued means that f(s) is a simple number, such as 0.3, while
s can be a more complicated object, for example a list of destination addresses in the case of the delivery
truck), which is called the fitness function or fitness landscape.
A high f(s) implies that s is a good solution. In the case of the delivery truck, f(s) could be the number
of deliveries per hour on route s. The best, or at least a very good, solution is then found in the following way:
initially, a population of random solutions is created. Then, the solutions are mutated and selected for those
with higher fitness, until a satisfying solution has been found.
Evolutionary optimization techniques are particularly useful in situations in which it is easy to
determine the quality of a single solution, but hard to go through all possible solutions one by one (it is easy
to determine the driving time for a particular route of the delivery truck, but it is almost impossible to check all
possible routes once the number of destinations grows to more than a handful).
The concept of a scalar valued fitness function f(s) also corresponds to the concept of a potential or
energy function in physics. The two concepts only differ in that physicists traditionally think in terms of
minimizing the potential function, while biologists prefer the notion that fitness is being maximized. Therefore,
taking the inverse of a potential function turns it into a fitness function, and vice versa.
Figure 1: Sketch of a fitness landscape. The arrows indicate the preferred flow of a population on the
landscape, and the points A and C are local optima. The red ball indicates a population that moves from a
very low fitness value to the top of a peak.
[edit] See also

• Fitness approximation
• Fitness function
• Epigenetic landscape
• Evolution
• Genetic algorithm
• Habitat (ecology)
• Hill climbing
• Natural selection
• NK model
• Potential function
• Self-organized criticality
[edit] References
1. ^ Wright, S. 1932 "The roles of mutation, inbreeding, crossbreeding, and selection in
evolution". In Proceedings of the Sixth International Congress on Genetics , pp. 355–366.

• Niko Beerenwinkel, Lior Pachter and Bernd Sturmfels. Epistasis and shapes of fitness
landscapes, 2006.
• Richard Dawkins. Climbing Mount Improbable. New York: Norton, 1996.
• Sergey Gavrilets. Fitness landscapes and the origin of species, 2004.
• Stuart Kauffman. At Home in the Universe: The Search for Laws of Self-Organization and
Complexity. New York: Oxford University Press, 1995.
• Melanie Mitchell. An Introduction to Genetic Algorithms . Cambridge, MA: MIT Press, 1996.
• Foundations of Genetic Programming, Chapter 2
• Stuart Kauffman, The Origins of Order, OUP, 1993


phenotype
Non-genetic
Developmental


Effects of


Genetic genealogy
Retrieved from "http://en.wikipedia.org/wiki/Fitness_landscape"
Categories: Population genetics | Selection

W000
Transgressive segregation
(Redirected from Transgressive phenotype)
It has been suggested that this article or section be merged with Transgressive
phenotype. (Discuss)
In genetics, transgressive segregation is the formation of extreme phenotypes, or transgressive
phenotypes, observed in segregated hybrid populations compared to phenotypes observed in the parental
lines.[1][2]
Hybrid offspring generally possess traits or characteristics seen in ancestral species. These traits
might be expected to be subdued or diluted when compared to the original species. Transgressive
segregation attempts to explain situations when the converse is true, hybrid offspring that appear to have
overstated traits when compared to the parental line.
Transgressive segregation may be a major source of novel adaptations in hybrids.[2]
There are many causes of transgressive segregation in hybrids such as: recombination of additive
alleles, an elevated mutation rate, reduced developmental stability, epistatic effects between alleles, or
overdominance caused by heterozygosity at specific loci or chromosome number variation.[2]
[edit] Notes
1. ^ Nolte, Arne W.; H David Sheets (2005-06-29). "Shape based assignment tests suggest
transgressive phenotypes in natural sculpin hybrids (Teleostei, Scorpaeniformes, Cottidae)".
Frontiers in Zoology 2: 11. doi: 10.1186/1742-9994-2-11.
2. ^ a b c Rieseberg, Loren H.; Margaret A. Archer and Robert K. Wayne (1999-07).
"Transgressive segregation, adaptation and speciation". Heredity 83: 363–372. doi:
10.1038/sj.hdy.6886170.

Genetic architecture Dominance relationship · Epistasis · Polygenic inheritance ·

Pleiotropy · Plasticity · Canalisation · Fitness landscape · Transgressive
phenotype
Non-genetic
Developmental

W000
Epigenetics

For the unfolding of an organism or the theory that plants and animals develop in this way, see
epigenesis (biology). For epigenetics in robotics, see developmental robotics.
In biology, and specifically genetics, epigenetics is the study of heritable changes in phenotype
(appearance) or gene expression caused by mechanisms other than changes in the underlying DNA
sequence, hence the name epi- (Greek: επί- over, above) -genetics. These changes may remain through cell
divisions for the remainder of the cell's life and may also last for multiple generations. However, there is no
change in the underlying DNA sequence of the organism;[1] instead, non-genetic factors cause the
organism's genes to behave (or "express themselves") differently.[2]
The best example of epigenetic changes in eukaryotic biology is the process of cellular
differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the
embryo which in turn become fully differentiated cells. In other words, a single fertilized egg cell – the zygote –
changes into the many cell types including neurons, muscle cells, epithelium, blood vessels etc. as it
continues to divide. It does so by activating some genes while inhibiting others.[3]
Contents
[hide]
• 1 Etymology and definitions
• 2 Molecular basis of epigenetics
• 3 Mechanisms
• 3.1 DNA methylation and chromatin remodeling
• 3.2 RNA transcripts and their encoded proteins
• 3.3 Prions
• 3.4 Structural inheritance systems
• 4 Functions and consequences
• 4.1 Development
• 4.2 Medicine
• 4.3 Evolution
• 5 Epigenetic effects in humans
• 5.1 Genomic imprinting and related disorders
• 5.2 Transgenerational epigenetic observations
• 5.3 Cancer and developmental abnormalities
• 5.3.1 Cancer Treatment
• 5.4 Twin studies
• 6 Epigenetics in microorganisms
• 7 See also
[edit] Etymology and definitions
epigenetic mechanisms
Epigenetics (as in "epigenetic landscape") was coined by C. H. Waddington in 1942 as a
portmanteau of the words genetics and epigenesis.[4] Epigenesis is an old[5] word which has more recently
been used (see preformationism for historical background) to describe the differentiation of cells from their
initial totipotent state in embryonic development. When Waddington coined the term the physical nature of
genes and their role in heredity was not known; he used it as a conceptual model of how genes might interact
with their surroundings to produce a phenotype.
Robin Holliday defined epigenetics as "the study of the mechanisms of temporal and spatial control
of gene activity during the development of complex organisms."[6] Thus epigenetic can be used to describe
anything other than DNA sequence that influences the development of an organism.
The modern usage of the word in scientific discourse is more narrow, referring to heritable traits (over
rounds of cell division and sometimes transgenerationally) that do not involve changes to the underlying DNA
sequence.[7] The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to"
genetics; thus epigenetic traits exist on top of or in addition to the traditional molecular basis for inheritance.
The similarity of the word to "genetics" has generated many parallel usages. The "epigenome" is a
parallel to the word "genome", and refers to the overall epigenetic state of a cell. The phrase "genetic code"
has also been adapted—the "epigenetic code" has been used to describe the set of epigenetic features that
create different phenotypes in different cells. Taken to its extreme, the "epigenetic code" could represent the
total state of the cell, with the position of each molecule accounted for in an epigenomic map, a diagrammatic
representation of the gene expression, DNA methylation and histone modification status of a particular
genomic region. More typically, the term is used in reference to systematic efforts to measure specific,
relevant forms of epigenetic information such as the histone code or DNA methylation patterns.
The psychologist Erik Erikson used the term epigenetic[when?] in his theory of psychosocial
development. That usage, however, is of primarily historical interest.[8]
[edit] Molecular basis of epigenetics

The molecular basis of epigenetics is complex. It involves modifications of the activation of certain
genes, but not the basic structure of DNA. Additionally, the chromatin proteins associated with DNA may be
activated or silenced. This accounts for why the differentiated cells in a multi-cellular organism express only
the genes that are necessary for their own activity. Epigenetic changes are preserved when cells divide. Most
epigenetic changes only occur within the course of one individual organism's lifetime, but, if a mutation in the
DNA has been caused in sperm or egg cell that results in fertilization, then some epigenetic changes are
inherited from one generation to the next.[9] This raises the question of whether or not epigenetic changes in
an organism can alter the basic structure of its DNA (see Evolution, below), a form of Lamarckism.
Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X
chromosome inactivation, position effect, reprogramming, transvection, maternal effects, the progress of
carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and
technical limitations affecting parthenogenesis and cloning.
Epigenetic research uses a wide range of molecular biologic techniques to further our understanding
of epigenetic phenomena, including chromatin immunoprecipitation (together with its large-scale variants
ChIP-on-chip and ChIP-seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes,
DNA adenine methyltransferase identification (DamID) and bisulfite sequencing. Furthermore, the use of
bioinformatic methods is playing an increasing role (computational epigenetics).
[edit] Mechanisms
Several types of epigenetic inheritance systems may play a role in what has become known as cell
memory:[10]
[edit] DNA methylation and chromatin remodeling
DNA associates with histone proteins to form chromatin.

Because the phenotype of a cell or individual is affected by which of its genes are transcribed,
heritable transcription states can give rise to epigenetic effects. There are several layers of regulation of gene
expression. One way that genes are regulated is through the remodeling of chromatin. Chromatin is the
complex of DNA and the histone proteins with which it associates. Histone proteins are little spheres that
DNA wraps around. If the way that DNA is wrapped around the histones changes, gene expression can
change as well. Chromatin remodeling is accomplished through two main mechanisms:
1. The first way is post translational modification of the amino acids that make up histone
proteins. Histone proteins are made up of long chains of amino acids. If the amino acids that are in
the chain are changed, the shape of the histone sphere might be modified. DNA is not completely
unwound during replication. It is possible, then, that the modified histones may be carried into each
new copy of the DNA. Once there, these histones may act as templates, initiating the surrounding
new histones to be shaped in the new manner. By altering the shape of the histones around it, these
modified histones would ensure that a differentiated cell would stay differentiated, and not convert
back into being a stem cell.
2. The second way is the addition of methyl groups to the DNA, mostly at CpG sites, to convert
cytosine to 5-methylcytosine. 5-Methylcytosine performs much like a regular cytosine, pairing up with
a guanine. However, some areas of genome are methylated more heavily than others and highly
methylated areas tend to be less transcriptionally active, through a mechanism not fully understood.
Methylation of cytosines can also persist from the germ line of one of the parents into the zygote,
marking the chromosome as being inherited from this parent (genetic imprinting).
The way that the cells stay differentiated in the case of DNA methylation is clearer to us than it is in
the case of histone shape. Basically, certain enzymes (such as DNMT1) have a higher affinity for the
methylated cytosine. If this enzyme reaches a "hemimethylated" portion of DNA (where methylcytosine is in
only one of the two DNA strands) the enzyme will methylate the other half.
Although histone modifications occur throughout the entire sequence, the unstructured N-termini of
histones (called histone tails) are particularly highly modified. These modifications include acetylation,
methylation, ubiquitylation, phosphorylation and sumoylation. Acetylation is the most highly studied of these
modifications. For example, acetylation of the K14 and K9 lysines of the tail of histone H3 by histone
acetyltransferase enzymes (HATs) is generally correlated with transcriptional competence.
One mode of thinking is that this tendency of acetylation to be associated with "active" transcription is
biophysical in nature. Because it normally has a positively charged nitrogen at its end, lysine can bind the
negatively charged phosphates of the DNA backbone. The acetylation event converts the positively charged
amine group on the side chain into a neutral amide linkage. This removes the positive charge, thus loosening
the DNA from the histone. When this occurs, complexes like SWI/SNF and other transcriptional factors can
bind to the DNA and allow transcription to occur. This is the "cis" model of epigenetic function. In other words,
changes to the histone tails have a direct affect on the DNA itself.
Another model of epigenetic function is the "trans" model. In this model changes to the histone tails
act indirectly on the DNA. For example, lysine acetylation may create a binding site for chromatin modifying
enzymes (and basal transcription machinery as well). This Chromatin Remodeler can then cause changes to
the state of the chromatin. Indeed, the bromodomain — a protein segment (domain) that specifically binds
acetyl-lysine — is found in many enzymes that help activate transcription, including the SWI/SNF complex (on
the protein polybromo). It may be that acetylation acts in this and the previous way to aid in transcriptional
activation.
The idea that modifications act as docking modules for related factors is borne out by histone
methylation as well. Methylation of lysine 9 of histone H3 has long been associated with constitutively
transcriptionally silent chromatin (constitutive heterochromatin). It has been determined that a chromodomain
(a domain that specifically binds methyl-lysine) in the transcriptionally repressive protein HP1 recruits HP1 to
K9 methylated regions. One example that seems to refute this biophysical model for acetylation is that tri-
methylation of histone H3 at lysine 4 is strongly associated with (and required for full) transcriptional
activation. Tri-methylation in this case would introduce a fixed positive charge on the tail.
It has been shown that the histone lysine methyltransferase (KMT) is responsible for this methylation
activity in the pattern of histones H3 & H4. This enzyme utilizes a catalytically active site called the SET
domain (Supressor of variegation, Enhancer of zeste, Trithorax). The SET domain is a 130-amino acid
sequence involved in modulating gene activities. This domain has been demonstrated to bind to the histone
tail and causes the methylation of the histone.[11]
Differing histone modifications are likely to function in differing ways; acetylation at one position is
likely to function differently than acetylation at another position. Also, multiple modifications may occur at the
same time, and these modifications may work together to change the behavior of the nucleosome. The idea
that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called
the histone code.
DNA methylation frequently occurs in repeated sequences, and helps to suppress the expression
and mobility of 'transposable elements':[12] Because 5-methylcytosine is chemically very similar to
thymidine, CpG sites are frequently mutated and become rare in the genome, except at CpG islands where
they remain unmethylated. Epigenetic changes of this type thus have the potential to direct increased
frequencies of permanent genetic mutation. DNA methylation patterns are known to be established and
modified in response to environmental factors by a complex interplay of at least three independent DNA
methyltransferases, DNMT1, DNMT3A and DNMT3B, the loss of any of which is lethal in mice.[13] DNMT1 is
the most abundant methyltransferase in somatic cells,[14] localizes to replication foci,[15] has a 10–40-fold
preference for hemimethylated DNA and interacts with the proliferating cell nuclear antigen (PCNA).[16] By
preferentially modifying hemimethylated DNA, DNMT1 transfers patterns of methylation to a newly
synthesized strand after DNA replication, and therefore is often referred to as the ‘maintenance'
methyltransferase.[17] DNMT1 is essential for proper embryonic development, imprinting and X-inactivation.
[13][18]
Histones H3 and H4 can also be manipulated through demethylation using histone lysine
demethylase (KDM). This recently identifited enzyme has a catalytically active site called the Jumonji domain
(JmjC). The demethylation occurs when JmjC utilizes multiple cofactors to hydroxylate the methyl group,
thereby removing it. JmjC is capable of demethylating mono-, di-, and tri-methylated substrates. .[19]
Chromosomal regions can adopt stable and heritable alternative states resulting in bistable gene
expression without changes to the DNA sequence. Epigenetic control is often associated with alternative
covalent modifications of histones.[20] The stability and heritability of states of larger chromosomal regions
are often thought to involve positive feedback where modified nucleosomes recruit enzymes that similarly
modify nearby nucleosomes. A simplified stochastic model for this type of epigenetics is found here [21] .
Because DNA methylation and chromatin remodeling play such a central role in many types of
epigenic inheritance, the word "epigenetics" is sometimes used as a synonym for these processes. However,
this can be misleading. Chromatin remodeling is not always inherited, and not all epigenetic inheritance
involves chromatin remodeling.[22]
It has been suggested that the histone code could be mediated by the effect of small RNAs. The
recent discovery and characterization of a vast array of small (21- to 26-nt), non-coding RNAs suggests that
there is an RNA component, possibly involved in epigenetic gene regulation. Small interfering RNAs can
modulate transcriptional gene expression via epigenetic modulation of targeted promoters.[23]
[edit] RNA transcripts and their encoded proteins

Sometimes a gene, after being turned on, transcribes a product that (either directly or indirectly)
maintains the activity of that gene. For example, Hnf4 and MyoD enhance the transcription of many liver- and
muscle-specific genes, respectively, including their own, through the transcription factor activity of the
proteins they encode. RNA signalling includes differential recruitment of a hierarchy of generic chromatin
modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and
development.[24] Other epigenetic changes are mediated by the production of different splice forms of RNA,
or by formation of double-stranded RNA (RNAi). Descendants of the cell in which the gene was turned on will
inherit this activity, even if the original stimulus for gene-activation is no longer present. These genes are
most often turned on or off by signal transduction, although in some systems where syncytia or gap junctions
are important, RNA may spread directly to other cells or nuclei by diffusion. A large amount of RNA and
protein is contributed to the zygote by the mother during oogenesis or via nurse cells, resulting in maternal
effect phenotypes. A smaller quantity of sperm RNA is transmitted from the father, but there is recent
evidence that this epigenetic information can lead to visible changes in several generations of offspring.[25]
[edit] Prions
For more details on this topic, see Prions.
Prions are infectious forms of proteins. Proteins generally fold into discrete units which perform
distinct cellular functions, but some proteins are also capable of forming an infectious conformational state
known as a prion. Although often viewed in the context of infectious disease, prions are more loosely defined
by their ability to catalytically convert other native state versions of the same protein to an infectious
conformational state. It is in this latter sense that they can be viewed as epigenetic agents capable of
inducing a phenotypic change without a modification of the genome.[26]
Fungal prions are considered epigenetic because the infectious phenotype caused by the prion can
be inherited without modification of the genome. PSI+ and URE3, discovered in yeast in 1965 and 1971, are
the two best studied of this type of prion.[27][28] Prions can have a phenotypic effect through the
sequestration of protein in aggregates, thereby reducing that protein's activity. In PSI+ cells, the loss of the
Sup35 protein (which is involved in termination of translation) causes ribosomes to have a higher rate of
read-through of stop codons, an effect which results in suppression of nonsense mutations in other genes.
[29] The ability of Sup35 to form prions may be a conserved trait. It could confer an adaptive advantage by
giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated
by premature stop codon mutations.[30][31]
[edit] Structural inheritance systems

For more details on this topic, see Structural inheritance.
In ciliates such as Tetrahymena and Paramecium, genetically identical cells show heritable
differences in the patterns of ciliary rows on their cell surface. Experimentally altered patterns can be
transmitted to daughter cells. It seems existing structures act as templates for new structures. The
mechanisms of such inheritance are unclear, but reasons exist to assume that multicellular organisms also
use existing cell structures to assemble new ones.[32]
[edit] Functions and consequences

[edit] Development
Somatic epigenetic inheritance, particularly through DNA methylation and chromatin remodeling, is
very important in the development of multicellular eukaryotic organisms. The genome sequence is static (with
some notable exceptions), but cells differentiate into many different types, which perform different functions,
and respond differently to the environment and intercellular signalling. Thus, as individuals develop,
morphogens activate or silence genes in an epigenetically heritable fashion, giving cells a "memory". In
mammals, most cells terminally differentiate, with only stem cells retaining the ability to differentiate into
several cell types ("totipotency" and "multipotency"). In mammals, some stem cells continue producing new
differentiated cells throughout life, but mammals are not able to respond to loss of some tissues, for example,
the inability to regenerate limbs, which some other animals are capable of. Unlike animals, plant cells do not
terminally differentiate, remaining totipotent with the ability to give rise to a new individual plant. While plants
do utilise many of the same epigenetic mechanisms as animals, such as chromatin remodeling, it has been
hypothesised that plant cells do not have "memories", resetting their gene expression patterns at each cell
division using positional information from the environment and surrounding cells to determine their fate.[33]
[edit] Medicine
Epigenetics has many and varied potential medical applications. Congenital genetic disease is well
understood, and it is also clear that epigenetics can play a role, for example, in the case of Angelman
syndrome and Prader-Willi syndrome. These are normal genetic diseases caused by gene deletions or
inactivation of the genes, but are unusually common because individuals are essentially hemizygous
because of genomic imprinting, and therefore a single gene knock out is sufficient to cause the disease,
where most cases would require both copies to be knocked out.[34]
[edit] Evolution
Although epigenetics in multicellular organisms is generally thought to be a mechanism involved in
differentiation, with epigenetic patterns "reset" when organisms reproduce, there have been some
observations of transgenerational epigenetic inheritance (e.g., the phenomenon of paramutation observed in
maize). Although most of these multigenerational epigenetic traits are gradually lost over several
generations, the possibility remains that multigenerational epigenetics could be another aspect to evolution
and adaptation. A sequestered germ line or Weismann barrier is specific to animals, and epigenetic
inheritance is expected to be far more common in plants and microbes. These effects may require
enhancements to the standard conceptual framework of the modern evolutionary synthesis.[35][36]
Epigenetic features may play a role in short-term adaptation of species by allowing for reversible
phenotype variability. The modification of epigenetic features associated with a region of DNA allows
organisms, on a multigenerational time scale, to switch between phenotypes that express and repress that
particular gene.[37] When the DNA sequence of the region is not mutated, this change is reversible. It has
also been speculated that organisms may take advantage of differential mutation rates associated with
epigenetic features to control the mutation rates of particular genes.[37] Interestingly, recent analysis have
suggested that members of the APOBEC family of cytosine deaminases are capable of simultaneously
mediating genetic and epigenetic inheritance using similar molecular mechanisms.[38]
Epigenetic changes have also been observed to occur in response to environmental exposure—for
example, mice given some dietary supplements have epigenetic changes affecting expression of the agouti
gene, which affects their fur color, weight, and propensity to develop cancer.[39][40]
More than 100 cases of transgenerational epigenetic inheritance phenomena have been reported in
a wide range of organisms, including prokaryotes, plants, and animals. [41]
[edit] Epigenetic effects in humans

[edit] Genomic imprinting and related disorders
Some human disorders are associated with genomic imprinting, a phenomenon in mammals where
the father and mother contribute different epigenetic patterns for specific genomic loci in their germ cells.[42]
The best-known case of imprinting in human disorders is that of Angelman syndrome and Prader-Willi
syndrome—both can be produced by the same genetic mutation, chromosome 15q partial deletion, and the
particular syndrome that will develop depends on whether the mutation is inherited from the child's mother or
from their father.[43] This is due to the presence of genomic imprinting in the region. Beckwith-Wiedemann
syndrome is also associated with genomic imprinting, often caused by abnormalities in maternal genomic
imprinting of a region on chromosome 11.
[edit] Transgenerational epigenetic observations

Marcus Pembrey and colleagues also observed in the Överkalix study that the paternal (but not
maternal) grandsons of Swedish boys who were exposed during preadolescence to famine in the 19th
century were less likely to die of cardiovascular disease; if food was plentiful then diabetes mortality in the
grandchildren increased, suggesting that this was a transgenerational epigenetic inheritance.[44] The
opposite effect was observed for females—the paternal (but not maternal) granddaughters of women who
experienced famine while in the womb (and their eggs were being formed) lived shorter lives on average.[45]
[edit] Cancer and developmental abnormalities

A variety of compounds are considered as epigenetic carcinogens—they result in an increased
incidence of tumors, but they do not show mutagen activity (toxic compounds or pathogens that cause
tumors incident to increased regeneration should also be excluded). Examples include diethylstilbestrol,
arsenite, hexachlorobenzene, and nickel compounds.
Many teratogens exert specific effects on the fetus by epigenetic mechanisms.[46][47] While
epigenetic effects may preserve the effect of a teratogen such as diethylstilbestrol throughout the life of an
affected child, the possibility of birth defects resulting from exposure of fathers or in second and succeeding
generations of offspring has generally been rejected on theoretical grounds and for lack of evidence.[48]
However, a range of male-mediated abnormalities have been demonstrated, and more are likely to exist.[49]
FDA label information for Vidaza(tm), a formulation of 5-azacitidine (an unmethylatable analog of cytidine
that causes hypomethylation when incorporated into DNA) states that "men should be advised not to father a
child" while using the drug, citing evidence in treated male mice of reduced fertility, increased embryo loss,
and abnormal embryo development. In rats, endocrine differences were observed in offspring of males
exposed to morphine.[50] In mice, second generation effects of diethylstilbesterol have been described
occurring by epigenetic mechanisms.[51]
Recent studies have shown that the Mixed Lineage Leukemia (MLL) gene causes leukemia by
rearranging and fusing with other genes in different chromosomes, which is a process under epigenetic
control.[52]
Other investigations have concluded that alterations in histone acetylation and DNA methylation
occur in various genes influencing prostate cancer.[53]
In 2008, the National Institutes of Health announced that $190 million had been earmarked for
epigenetics research over the next five years. In announcing the funding, government officials noted that
epigenetics has the potential to explain mechanisms of aging, human development, and the origins of
cancer, heart disease, mental illness, as well as several other conditions. Some investigators, like Randy
Jirtle, PhD, of Duke University Medical Center, think epigenetics may ultimately turn out to have a greater
role in disease than genetics.[54]
[edit] Cancer Treatment

Current research has shown that epigenetic pharmaceuticals could be a putative replacement or
adjuvant therapy for currently accepted treatment methods such as radiation and chemotherapy, or could
enhance the effects of these current treatments.[55] It has been shown that the epigenetic control of the
proto-onco regions and the tumor suppressor sequences by conformational changes in histones directly
affects the formation and progression of cancer [56] Epigenetics also has the factor of reversibility, a
characteristic that other cancer treatments do not offer.[53]
Drug development has mainly focused on Histone Acetyltransferase (HAT) and Histone Deactylase
(HDAC), including the introduction of the new pharmaceutical Vorinostat, a HDAC inhibitor, to the market.[57]
HDAC specifically has been shown to play an integral role in the progression of oral squamous cancer [56]
Current front-runner candidates for new drug targets are Histone Lysine Methyltransferases (KMT)
and Protein Arginine Methyltransferases (PRMT).[58]
[edit] Twin studies

Recent studies involving both dizygotic and monozygotic twins have produced some evidence of
epigenetic influence in humans.[59][60][61]
[edit] Epigenetics in microorganisms

Bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-
protein interactions. Bacteria make use of DNA adenine methylation (rather than DNA cytosine methylation)
as an epigenetic signal. DNA adenine methylation is important in bacteria virulence in organisms such as
Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria,
methylation of adenine regulates the cell cycle and couples gene transcription to DNA replication. In
Gammaproteobacteria, adenine methylation provides signals for DNA replication, chromosome segregation,
mismatch repair, packaging of bacteriophage, transposase activity and regulation of gene expression.[62][63]
The filamentous fungus Neurospora crassa is a prominent model system for understanding the
control and function of cytosine methylation. In this organisms, DNA methylation is associated with relics of a
genome defense system called RIP (repeat-induced point mutation) and silences gene expression by
inhibiting transcription elongation.[64]
The yeast prion PSI is generated by a conformational change of a translation termination factor,
which is then inherited by daughter cells. This can provide a survival advantage under adverse conditions.
This is an example of epigenetic regulation enabling unicellular organisms to respond rapidly to
environmental stress. Prions can be viewed as epigenetic agents capable of inducing a phenotypic change
without modification of the genome.[63]
[edit] See also

• B chromosome
• Epigenetic Theory
• Baldwin effect
• Centromere
• Computational epigenetics
• Dutch famine of 1944 (scientific legacy)
• Evolutionary developmental psychology
• Emergenesis
• Histone code
• Human genome
• Molecular biology
• Preformationism
• Somatic epitype
• Synthetic genetic array
• Weismann barrier
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18.^ Li, E; Beard C and Jaenisch R (December 1993). "Role for DNA methylation in genomic
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doi:10.1016/j.cell.2007.02.053. PMID 17512413.
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R236. doi:10.1016/j.cub.2007.02.030
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Gene Expression: A Hidden Layer of Complexity. Caister Academic Press. ISBN 978-1-904455-25-7.
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Evolution of Biology Oxford University Press, 2003. Cycles of Contingency: Developmental Systems
and Evolution |last=Oyama |first=Susan |coauthors=Paul E. Griffiths, Russell D. Gray |year=2001 |
publisher=MIT Press |isbn=0262650630 }}
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in Cell Biology 17 (3): 101–106. doi:10.1016/j.tcb.2006.12.005. PMID 17194589.
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35.^ Jablonka, Eva; Marion J. Lamb (2005). Evolution in Four Dimensions. MIT Press. ISBN 0-
262-10107-6.
36.^ See also Denis Noble The Music of Life see esp pp93-8 and p48 where he cites Jablonka &
Lamb and Massimo Pigliucci's review of Jablonka and Lamb in Nature 435, 565-566 (2 June 2005)
37.^ a b O.J. Rando and K.J. Verstrepen (2007). "Timescales of Genetic and Epigenetic
Inheritance". Cell 128 (4): 655–668. doi:10.1016/j.cell.2007.01.023. PMID 17320504.
38.^ Chahwan R., Wontakal S.N., and Roa S. (2010). "Crosstalk between genetic and
epigenetic information through cytosine deamination". Trends in Genetics 26 (10): 443–448.
doi:10.1016/j.tig.2010.07.005. PMID 20800313.
39.^ Cooney, CA, Dave, AA, and Wolff, GL (2002). "Maternal Methyl Supplements in Mice Affect
Epigenetic Variation and DNA Methylation of Offspring". Journal of Nutrition 132 (8 Suppl): 2393S–
2400S. PMID 12163699. available online
40.^ Waterland RA and Jirtle RL (August 2003). "Transposable elements: Targets for early
nutritional effects on epigenetic gene regulation". Molecular and Cellular Biology 23 (15): 5293–5300.
doi:10.1128/MCB.23.15.5293-5300.2003. PMID 12861015. PMC 165709.
http://mcb.asm.org/cgi/content/full/23/15/5293.
41.^ Jablonka, Eva; Gal Raz (June 2009). "Transgenerational Epigenetic Inheritance:
Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution". The Quarterly
Review of Biology 84 (2): 131–176. doi:10.1086/598822.
http://www.journals.uchicago.edu/doi/abs/10.1086/598822.
42.^ A.J. Wood and A.J. Oakey (2006). "Genomic imprinting in mammals: Emerging themes and
established theories". PLOS Genetics 2 (11): 1677–1685. doi:10.1371/journal.pgen.0020147.
PMID 17121465. available online
43.^ J.H.M. Knoll, R.D. Nicholls, R.E. Magenis, J.M. Graham Jr, M. Lalande, S.A. Latt (1989).
"Angelman and Prader-Willi syndromes share a common chromosome deletion but differ in parental
origin of the deletion". American Journal of Medical Genetics 32 (2): 285–290.
doi:10.1002/ajmg.1320320235. PMID 2564739.
44.^ Pembrey ME, Bygren LO, Kaati G, et al.. Sex-specific, male-line transgenerational
responses in humans. Eur J Hum Genet 2006; 14: 159-66. PMID 16391557. Robert Winston refers to
this study in a lecture; see also discussion at Leeds University, here
45.^ http://www.pbs.org/wgbh/nova/transcripts/3413_genes.html
46.^ Bishop, JB; Witt KL and Sloane RA (December 1997). "Genetic toxiticities of human
teratogens". Mutat Res 396 (1-2): 9–43. http://www.sciencedirect.com/science?
_ob=ArticleURL&_udi=B6T2C-3TGW0WR-
19&_coverDate=12%2F12%2F1997&_alid=515200131&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi
=4915&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=991625
903beeedc77a9455d6fa2382a9.
47.^ Gurvich, N; Berman MG, Wittner BS et al. (July 2004). "Association of valproate-induced
teratogenesis with histone deacetylase inhibition in vivo". FASEB J 19 (9): 1166–1168.
doi:10.1096/fj.04-3425fje. PMID 15901671. http://www.fasebj.org/cgi/reprint/04-3425fjev1.
48.^ Smithells, D (November 1998). "Does thalidomide cause second generation birth defects?".
Drug Saf 19 (5): 339–341. doi:10.2165/00002018-199819050-00001. PMID 9825947.
49.^ Friedler, G (December 1996). "Paternal exposures: impact on reproductive and
developmental outcome. An overview". Pharmacol Biochem Behav 55 (4): 691–700.
doi:10.1016/S0091-3057(96)00286-9. PMID 8981601.
50.^ Cicero, TJ; Adams NL, Giodarno A et al. (March 1991). "Influence of morphine exposure
during adolescence on the sexual maturation of male rats and the development of their offspring". J
Pharmacol Exp Ther. 256 (3): 1086–1093. PMID 2005573.
51.^ Newbold, RR; Padilla-Banks E and Jefferson WN (June 2006). "Adverse effects of the
model environmental estrogen diethylstilbestrol are transmitted to subsequent generations".
Endocrinology 147 (6 Suppl): S11–S17. doi:10.1210/en.2005-1164. PMID 16690809.
52.^ Mandall, SS (2010). "Mixed lineage leukemia: versatile player in epigenetics and human
disease". The FEBS Journal 227 (8): 1789. doi:10.1111/j.1742-4658.2010.07605.x.
PMID 20236314.
53.^ a b Li, LC; Carroll, PR; Dahiya, R (2005). "Epigenetic changes in prostate cancer:
implication for diagnosis and treatment". Journal of the National Cancer Institute 2 (97): 103–15.
doi:10.1093/jnci/dji010. PMID 15657340.
54.^ Beil, Laura (Winter, 2008). "Medicine's New Epicenter? Epigenetics: New field of
epigenetics may hold the secret to flipping cancer's "off" switch.". CURE (Cancer Updates, Research
and Education). http://www.curetoday.com/index.cfm/fuseaction/article.show/id/2/article_id/949.
55.^ Wang, LG; Chiao, JW (2010). "Prostate cancer chemopreventive activity of phenethyl
isothiocyanate through epigenetic regulation (review)". International Journal of Oncology 3 (37): 533–
9. PMID 20664922.
56.^ a b Iglesias-Linares, A; Yañez-Vico, RM; González-Moles, MA (2010). "Potential role of
HDAC inhibitors in cancer therapy: insights into oral squamous cell carcinoma". Oral Oncology 5
(46): 323–9. doi:10.1016/j.oraloncology.2010.01.009. PMID 20207580.
57.^ Spannhoff, A; Sippl, W; Jung, M (2009). "Cancer treatment of the future: Inhibitors of
histone methyltransferases". The International Journal of Biochemistry & Cell Biology 1 (41): 4–11.
doi:10.1016/j.biocel.2008.07.024. PMID 18773966.
58.^ "Toward the development of potent and selective bisubstrate inhibitors of protein arginine
methyltransferases". Bioorganic & Medicinal Chemistry Letters 7 (20): 2103–5.
doi:10.1016+pmid=20219369.
59.^ O'Connor, Anahad (2008-03-11). "The Claim: Identical Twins Have Identical DNA". New
York Times. http://www.nytimes.com/2008/03/11/health/11real.html. Retrieved 2010-05-02.
60.^ Kaminsky, Zachary A; Tang, T; Wang, SC; Ptak, C; Oh, GH; Wong, AH; Feldcamp, LA;
Virtanen, C et al. (2009). "DNA methylation profiles in monozygotic and dizygotic twins". Nature
Genetics 41 (2): 240–5. doi:10.1038/ng.286. PMID 19151718.
61.^ Fraga, M. F.; Ballestar, E; Paz, MF; Ropero, S; Setien, F; Ballestar, ML; Heine-Suñer, D;
Cigudosa, JC et al. (2005). "Epigenetic differences arise during the lifetime of monozygotic twins".
PMID 16009939. PMC 1174919. http://www.pnas.org/content/102/30/10604.full.
62.^ Casadesus J and Low D (September 2006). "Epigenetic Gene Regulation in the Bacterial
World". Microbiol Mol Biol Rev 70 (3): 830–856. doi:10.1128/MMBR.00016-06. PMID 16959970.
63.^ a b Tost J (editor). (2008). Epigenetics. Caister Academic Press. ISBN 978-1-904455-23-3 .
ISBN 1904455239. http://www.horizonpress.com/epi.
64.^ Genome Res. 2009. 19: 427-437/doi: 10.1101/gr.086231.108

• The Human Epigenome Project (HEP)
• The Epigenome Network of Excellence (NoE)
• The Epigenome Network of Excellence (NoE)- public international site
• DNA Is Not Destiny - Discover Magazine cover story
• BBC - Horizon - 2005 - The Ghost In Your Genes
• Epigenetics article at Hopkins Medicine
• Towards a global map of epigenetic variation
[hide]v · d · eGene expression
Introduction to General flow: DNA > RNA > Protein

genetics
special transfers (RNA > RNA, RNA > DNA, Protein > Protein)
Genetic code
(Transcription factors, RNA Polymerase,promoter) Prokaryotic /

Archaeal / Eukaryotic
Transcription
post-transcriptional modification (hnRNA,5'
capping,Splicing,Polyadenylation)
(Ribosome,tRNA) Prokaryotic / Archaeal / Eukaryotic

Translation
post-translational modification (functional groups, peptides, structural
changes)
epigenetic regulation (Genomic imprinting)

transcriptional regulation
Gene regulation post-transcriptional regulation (sequestration, alternative splicing,
miRNA)
translational regulation
post-translational regulation (reversible, irreversible)


phenotype
Non-genetic
Developmental

[hide]v · d · eMolecular biology
Computational biology • Developmental biology • Functional Biology
History of molecular biology • DNA Replication (DNA),

Dogma
Transcription (RNA) - Translation (protein)
(Genetic • Heredity)
Promoter (Pribnow box, TATA box) • Operon (gal operon, lac
Overview Element operon, trp operon) • Intron • Exon • Terminator • Enhancer •
Repressor (lac repressor, trp repressor) • Silencer • Histone
methylation
Linked Cell Biology • Biochemistry • Computational Biology •

Life Genetics
Engineering mitosis • cell signalling • Post-transcriptional

Concept modification and Post-translational modification • Dry Lab/Wet
lab
Cell culture • model organisms (such as C57BL/6
mice) • method (Nucleic acid • Protein) • Fluorescence, Pigment
& Radioactivity
Technique
High-throughput Technique (-omics): DNA
microarray • Mass spectrometry • Lab-on-a-chip
Gene Epigenetic • genetic • post-transcriptional • post-

regulation translational regulation
Glossary
Retrieved from "http://en.wikipedia.org/wiki/Epigenetics"
Categories: Epigenetics | Genetic mapping

W000
Maternal effect

This article concerns the legitimate scientific concept of genes that are expressed only when
carried by the female parent. It is not to be confused with the generally discredited theory of maternal
impression.
A maternal effect is a situation where the phenotype of an organism is determined not only by the
environment it experiences and its genotype, but also by the environment and phenotype of its mother. In
genetics, maternal effects occur when an organism shows the phenotype expected from the genotype of the
mother, irrespective of its own genotype, often due to the mother supplying mRNA or proteins to the egg.
Maternal effects can also be caused by the maternal environment independent of genotype, sometimes
controlling the size, sex, or behaviour of the offspring. It has been proposed that maternal effects are
important for the evolution of adaptive responses to environmental heterogeneity.
Contents
[hide]
• 1 Maternal effects in genetics
• 1.1 Example: maternal effect genes in Drosophila
early embryogenesis
• 2 Environmental maternal effects
• 3 Paternal effect genes
• 4 See also
• 5 References
[edit] Maternal effects in genetics

In genetics, a maternal effect occurs when the phenotype of an organism is determined by the
genotype of its mother.[1] For example, if a mutation is maternal effect recessive, then a female homozygous
for the mutation may appear phenotypically normal, however her offspring will show the mutant phenotype,
even if they are heterozygous for the mutation.
Genetic crosses involving a maternal effect recessive mutation, m. The maternal genotype
determines the phenotype of the offspring.
Maternal effect
All offspring show the wild-type phenotype All offspring show the muta
Maternal effects often occur because the mother supplies a particular mRNA or protein to the oocyte,
hence the maternal genome determines whether the molecule is functional. Maternal supply of mRNAs to the
early embryo is important, as in many organisms the embryo is initially transcriptionally inactive.[2] Because
of the inheritance pattern of maternal effect mutations, special genetic screens are required to identify them.
These typically involve examining the phenotype of the organisms one generation later than in a
conventional (zygotic) screen, as their mothers will be potentially homozygous for maternal effect mutations
that arise.[3][4]
[edit] Example: maternal effect genes in Drosophila early embryogenesis
Protein and RNA are transported in particles (white dots) from the nurse cells (maternal) to the
developing oocyte in Drosophila melanogaster. Scale bar shows 10µm.
For more details on the role of the maternal effect genes, see Drosophila embryogenesis.
A Drosophila melanogaster oocyte develops in an egg chamber in close association with a set of
cells called nurse cells. Both the oocyte and the nurse cells are descended from a single germline stem cell,
however cytokinesis is incomplete in these cell divisions, and the cytoplasm of the nurse cells and the oocyte
is connected by structures known as ring canals.[5] Only the oocyte undergoes meiosis and contributes DNA
to the next generation.
Many maternal effect Drosophila mutants have been found that affect the early steps in
embryogenesis such as axis determination, including bicoid, dorsal, gurken and oskar.[6][7][8] For example,
embryos from homozygous bicoid mothers fail to produce head and thorax structures.
Once the gene that is disrupted in the bicoid mutant was identified, it was shown that bicoid mRNA is
transcribed in the nurse cells and then relocalized to the oocyte.[9]. Other maternal effect mutants either
affect products that are similarly produced in the nurse cells and act in the oocyte, or parts of the
transportation machinery that are required for this relocalization.[10] Since these genes are expressed in the
(maternal) nurse cells and not in the oocyte or fertilised embryo, the maternal genotype determines whether
they can function.
[edit] Environmental maternal effects

The environment or condition of the mother can also in some situations influence the phenotype of
her offspring, independent of the offspring's genotype.
[edit] Paternal effect genes

In contrast, a paternal effect is when a phenotype results from the genotype of the father, rather than
the genotype of the individual.[11] The genes responsible for these effects are components of sperm that are
involved in fertilization and early development.[12] An example of a paternal-effect gene is the ms(3)sneaky
in Drosophila, males with a mutant allele of this gene produce sperm that are able to fertilize an egg, but the
snky-inseminated eggs do not develop normally. However, females with this mutation produce eggs that
undergo normal development when fertilized.[13]
[edit] See also
• Maternal effect dominant embryonic arrest
[edit] References
1. ^ Griffiths, Anthony J. F. (1999). An Introduction to genetic analysis. New York: W.H.
Freeman. ISBN 071673771X. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?
highlight=maternal,effect&rid=iga.section.3739#3740.
2. ^ Schier AF (April 2007). "The maternal-zygotic transition: death and birth of RNAs". Science
316 (5823): 406–7. doi:10.1126/science.1140693. PMID 17446392.
3. ^ Jorgensen EM, Mango SE (May 2002). "The art and design of genetic screens:
Caenorhabditis elegans". Nat. Rev. Genet. 3 (5): 356–69. doi:10.1038/nrg794. PMID 11988761.
4. ^ St Johnston D (March 2002). "The art and design of genetic screens: Drosophila
melanogaster". Nat. Rev. Genet. 3 (3): 176–88. doi:10.1038/nrg751. PMID 11972155.
5. ^ Bastock R, St Johnston D (December 2008). "Drosophila oogenesis". Curr. Biol. 18 (23):
R1082–7. doi:10.1016/j.cub.2008.09.011. PMID 19081037.
6. ^ Nüsslein-Volhard C, Lohs-Schardin M, Sander K, Cremer C (January 1980). "A dorso-
ventral shift of embryonic primordia in a new maternal-effect mutant of Drosophila". Nature 283
(5746): 474–6. doi:10.1038/283474a0. PMID 6766208.
7. ^ Schüpbach T, Wieschaus E (February 1986). "Germline autonomy of maternal-effect
mutations altering the embryonic body pattern of Drosophila". Dev. Biol. 113 (2): 443–8.
doi:10.1016/0012-1606(86)90179-X. PMID 3081391.
8. ^ Nüsslein-Volhard C, Frohnhöfer HG, Lehmann R (December 1987). "Determination of
anteroposterior polarity in Drosophila". Science 238 (4834): 1675–81. doi:10.1126/science.3686007.
PMID 3686007.
9. ^ Berleth T, Burri M, Thoma G, et al. (June 1988). "The role of localization of bicoid RNA in
organizing the anterior pattern of the Drosophila embryo". EMBO J. 7 (6): 1749–56. PMID 2901954.
10.^ Ephrussi A, St Johnston D (January 2004). "Seeing is believing: the Bicoid morphogen
gradient matures". Cell 116 (2): 143–52. doi:10.1016/S0092-8674(04)00037-6. PMID 14744427.
11.^ Yasuda GK, Schubiger G, Wakimoto BT (1 May 1995). "Genetic characterization of ms (3)
K81, a paternal effect gene of Drosophila melanogaster". Genetics 140 (1): 219–29. PMID 7635287.
PMC 1206549. http://www.genetics.org/cgi/reprint/140/1/219.
12.^ Fitch KR, Yasuda GK, Owens KN, Wakimoto BT (1998). "Paternal effects in Drosophila:
implications for mechanisms of early development". Curr. Top. Dev. Biol. 38: 1–34.
doi:10.1016/S0070-2153(08)60243-4. PMID 9399075.
13.^ Fitch KR, Wakimoto BT (1998). "The paternal effect gene ms(3)sneaky is required for
sperm activation and the initiation of embryogenesis in Drosophila melanogaster". Dev. Biol. 197 (2):
270–82. doi:10.1006/dbio.1997.8852. PMID 9630751.


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Maternal_effect"
Categories: Developmental biology | Ecology | Evolutionary biology | Genetics

W000
Dual inheritance theory


Dual inheritance theory (DIT), also known as gene-culture coevolution, was developed in the late
1970s and early 1980s to explain how human behavior is a product of two different and interacting
evolutionary processes: genetic evolution and cultural evolution. DIT is a "middle-ground" between much of
social science, which views culture as the primary cause of human behavioral variation, and human
sociobiology and evolutionary psychology which view culture as an insignificant by-product of genetic
selection.[1] In DIT, culture is defined as information in human brains that got there by social learning.
Cultural evolution is considered a Darwinian selection process that acts on cultural information. Dual
Inheritance Theorists often describe this by analogy to genetic evolution, which is a Darwinian selection
process acting on genetic information.[2]
Because genetic evolution is relatively well understood, most of DIT examines cultural evolution and
the interactions between cultural evolution and genetic evolution.
Contents
[hide]
• 1 Theoretical basis
• 1.1 Culture capacities are adaptations
• 1.2 Culture evolves
• 1.3 Genes and culture coevolve
• 2 View of culture
• 3 Genetic influence on cultural evolution
• 4 Cultural influences on genetic evolution
• 5 Mechanisms of cultural evolution
• 5.1 Natural selection
• 5.2 Random variation
• 5.3 Cultural drift
• 5.4 Guided variation
• 5.5 Biased transmission
• 5.5.1 Content bias
• 5.5.2 Context bias
• 5.5.2.1 Model-based biases
• 5.5.2.2 Frequency-dependent
biases
• 6 Social learning and cumulative cultural evolution
• 7 Cultural group selection
[edit] Theoretical basis
DIT holds that genetic and cultural evolution interact in the evolution of Homo sapiens. DIT
recognizes that the natural selection of genotypes is an important component of the evolution of human
behavior and that cultural traits can be constrained by genetic imperatives. However, DIT also recognizes
that genetic evolution has endowed the human species with a parallel evolutionary process of cultural
evolution. DIT makes three main claims:[3]
[edit] Culture capacities are adaptations

The human capacity to store and transmit culture arose from genetically evolved psychological
mechanisms. This implies that at some point during the evolution of the human species a type of social
learning leading to cumulative cultural evolution was evolutionarily advantageous.
[edit] Culture evolves

Social learning processes give rise to cultural evolution. Cultural traits are transmitted differently than
genetic traits and, therefore, result in different population-level effects. These effects can help explain human
behavioral variation.
[edit] Genes and culture coevolve

Cultural traits alter the social and physical environments under which genetic selection operates. For
example, the cultural adoptions of agriculture and dairying have, in humans, caused genetic selection for the
traits to digest starch and lactose, respectively.[4][5][6][7][8][9] As another example, it is likely that once
culture became adaptive, genetic selection caused a refinement of the cognitive architecture that stores and
transmits cultural information. This refinement may have further influenced the way culture is stored and the
biases that govern its transmission.
DIT also predicts that, under certain situations, cultural evolution may select for traits that are
genetically maladaptive. An example of this is the demographic transition, which describes the fall of birth
rates within industrialized societies. Dual Inheritance Theorists hypothesize that the demographic transition
may be a result of a prestige bias, where individuals that forgo reproduction to gain more influence in
industrial societies are more likely to be chosen as cultural models.[10][11]
[edit] View of culture

People have defined the word "culture" to describe a large set of different phenomena.[12][13] A
definition that sums up what is meant by "culture" in DIT is:
Culture is information stored in individuals' brains that is capable of affecting behavior and that
got there through social learning.[14][15]
This view of culture emphasizes population thinking by focusing on the process by which culture is
generated and maintained. It also views culture as a dynamic property of individuals, as opposed to the more
standard social science view of culture as a superorganic entity to which individuals must conform.[16] This
view's main advantage is that it connects individual-level processes to population-level outcomes.[17]
[edit] Genetic influence on cultural evolution

Genes have an impact on cultural evolution via psychological predispositions on cultural learning.
Genes encode much of the information needed to form the human brain. Genes constrain the brain's
structure and, hence, the ability of the brain to acquire and store culture. Genes may also endow individuals
with certain types of transmission bias (described below).
[edit] Cultural influences on genetic evolution

Culture can profoundly influence gene frequencies in a population. One of the best known examples
is the prevalence of the genotype for adult lactose absorption in human populations, such as Northern
Europeans and some African societies, with a long history of raising cattle for milk. Other societies such as
East Asians and Amerindians, retain the typical mammalian genotype in which the body shuts down lactase
production shortly after the normal age of weaning. This implies that the cultural practice of raising cattle for
milk led to a selection for genetic traits for lactose digestion.[18] Recently, analysis of natural selection on the
human genome suggests that civilization has accelerated genetic change in humans over the past 10,000
years.[19]
[edit] Mechanisms of cultural evolution

In DIT, the evolution and maintenance of cultures is described by five major mechanisms, natural
selection of cultural variants, random variation, cultural drift, guided variation and transmission bias.
[edit] Natural selection

Cultural differences among individuals can lead to differential survival of individuals, with those that
survive more likely to have their cultural variants adopted by others. The patterns of this selective process
depend on transmission biases and can result in behavior that is more adaptive to a given environment.
[edit] Random variation
Random variation arises from errors in the learning, display or recall of cultural information.
[edit] Cultural drift

Cultural drift is a process roughly analogous to genetic drift in evolutionary biology.[20] In cultural
drift, the frequency of cultural traits in a population may be subject to random fluctuations due to chance
variations in which traits are observed and transmitted (sometimes called "sampling error").[21] These
fluctuations might cause cultural variants to disappear from a population. This effect should be especially
strong in small populations.[22]
An example of cultural drift would be dialects of song birds. If a group of songbirds are culturally split
(viz, no interactions with their songs), then distinct dialects will form from the original mating songs of the
male birds. This is thought to happen due to errors in songbird singing and acquisition by successive
generations, which, while still functional, do not maintain fidelity with the original song of the first generation.
[23]
[edit] Guided variation

Cultural traits may be gained in a population through the process of individual learning. Once an
individual learns a novel trait, it can be transmitted to other members of the population. The process of
guided variation depends on an adaptive standard that determines what cultural variants are learned.
[edit] Biased transmission
Understanding the different ways that culture traits can be transmitted between individuals has been
an important part of DIT research since the 1970s.[24][25] Transmission biases occur when some cultural
variants are favored over others during the process of cultural transmission.[26] Boyd and Richerson (1985)
[27] defined and analytically modeled a number of possible transmission biases. The list of biases has been
refined over the years, especially by Henrich and McElreath.[28]
[edit] Content bias

Content biases result from situations where some aspect of a cultural variant's content makes them
more likely to be adopted.[29] Content biases can result from genetic preferences, preferences determined
by existing cultural traits, or a combination of the two. For example, food preferences can result from genetic
preferences for sugary or fatty foods and socially-learned eating practices and taboos.[30] Content biases
are sometimes called "direct biases."[31]
[edit] Context bias

Context biases result from individuals using clues about the social structure of their population to
determine what cultural variants to adopt. This determination is made without reference to the content of the
variant. There are two major categories of context biases: (1) model-based biases, and (2) frequency-
dependent biases.
[edit] Model-based biases

Model-based biases result when an individual is biased to choose a particular "cultural model" to
imitate. There are four major categories of model-based biases: (1) prestige bias, (2) skill bias, (3) success
bias, (4) similarity bias.[32][33] A "prestige bias" results when individuals are more likely to imitate cultural
models that are seen as having more prestige. A measure of prestige could be the amount of deference
shown to a potential cultural model by other individuals. A "skill bias" results when individuals can directly
observe different cultural models performing a learned skill and are more likely to imitate cultural models that
perform better at the specific skill. A "success bias" results from individuals preferentially imitating cultural
models that they determine are most generally successful (as opposed to successful at a specific skill as in
the skill bias.) A "similarity bias" results when individuals are more likely to imitate cultural models that are
perceived as being similar to the individual based on specific traits.
[edit] Frequency-dependent biases

Frequency-dependent biases result when an individual is biased to choose particular cultural variants
based on their perceived frequency in the population. The most explored frequency-dependent bias is the
"conformity bias." Conformity biases result when individuals attempt to copy the mean or the mode cultural
variant in the population. Another possible frequency dependent bias is the "rarity bias." The rarity bias
results when individuals preferentially choose cultural variants that are less common in the population. The
rarity bias is also sometimes called a "nonconformist bias".
[edit] Social learning and cumulative cultural evolution

In DIT, the evolution of culture is dependent on the evolution of social learning. Analytic models show
that social learning becomes evolutionarily beneficial when the environment changes with enough frequency
that genetic inheritance can not track the changes, but not fast enough that individual learning is more
efficient.[34] While other species have social learning, and thus some level of culture, only humans, some
birds and chimpanzees are known to have cumulative culture.[35] Boyd and Richerson argue that the
evolution of cumulative culture depends on observational learning and is uncommon in other species
because it is ineffective when it is rare in a population. They propose that the environmental changes
occurring in the Pleistocene may have provided the right environmental conditions.[36] Michael Tomasello
argues that cumulative cultural evolution results from a "ratchet effect" that began when humans developed
the cognitive architecture to understand others as mental agents.[37] Furthermore Tomasello proposed in the
80s that there are some disparities between the observational learning mechanisms found in humans and
great apes - which go some way to explain the observable difference between great ape traditions and
human types of culture (see Emulation (observational learning)).
[edit] Cultural group selection

Although group selection is commonly thought to be nonexistent or unimportant in genetic evolution,
[38][39][40] DIT predicts that, due to the nature of cultural inheritance, it may be an important force in cultural
evolution. The reason group selection is thought to operate in cultural evolution is because of conformist
biases (see above section on transmission biases). Conformist biases make it difficult for novel cultural traits
to spread through a population. Conformist bias also helps maintain variation between groups. These two
properties, rare in genetic transmission, are necessary for group selection to operate.[41] Based on an earlier
model by Cavalli-Sforza and Feldman,[42] Boyd and Richerson show that conformist biases are almost
inevitable when traits spread through social learning,[43] implying that group selection is common in cultural
evolution. Analysis of small groups in New Guinea imply that cultural group selection might be a good
explanation for slowly changing aspects of social structure, but not for rapidly changing fads.[44] The ability
of cultural evolution to maintain intergroup diversity is what allows for the study of cultural phylogenetics.[45]
The idea that human cultures undergo a similar evolutionary process as genetic evolution goes back
at least to Darwin[46] In the 1960s, Donald T. Campbell published some of the first theoretical work that
adapted principles of evolutionary theory to the evolution of cultures.[47] In 1976, two developments in
cultural evolutionary theory set the stage for DIT. In that year Richard Dawkins's The Selfish Gene introduced
ideas of cultural evolution to a popular audience. Although one of the best-selling science books of all time,
because of its lack of mathematical rigor, it had little impact on the development of DIT. Also in 1976,
geneticists Marcus Feldman and Luigi Luca Cavalli-Sforza published the first dynamic models of gene-
culture coevolution.[48] These models were to form the basis for subsequent work on DIT, heralded by the
publication of three seminal books in 1980 and 1981.
The first was Charles Lumsden and E.O. Wilson's Genes, Mind and Culture.[49] This book outlined a
series of mathematical models of how genetic evolution might favor the selection of cultural traits and how
cultural traits might, in turn, affect the speed of genetic evolution. While it was the first book published
describing how genes and culture might coevolve, it had relatively little impact on the further development of
DIT.[50] Some critics felt that their models depended too heavily on genetic mechanisms at the expense of
cultural mechanisms.[51] Controversy surrounding Wilson's sociobiological theories may also have
decreased the lasting impact of this book.[52]
The second 1981 book was Cavalli-Sforza and Feldman's Cultural Transmission and Evolution: A
Quantitative Approach.[53] Borrowing heavily from population genetics and epidemiology, this book built a
mathematical theory concerning the spread of cultural traits. It describes the evolutionary implications of
vertical transmission, passing cultural traits from parents to offspring; oblique transmission, passing cultural
traits from any member of an older generation to a younger generation; and horizontal transmission, passing
traits between members of the same population.
The next significant DIT publication was Robert Boyd and Peter Richerson's 1985 Culture and the
Evolutionary Process.[54] This book presents the now-standard mathematical models the evolution of social
learning under different environmental conditions, the population effects of social learning, various forces of
selection on cultural learning rules, different forms of biased transmission and their population-level effects,
and conflicts between cultural and genetic evolution. The book's conclusion also outlined areas for future
research that are still relevant today.
[edit] Current and future research

In their 1985 book, Boyd and Richerson outlined an agenda for future DIT research. This agenda,
outlined below, called for the development of both theoretical models and empirical research. DIT has since
built a rich tradition of theoretical models over the past two decades.[55] However, there has not been a
comparable level of empirical work.
In a 2006 interview Harvard biologist E.O. Wilson expressed disappointment at the little attention
afforded to DIT:
"...for some reason I haven't fully fathomed, this most promising frontier of scientific research
has attracted very few people and very little effort." [56]
Kevin Laland and Gillian Brown attribute this lack of attention to DIT's heavy reliance on formal
modeling, which doesn't attract the media attention of less rigorous approaches to human behavioral
evolution, such as evolutionary psychology:
"In many ways the most complex and potentially rewarding of all approaches, [DIT], with its
multiple processes and cerebral onslaught of sigmas and deltas, may appear too abstract to all
but the most enthusiastic reader. Until such a time as the theoretical hieroglyphics can be
translated into a respectable empirical science most observers will remain immune to its
message."[57]
Economist Herbert Gintis disagrees with this critique, citing existing empirical work as well as more
recent work using techniques from behavioral economics.[58] These behavioral economic techniques have
been adapted to test predictions of cultural evolutionary models in laboratory settings [59][60][61] as well as
studying differences in cooperation in fifteen small-scale societies in the field.[62]
Since one of the goals of DIT is to explain the distribution of human cultural traits, ethnographic and
ethnologic techniques may also be useful for testing hypothesis stemming from DIT. Although findings from
traditional ethnologic studies have been used to buttress DIT arguments,[63][64] thus far there have been
little ethnographic fieldwork designed to explicitly test these hypotheses.[65][66][67] A major difficulty in using
existing ethnographic data to test DIT is that, due to cultural anthropology's assumption of culture as a
superorganic entity, ethnographic data tends to ignore individual and intragroup cultural variation and focus
almost entirely on intergroup variation.
DIT has been viewed as having great potential for unifying diverse academic fields under one
overarching theory. Mesoudi, et al. have identified DIT as the ideal way to build a comprehensive theory of
cultural evolution to answer questions about human behavior at different temporal and spacial scales.[68]
Along with game theory, Herb Gintis has named DIT one of the two major conceptual theories with potential
for unifying the behavioral sciences, including economics, biology, anthropology, sociology, psychology and
political science. Because it addresses both the genetic and cultural components of human inheritance,
Gintis sees DIT models as providing the best explanations for the ultimate cause of human behavior and the
best paradigm for integrating those disciplines with evolutionary theory.[69] In a review of competing
evolutionary perspectives on human behavior, Laland and Brown see DIT as the best candidate for uniting
the other evolutionary perspectives under one theoretical umbrella.[70]
[edit] Relation to other fields

[edit] Sociology and cultural anthropology
Two major topics of study in both sociology and cultural anthropology are human cultures and
cultural variation. However, Dual Inheritance theorists charge that both disciplines too often treat culture as a
static superorganic entity that dictates human behavior.[71][72] Cultures are defined by a suite of common
traits shared by a large group of people, without regard to variation in cultural traits at the individual level.
This is in sharp contrast to DIT, which models human culture at the individual level and views culture as the
result of a dynamic evolutionary process at the population level.[73][74]
[edit] Human sociobiology and evolutionary psychology

Human sociobiologists and evolutionary psychologists try to understand how maximizing genetic
fitness, in either the modern era or past environments, can explain human behavior. To the human
sociobiologist and evolutionary psychologist, culture is either trivial or so bound by genetic fitness that it is
unimportant. When faced with a common and seemingly maladaptive trait, practitioners from these
disciplines try to determine how the trait actually increases genetic fitness (maybe through kin selection or by
speculating about early evolutionary environments). Dual Inheritance theorists, in contrast, will consider a
variety of genetic and cultural processes in addition to natural selection on genes.
[edit] Human behavioral ecology
Human behavioral ecology (HBE) and DIT have a similar relationship to what ecology and
evolutionary biology have in the biological sciences. HBE is more concerned about ecological process and
DIT more focused on historical process. One difference is that human behavioral ecologists often assume
that culture is a system that produces the most adaptive outcome in a given environment. This implies that
similar behavioral traditions should be found in similar environments. However, this is not always the case. A
study of African cultures showed that cultural history was a better predictor of cultural traits than local
ecological conditions.[75]
[edit] Memetics
Memetics, which comes from the meme idea described in Dawkins's The Selfish Gene, is similar to
DIT in that it treats culture as an evolutionary process that is distinct from genetic transmission. However,
there are some philosophical differences between memetics and DIT.[76] One difference is that memetics'
focus is on the selection potential of discrete replicators (memes), where DIT allows for transmission of both
non-replicators and non-discrete cultural variants. DIT does not assume that replicators are necessary for
cumulative adaptive evolution. DIT also more strongly emphasizes the role of genetic inheritance in shaping
the capacity for cultural evolution. But perhaps the biggest difference is a difference in academic lineage.
Memetics as a label is more influential in popular culture than in academia. Critics of memetics argue that it is
lacking in empirical support or is conceptually ill-founded, and question whether there is hope for the memetic
research program succeeding. Proponents point out that many cultural traits are discrete, and that many
existing models of cultural inheritance assume discrete cultural units, and hence involve memes.[77]
[edit] See also
• Nature versus nurture
• Adaptive bias
• Cultural selection theory
• Memetics
[edit] References
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2. ^ Not By Genes Alone: How Culture Transformed Human Evolution . Chicago: University of
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3. ^ McElreath, R. & Henrich, J. 2007. Dual inheritance theory: the evolution of human cultural
capacities and cultural evolution. In R. Dunbar and L. Barrett, (Eds.), Oxford Handbook of
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4. ^ Simoons, F. 1969. Primary adult lactose intolerance and the milking habit: A problem in
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5. ^ Simoons, F. 1970. Primary adult lactose intolerance and the milking habit: A problem in
biologic and cultural interrelations: II. A culture historical hypothesis. The American Journal of
Digestive Diseases 15:695-710.
6. ^ Cavalli-SFornza, L., P. Menozzi and A. Piazza. 1994. The history and geography of human
genes Princeton: Princeton University Press
7. ^ Holden, C. and R. Mace. 1997. Phylogenetic analysis of the evolution of lactose digestion
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8. ^ Durham, W. 1991. Coevolution: Genes, culture and human diversity. Stanford: Stanford
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11.^ Richerson, P. J. and R. Boyd. 2005. Not By Genes Alone: How Culture Transformed
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12.^ Kroeberm A. and C. Kluckhohn. 1952. Culture; A Critical Review of Concepts and
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13.^ Fox, R. and B. King. 2002. Anthropology Beyond Culture Oxford: Berg.
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Evolution Chicago: University of Chicago Press. pg 6.
15.^ Boyd, R. and P. Richerson. 2000. Memes: Universal Acid or a Better Mouse Trap? In R.
Aunger, Ed. Darwinizing Culture: The Status of Memetics as a Science. Oxford: Oxford University
Press. pp. 143-162. Full text
16.^ Richerson, P.J. and R. Boyd. 2001. Culture is Part of Human Biology: Why the
Superorganic Concept Serves the Human Sciences Badly. In Science Studies: Probing the
Dynamics of Scientific Knowledge, In S. Maasen and M. Winterhager, Ed. Bielefeld: Verlag.[1]
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18.^ Laland, K. N. and G. R. Brown. 2002. Sense & Nonsense: Evolutionary Perspectives on
Human Behavior. Oxford: Oxford University Press. pg. 260
19.^ Cochran, G. and H. Harpending. 2009. The 10,000 Year Explosion: How Civilization
Accelerated Human Evolution. Basic Books.
20.^ Bentley, R.A., M.W. Hahn and S.J. Shennan. 2004. Random drift and culture change.
Proceedings of the Royal Society B 271: 1443-1450. Full text
21.^ Hahn, M.W. and R. A. Bentley. 2003. Drift as a mechanism for cultural change: An example
from baby names. Proceedings of the Royal Society B 271: S353-S356. Full text
University of Chicago Press. pp.9, 69
23.^ P.J.B. Slater, V.M. Janik. Vocal Learning. In "Encyclopedia of Animal Behavior", 2010,
Pages 551-557. http://www.sciencedirect.com/science/referenceworks/9780080453378
24.^ Feldman, M. and L. Cavalli-Sfornza. 1976. Cultural and biological evolutionary processes,
selection for a trait under complex transmission. Theoretical Population Biology 9: 238-259.
25.^ Feldman, M and L. Cavalli-Sfornza. 1977. The evolution of continuous variation: II, complex
transmission and assortive mating. Theoretical Population Biology 11:161-181.
26.^ Boyd, R., and P. Richerson. 1985. Culture and the Evolutionary Process . Chicago: The
University of Chicago Press.
28.^ "The Evolution of Cultural Evolution". Evolutionary Anthropology (12): 123–135. 2003.
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%20inheritance%20theorypdf'.
29.^ Henrich, J. and R. McElreath. 2007. Dual inheritance theory: the evolution of human
cultural capacities and cultural evolution. Oxford Handbook of Evolutionary Psychology, R. Dunbar
and L. Barrett, eds., Ch. 38. Oxford: Oxford Univ Press.
30.^ Henrich, J. and R. McElreath. 2007. Dual inheritance theory: the evolution of human
cultural capacities and cultural evolution. Oxford Handbook of Evolutionary Psychology, R. Dunbar
and L. Barrett, eds., Ch. 38. Oxford: Oxford Univ Press.
32.^ Henrich, J. and R. McElreath. 2003. The evolution of cultural evolution. Evolutionary
Anthropology 12:123-135.
33.^ McElreath, R. & Henrich, J. 2007. Dual inheritance theory: the evolution of human cultural
34.^ Richerson, P.J. and R. Boyd. 2000. Climate, culture, and the evolution of cognition. In C.M.
Heyes and L. Huber, (Eds), The Evolution of Cognition. Massachusetts: MIT Press.
35.^ Tomasello, M. 1999. The Cultural Origins of Human Cognition. Cambridge, Massachusetts:
36.^ Richerson, P. J. and R. Boyd. 2000. The Pleistocene and the origins of human culture: built
for speed. Perspectives in Ethology 13:1-45, 2000.
37.^ Tomasello, M. 1999. The Cultural Origins of Human Cognition. Cambridge, MA: Harvard
University Press.
38.^ Williams, G.C. 1972. Adaptation and Natural Selection: A Critique of Some Current
Evolutionary Thought. Princeton: Princeton University Press. ISBN 0-691-02357-3
39.^ Williams, G.C.. 1986. Evolution Through Group Selection. Blackwell. ISBN 0-632-01541-1
40.^ Maynard Smith, J.. 1964. Group selection and kin selection 'Nature' 201:1145–1147
41.^ Uyenoyama, M. and M. W. Feldman. 1980. Theories of kin and group selection: a
population genetics perspective. Theoretical Population Biology 17:380-414.
42.^ Cavalli-Sforza, L. L. and M. W. Feldman. 1973. Models for cultural inheritance. I. Group
mean and within group variation. Theoretical Population Biology 4:42-44.
University of Chicago Press. pg. 227-240.
44.^ Soltis, J., Boyd, R. and P. J. Richerson. 1995. Can group-functional behaviors evolve by
cultural group selection? An empirical test Current Anthropology 36:473-494
45.^ Mace, R., C. Holden, and S. Shennan (Eds.) 2005. The evolution of cultural diversity: a
phylogenetic approach. London:University College London Press.
46.^ Darwin, C. 1874. The descent of man and selection in relation to sex. 2nd ed. 2 vols. New
York: American Home Library.
47.^ Campbell, D. 1965. Variation and selective retention in socio-cultural evolution. In Social
change in developing areas: A reinterpretation of evolutionary theory , ed. H. Barringer, G. Blanksten,
and R. Mack, 19-49. Cambridge, MA: Schenkman Publishing Company.
48.^ Feldman, M. and Cavalli-Sforna L. 1976. Cultural and biological evolutionary processes,
selection for a trait under complex transmission. Theoretical Population Biology, 9:238-59.
49.^ Lumsden C., and E. Wilson. 1981. Genes, Mind and Culture: The Coevolutionary Process.
Cambridge, MA: Harvard University Press.
50.^ Laland K. and G. Brown. 2002. Sense and Nonsense: Evolutionary Perspectives on
Human Behavior. Oxford: Oxford University Press.
51.^ Boyd, R. and Richardson, P. 1983. The cultural transmission of acquired variation: effects
on genetic fitness. Journal of Theoretical Biology 100:567-96.
52.^ Laland K. and G. Brown. 2002. Sense and Nonsense: Evolutionary Perspectives on
53.^ Cavalli-Sfornza, L. and M. Feldman. 1981. Cultural Transmission and Evolution: A
Quantitative Approach. Princeton, New Jersey: Princeton University Press.
55.^ Boyd, R. and P. J. Richerson. 2005. The Origin and Evolution of Cultures . Oxford: Oxford
University Press. pg. 294-299.
56.^ Haag, Allison. 2006. The synthesizer. SEED, 2(7): 46.
Human Behavior. Oxford: Oxford University Press. pg 290.
58.^ Herb Gintis Amazon.com review: http://www.amazon.com/review/product/0198508840/
59.^ McElreath, R., M. Lubell, P. J. Richerson, T. M. Waring, W. Baum, E. Edsten, C. Efferson,
and B. Paciotti. 2005. Applying formal models to the laboratory study of social learning: The impact of
task difficulty and environmental fluctuation. Evolution and Human Behavior 26: 483-508.
60.^ Efferson, C, R. Lalive, P. J. Richerson, R. McElreath, and M. Lubell. Conformists and
mavericks in the lab: The structure of frequency-dependent social learning. Evolution and Human
Behavior (in press).
61.^ Baum, W. M., P. J. Richerson, C. M. Efferson, B. M. Paciotti. 2004. Cultural evolution in
laboratory micro-societies including traditions of rule-giving and rule-following. Evolution and Human
Behavior 25: 305-326. 2004.
62.^ Henrich, J., R. Boyd, S. Bowles, C. Camerer, E. Fehr, H. Gintis (Eds). 2004. Foundations
of Human Sociality: Economic Experiments and Ethnographic Evidence from Fifteen Small-Scale
Societies Oxford: Oxford University Press.
63.^ Cavalli-Sfornza, L. L. and M. Feldman. 1981. Cultural Transmission and Evolution: A
65.^ McElreath, R. 2004. Social learning and the maintenance of cultural variation: An
evolutionary model and data from East Africa. American Anthropologist 106:308-321.
66.^ Henrich, J., R. Boyd, S. Bowles, C. Camerer, E. Fehr, H. Gintis (Eds). 2004. Foundations
of Human Sociality: Economic Experiments and Ethnographic Evidence from Fifteen Small-Scale
Societies Oxford: Oxford University Press.
67.^ Soltis, J., Boyd, R. and P. J. Richerson. 1995. Can group-functional behaviors evolve by
cultural group selection? An empirical test Current Anthropology 36:473-494
68.^ Mesoudi, A., A. Whiten, and K. N. Laland. 2006. Towards a unified science of cultural
evolution. Behavioral and Brain Sciences 29:329-383.
69.^ Gintis, H. 2006. Behavioral and Brain Sciences A framework for the integration of the
behavioral sciences Behavioral and Brain Sciences 30:1-61
71.^ Richerson, P. and R. Boyd. 2001. Culture is part of human biology: Why the superorganic
concept serves the human sciences badly. In M. Goodman and A. S. Moffat(Eds.) Probing Human
Origins. Cambridge, Massachusetts: The American Academy of Arts & Sciences.
72.^ Gintis, H. 2007. A framework for the unification of the behavioral sciences. Behavioral and
Brain Sciences. 30:1-61.
73.^ Richerson, P. J. and R. Boyd. 2005. Not By Genes Alone: How Culture Transformed
Human Evolution. Chicago: University of Chicago Press. pg. 5-8
74.^ Richerson, P. and R. Boyd. 2001. Culture is part of human biology: Why the superorganic
concept serves the human sciences badly. In M. Goodman and A. S. Moffat(Eds.) Probing Human
Origins. Cambridge, Massachusetts: The American Academy of Arts & Sciences.
75.^ Guglielmino, C. R., Viganotti, C., Hewlett, B., and Cavalli-Sforza, L.L. 1995. Cultural
variation in Africa: role of mechanism of transmission and adaptation. Proceedings of the National
Academy of Sciences USA 92:7585-7589.
76.^ Boyd, R. and P.J. Richerson. 2000. Memes: universal acid or better mouse trap. In R.
Aunger (Ed), Darwinizing Culture: The Status of Memetics as a Science . Oxford: Oxford University
Press. pg 143–162.

[edit] Books
• Lumsden, C. J. and E. O. Wilson. 1981. Genes, Mind, and Culture: The Coevolutionary
Process. Cambridge, Massachusetts: Harvard University Press.
• Cavalli-Sfornza, L. L. and M. Feldman. 1981. Cultural Transmission and Evolution: A
• Boyd, R. and P. J. Richerson. 1985. Culture and the Evolutionary Process . Chicago:
• Durham, W. H. 1991. Coevolution: Genes, Culture and Human Diversity . Stanford, California:
Stanford University Press. ISBN 0-8047-1537-8
• Tomasello, M. 1999. The Cultural Origins of Human Cognition. Cambridge, Massachusetts:
• Shennan, S. J. 2002. Genes, Memes and Human History: Darwinian Archaeology and
Cultural Evolution. London: Thames and Hudson.
• Laland, K. N. and G. R. Brown. 2002. Sense & Nonsense: Evolutionary Perspectives on
• Boyd, R. and P. J. Richerson. 2005. The Origin and Evolution of Cultures . Oxford: Oxford
University Press.
• Richerson, P. J. and R. Boyd. 2005. Not By Genes Alone: How Culture Transformed Human
Evolution. Chicago: University of Chicago Press.
[edit] Reviews
• Smith, E. A. 1999. Three styles in the evolutionary analysis of human behavior. In L. Cronk,
N. Chagnon, and W. Irons, (Eds.) Adaptation and Human Behavior: An Anthropological Perspective
New York: Aldine de Gruyter.
• Henrich, J. and R. McElreath. 2003. The evolution of cultural evolution. Evolutionary
Anthropology 12:123-135.
• Mesoudi, A., A. Whiten, and K. N. Laland. 2006. Towards a unified science of cultural
evolution. Behavioral and Brain Sciences 29:329-383
• Gintis, H. 2006. A framework for the integration of the behavioral sciences Behavioral and
Brain Sciences 30:1-61
• Bentley, R.A., C. Lipo, H.D.G. Maschner and B. Marler 2007. Darwinian Archaeologies. In
R.A. Bentley, H.D.G. Maschner & C. Chippendale (Eds.) Handbook of Archaeological Theories.
Lanham (MD): AltaMira Press.
• McElreath, R. & Henrich, J. 2007. Modeling cultural evolution. In R. Dunbar and L. Barrett,
(Eds.), Oxford Handbook of Evolutionary Psychology Oxford: Oxford University Press.
• McElreath, R. & Henrich, J. 2007. Dual inheritance theory: the evolution of human cultural
• Sterelny, Kim (2002). Review Genes, Memes and Human History. Stephen Shennan.
London: Thames and Hudson. pp. 304. http://www.vuw.ac.nz/phil/staff/documents/sterelny-
papers/tripod.pdf#search='dual%20inheritance%20theorypdf'.
• Laland, K.N., Odling-Smee, J. & Myles, S. 2010. How culture shaped the human genome:
bringing genetics and the human sciences. Nature Reviews: Genetics 11:137-148
[edit] Journal articles

• "Culture, Adaptation, and Innateness" . The Innate Mind: Culture and Cognition .
http://www.sscnet.ucla.edu/anthro/faculty/boyd/Innateness%20ver%204.1.pdf.
• "Built for Speed, Not for Comfort: Darwinian Theory and Human Culture" . History and
Philosophy of the Life Sciences (23): 425–465. 2001.
http://www.sscnet.ucla.edu/anthro/faculty/boyd/Built%20for%20Speed,%20Not%20for
%20Comfort.pdf.

[edit] Current DIT researchers
• Rob Boyd, Department of Anthropology, UCLA
• Marcus Feldman, Department of Biological Sciences, Stanford
• Joe Henrich, Departments of Psychology and Economics, University of British Columbia
• Richard McElreath, Anthropology Department, UC Davis
• Peter J. Richerson, Department of Environmental Science and Policy, UC Davis
[edit] Related researchers

• Herb Gintis, Emeritus Professor of Economics, University of Massachusetts & Santa Fe
Institute
• Kevin Laland, School of Biology, University of St. Andrews
• Ruth Mace, Department of Anthropology, University College London
• Michael Tomasello, Department of Developmental and Comparative Psychology, Max
Planck Institute for Evolutionary Anthropology
Retrieved from "http://en.wikipedia.org/wiki/Dual_inheritance_theory"
Categories: Anthropology | Cultural anthropology | Demography | Human evolution | Interdisciplinary

fields | Population genetics | Sociobiology
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Segmentation (biology)

Vertebrates have a segmented vertebral column and brain.
Segmentation in biology refers to either (1) a type of gastrointestinal motility ("mixing" movements (in
contrast to "propulsive" movements)) or (2) the division of some animal and plant body plans into a series of
repetitive segments. This article will focus on the segmentation of animal body plans, specifically using the
examples of the phyla Arthropoda, Vertebrata, and Annelida. These three phyla form segments by using a
“growth zone” to direct and define the segments. While all three have a generally segmented body plan and
use a “growth zone,” they use different mechanisms for generating this patterning. Even within these phyla,
different organisms have different mechanisms for segmenting the body. Segmentation of the body plan is
important for allowing different regions of the body to develop differentially for different uses.
While many details will be discussed here, there are other details about the process of establishing
such a segmented body pattern in morphogenesis.
Contents
[hide]
• 1 Animals
• 1.1 Arthropods: Drosophila
• 1.2 Annelids: Leech
• 1.3 Chordates: Zebrafish
• 2 References
[edit] Animals
Segmentation in animals typically falls into three types characteristic of the different phyla:
Arthropoda, Vertebrata, and Annelida. The three will be discussed here in using an example from each phyla,
drosophila, zebrafish, and leech, respectively. Drosophila form segments from a field of equivalent cells
based on transcription factor gradients. Zebrafish, and other vertebrates, use oscillating gene expression to
define segments known as somites. Leech embryos, and other annelids, use smaller cells budded off from
teloblast cells to define segments. [1]
[edit] Arthropods: Drosophila

Although drosophila segmentation is not representative of the arthropod phylum in general, it is the
most highly studied. The drosophila as a model organism is ideal for genetic screens. Early screens to
identify genes involved in cuticle development led to the discovery of a class of genes that was necessary for
proper segmentation of the ‘’drosophila’’ embryo.[2]
To properly segment the drosophila embryo, the anterior-posterior axis is defined by maternally supplied
transcripts giving rise to gradients of these proteins.[1][2][3] This gradient then defines the expression pattern
for gap genes, which set up the boundaries between the different segments. The gradients produced from
gap gene expression then define the expression pattern for the pair-rule genes.[1][3]The pair-rule genes are
mostly transcription factors, expressed in regular stripes down the length of the embryo.[3] These
transcription factors then regulate the expression of segment polarity genes, which define the polarity of each
segment. Boundaries and identities of each segment are later defined.[3]
[edit] Annelids: Leech
While not as well studied as in drosophila and zebrafish, segmentation in leech has been described
as “budding” segmentation. Early divisions within the leech embryo result in teloblast cells, which are stem
cells that divide asymmetrically to create bandlets of blast cells.[1] Furthermore, there are five different
teloblast lineages (N, M, O, P, and Q), with one set for each side of the midline. The N and Q lineages
contribute two blast cells for each segment, while the M, O, and P lineages only contribute one cell per
segment.[4] Finally, the number of segments within the embryo is defined by the number of divisions and
blast cells.[1] Segmentation appears to be regulated by the gene Hedgehog, suggesting its common
evolutionary origin in the ancestor of arthropods and annelids.[5]
[edit] Chordates: Zebrafish

Zebrafish form segments known as somites through a process that is reliant upon gradients of
retinoic acid and FGF, as well as periodic oscillation of gene expression.
Perhaps not as well studied as segmentation in drosophila, segmentation in zebrafish is actively
studied. The process is similar in zebrafish and other chordates, such as the chicken and the mouse.
Segmentation in chordates is characterized as the formation of a pair of somites on either side of the midline.
This is often referred to as somitogenesis.
In the zebrafish, segmentation is coordinated by the “clock and wavefront.” The “clock” refers to the
periodic oscillation of specific genes, such as Her1, a hairy/Enhancer of split- gene. Expression starts that the
posterior end of the embryo and moves towards the anterior. The “wavefront” refers to the location where the
somites mature, which is defined by gradients of retinoic acid and FGF. Retinoic acid is high in the anterior
and FGF is high in the posterior; the “wavefront” is the point at which both concentrations are at their lowest.
Cells at this point will mature and form a pair of somites.[6]
[edit] References
1. ^ a b c d e Tautz, D (2004). "Segmentation". Dev Cell 7 (3): 301–312.
doi:10.1016/j.devcel.2004.08.008. PMID 15363406.
2. ^ a b Pick, L (1998). "Segmentation: Painting Stripes From Flies to Vertebrates". Dev Genet
23 (1): 1–10. doi:10.1002/(SICI)1520-6408(1998)23:1<1::AID-DVG1>3.0.CO;2-A. PMID 9706689.
3. ^ a b c d Peel AD, Chipman AD, Akam M (2005). "Arthropod Segmentation: Beyond The
Drosophila Paradigm". Nat Rev Genet 6 (12): 905–916. doi:10.1038/nrg1724. PMID 16341071.
4. ^ Weisblat DA, Shankland M (1985). "Cell lineage and segmentation in the leech". Philos
Trans R Soc Lond B Biol Sci. 312 (1153): 39–56. doi:10.1098/rstb.1985.0176. PMID 2869529.
5. ^ Dray, N.; Tessmar-Raible, K.; Le Gouar, M.; Vibert, L.; Christodoulou, F.; Schipany, K.;
Guillou, A.; Zantke, J. et al. (2010). "Hedgehog signaling regulates segment formation in the annelid
Platynereis". Science (New York, N.Y.) 329 (5989): 339–342. doi:10.1126/science.1188913.
PMID 20647470. edit
6. ^ Cinquin O (2007). "Understanding the somitogenesis clock: what's missing?". Mech Dev
124 (7-8): 501–517. doi:10.1016/j.mod.2007.06.004. PMID 17643270.


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Segmentation_(biology)"
Categories: Developmental biology

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Modularity (biology)

For other uses of "Modularity", see Modularity (disambiguation).
Many organisms consist of modules, both anatomically and in their metabolism. Anatomical modules
are usually segments or organs. When we look at illustrations of metabolic reactions, we find that they, too,
are modular: we can clearly identify, for instance, the citric acid cycle as a complex network that has only a
few interfaces with other such modules. This principle holds true at various different scales: we can identify
smaller modules within such larger networks that are similarly self-contained. We say that metabolic
modularity is scale-free.
In addition to showing scalefree and small world properties, biological networks appear to exhibit
modularity in topological structure. In the field of network biology, the definition of nodes and edges in a given
network depends on the type of network examined. For example, in a protein interaction network, nodes
correspond with individual proteins and edges represent the interactions between them (either through direct
physical interaction, or compound-mediated). Metabolic networks, on the other hand, contain metabolite
nodes and edges that represent the specific enzymes that connect them (in catalyzing biochemical
reactions). As with any type of network, modularity in biological networks allows sub-groups of nodes and
edges to function in a semi-autonomous fashion.
The concept of modularity resurfaces at the scale of organs and developmental units. Why are there
distinct cell types organised into spatial aggregations (organs), and what are the benefits of having a
segmented body plan, containing different modules (for instance, thoracic and abdominal segments in an
arthropod) and where one of the possible differences between species is in the number of each type of
module they possess?
Interestingly, this property has led researchers to suggest that modularity imparts a certain degree of
evolvability to a system by allowing specific features (i.e. network sub-groups) to undergo changes without
substantially altering the functionality of the entire system. Essentially, each module is free to evolve within,
so long as the interfaces between modules remain consistent. This would suggest that the metabolic
pathways at the edges between modules are more constrained. It is thought that there exists an optimal
degree of modularity for each given organism.

• Homologues, Natural Kinds, and the Evolution of Modularity
• Modules: Key Pieces in the Integration of Developmental and Evolutionary Biology
• Modularity in Animal Development and Evolution: Elements of a Conceptual Framework for
EvoDevo
Processes of
Population genetic
Evolutionary
developmental
concepts
Modes of


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Modularity_(biology)"

Categories: Biology terminology
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Evolvability

Evolvability is defined as the ability of a population of organisms to generate genetic diversity and
evolve through natural selection.[1][2]
In order for a biological organism to evolve by natural selection, there must be a certain minimum
probability that new, heritable variants are beneficial. Random mutations, unless they occur in DNA
sequences with no function, are expected to be mostly detrimental. Beneficial mutations are always rare, but
if they are too rare, then adaptation cannot occur. Random mutations seem to be beneficial more often than
random changes to a typical computer program are.[3] This means that biological genomes are structured in
ways that make beneficial changes less unlikely than they would otherwise be. This has been taken as
evidence that evolution has created not just fitter organisms, but populations of organisms that are better
able to evolve.
Contents
[hide]
• 1 Alternative definitions
• 1.1 Example
• 2 Generating more variation
• 3 Enhancement of Selection
• 4 Robustness and evolvability
• 5 Exploration ahead of time
• 6 Modularity
• 7 Evolution of evolvability
• 8 References
[edit] Alternative definitions

Wagner (2005) describes two definitions of evolvability. According to the first definition, a biological
system is evolvable
• if its properties show heritable genetic variation, and
• if natural selection can thus change these properties.
According to the second definition, a biological system is evolvable
• if it can acquire novel functions through genetic change, functions that help the organism
survive and reproduce.
These definitions can be applied on all levels of biological organisation, from macromolecules to
mammals. Not all systems that are evolvable in the first sense are evolvable in the second sense. (See
example below from Wagner (2005)).
Pigliucci[4] recognizes three classes of definition, depending on timescale. The first corresponds to
Wagner's first, and represents the very short timescales that are described by quantitative genetics. He
divides Wagner's second definition into two categories, one representing the intermediate timescales that
can be studied using population genetics, and one representing exceedingly rare long-term innovations of
form.
[edit] Example
Consider an enzyme with multiple alleles in the population. Each allele catalyzes the same reaction,
but with a different level of activity. However, even after millions of years of evolution, exploring many
sequences with similar function, no mutation might exist that gives this enzyme the ability to catalyze a
different reaction. Thus, although the enzyme’s activity is evolvable in the first sense, that does not mean that
the enzyme's function is evolvable in the second sense. However, every system evolvable in the second
sense must also be evolvable in the first.
[edit] Generating more variation
More heritable phenotypic variation means more evolvability. While mutation is the ultimate source of
heritable variation, its permutations and combinations also make a big difference. Sexual reproduction
generates more variation (and thereby evolvability) relative to asexual reproduction (see evolution of sexual
reproduction). Evolvability is further increased by generating more variation when an organism is stressed,
and thus likely to be less well adapted, but less variation when an organism is doing well. The amount of
variation generated can be adjusted in many different ways, for example via the mutation rate, via the
probability of sexual vs. asexual reproduction, via the probability of outcrossing vs. inbreeding, and via
dispersal.
[edit] Enhancement of Selection

Rather than creating more phenotypic variation, some mechanisms increase the intensity and
effectiveness with which selection acts on existing phenotypic variation. For example:
• Mating rituals that allow sexual selection on "good genes", and so intensify natural selection
• Large population size
• Recombination decreasing the importance of the Hill-Robertson effect, where different
genotypes contain different adaptive mutations. Recombination brings the two alleles together,
creating a super-genotype in place of two competing lineages.
• Shorter generation time
[edit] Robustness and evolvability
Robustness will not increase evolvability in the first sense. In organisms with a high level of
robustness, mutations will have smaller phenotypic effects than in organisms with a low level of robustness.
Thus, robustness reduces the amount of heritable genetic variation on which selection can act. However,
robustness may allow exploration of large regions of genotype space, increasing robustness according to the
second sense.[5][6]
For example, one reason many proteins are less robust to mutation is that they have marginal
thermodynamic stability, and most mutations reduce this stability further. Proteins that are more thermostable
can tolerate a wider range of mutations, and are more evolvable.[7]
[edit] Exploration ahead of time

When mutational robustness exists, many mutants will persist in a cryptic state. Mutations tend to fall
into two categories, having either a very bad effect or very little effect: few mutations fall somewhere in
between.[8] Sometimes, these mutations will not be completely invisible, but still have rare effects, with very
low penetrance. When this happens, natural selection weeds out the really bad mutations, while leaving the
other mutations relatively unaffected.[9] While evolution has no "foresight" to know which environment will be
encountered in the future, some mutations cause major disruption to a basic biological process, and will
never be adaptive in any environment. Screening these out in advance leads to preadapted stocks of cryptic
genetic variation.
Another way that phenotypes can be explored, prior to strong genetic commitment, is through
learning. An organism that learns gets to "sample" several different phenotypes during its early development,
and later sticks to whatever worked best. Later in evolution, the optimal phenotype can be genetically
assimilated so it becomes the default behavior rather than a rare behavior. This is known as the Baldwin
effect, and it can increase evolvability.[10][11]
Learning biases phenotypes in a beneficial direction. But an exploratory flattening of the fitness
landscape can also increase evolvability even when it has no direction, for example when the flattening is a
result of random errors in molecular and/or developmental processes. This increase in evolvability can
happen when evolution is faced with crossing a "valley" in an adaptive landscape. This means that two
mutations exist that are deleterious by themselves, but beneficial in combination. These combinations can
evolve more easily when the landscape is first flattened, and the discovered phenotype is then fixed by
genetic assimilation.[12][13][14]
[edit] Modularity
If every mutation affected every trait, then a mutation that was an improvement for one trait would be
a disadvantage for other traits. This means that almost no mutations would be beneficial overall. But if
pleiotropy is restricted to within functional modules, then mutations affect only one trait at a time, and
adaptation is much easier.
[edit] Evolution of evolvability

While variation yielding high evolvability could be useful in the long term, in the short term most of
that variation is likely to be deleterious. For example, naively it would seem that increasing the mutation rate
via a mutator allele would increase evolvability. But as an extreme example, if the mutation rate is too high
then all individuals will be dead or at least carry a heavy mutation load. Short-term selection for low variation
most of the time is usually thought likely to be more powerful than long-term selection for evolvability, making
it difficult for natural selection to cause the evolution of evolvability.
When recombination is low, mutator alleles may still sometimes hitchhike on the success of adaptive
mutations that they cause. In this case, selection can take place at the level of the lineage.[15] This may
explain why mutators are often seen during experimental evolution of microbes. Mutator alleles can also
evolve more easily when they only increase mutation rates in nearby DNA sequences, not across the whole
genome: this is known as a contingency locus.
The evolution of evolvability is less controversial if it occurs via the evolution of sexual reproduction,
or via the tendency of variation-generating mechanisms to become more active when an organism is
stressed. The yeast prion [PSI+] may also be an example of the evolution of evolvability through evolutionary
capacitance.[16][17] An evolutionary capacitor is a switch that turns genetic variation on and off. This is very
much like bet-hedging the risk that a future environment will be similar or different.[18] Theoretical models
also predict the evolution of evolvability via modularity.[19]
[edit] References
1. ^ Colegrave N, Collins S (May 2008). "Experimental evolution: experimental evolution and
evolvability". Heredity 100 (5): 464–70. doi:10.1038/sj.hdy.6801095. PMID 18212804.
2. ^ Kirschner M, Gerhart J (1998). "Evolvability". Proceedings of the National Academy of
Sciences of the United States of America 95 (15): 8420–8427. doi:10.1073/pnas.95.15.8420.
PMID 9671692.
3. ^ Wagner GP, Alternberg L (1996). "Complex adaptations and the evolution of evolvability".
Evolution 50 (3): 967–976. doi:10.2307/2410639. http://jstor.org/stable/2410639.
4. ^ Pigliucci M (2008). "Is evolvability evolvable?". Nature Reviews Genetics 9 (1): 75–82.
doi:10.1038/nrg2278. PMID 18059367.
5. ^ Masel J, Trotter MV (2010). "Robustness and evolvability". Trends in Genetics 26 (9): 406–
414. doi:10.1016/j.tig.2010.06.002. PMID 20598394.
6. ^ Wagner A (2005). Robustness and evolvability in living systems . Princeton Studies in
Complexity. Princeton University Press. ISBN 0691122407.
7. ^ Bloom JD, Labthavikul ST, Otey, CR, Arnold FH (2006). "Protein stability promotes
evolvability". Proceedings of the National Academy of Sciences of the United States of America 103
(15): 5869–5874. doi:10.1073/pnas.0510098103. PMID 16581913. PMC 1458665.
http://www.pnas.org/cgi/content/abstract/103/15/5869.
8. ^ Eyre-Walker A, Keightley, PD (2007). "The distribution of fitness effects of new mutations".
9. ^ Masel, Joanna (March 2006). "Cryptic Genetic Variation Is Enriched for Potential
Adaptations". Genetics (Genetics Society of America) 172 (3): 1985–1991.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artid=1456269.
10.^ Hinton GE, Nowlan SJ (1987). "How learning can guide evolution". Complex Systems 1:
495–502.
11.^ Borenstein E, Meilijson I, Ruppin E (2006). "The effect of phenotypic plasticity on evolution
in multipeaked fitness landscapes". Journal of Evolutionary Biology 19 (5): 1555–1570.
doi:10.1111/j.1420-9101.2006.01125.x. PMID 16910985.
12.^ Kim Y (2007). "Rate of adaptive peak shifts with partial genetic robustness". Evolution 61
(8): 1847–1856. doi:10.1111/j.1558-5646.2007.00166.x. PMID 17683428.
13.^ Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E (2008). "The look-ahead
effect of phenotypic mutations". Biology Direct 3: 18. doi:10.1186/1745-6150-3-18. PMID 18479505.
PMC 2423361. http://www.biology-direct.com/content/3/1/18.
14.^ Griswold CK, Masel J (2009). "Complex adaptations can drive the evolution of the capacitor
[PSI+, even with realistic rates of yeast sex"]. PLoS Genetics 5 (6): e1000517.
doi:10.1371/journal.pgen.1000517. PMID 19521499. PMC 2686163.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000517.
15.^ Eshel I (1973). "Clone-selection and optimal rates of mutation". Journal of Applied
Probability 10 (4): 728–738. doi:10.2307/3212376. http://jstor.org/stable/3212376.
16.^ Masel J, Bergman A, (2003). "The evolution of the evolvability properties of the yeast prion
[PSI+]". Evolution 57 (7): 1498–1512. PMID 12940355.
17.^ Lancaster AK, Bardill JP, True HL, Masel J (2010). "The Spontaneous Appearance Rate of
the Yeast Prion [PSI+ and Its Implications for the Evolution of the Evolvability Properties of the [PSI+]
System"]. Genetics 184 (2): 393–400. doi:10.1534/genetics.109.110213. PMID 19917766.
18.^ King O, Masel J (2007). "The evolution of bet-hedging adaptations to rare scenarios".
Theoretical Population Biology 72 (4): 560–575. doi:10.1016/j.tpb.2007.08.006. PMID 17915273.
19.^ Draghi J, Wagner G (2008). "Evolution of evolvability in a developmental model".
Theoretical Population Biology 62: 301–315.


phenotype
Non-genetic Epigenetics · Maternal effect · Dual inheritance theory

influences
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Evolvability"

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Mutational robustness

Mutational robustness describes the extent to which an organism's phenotype remains constant in
spite of mutation. Selection can directly induce the evolution of mutational robustness only when mutation
rates are high and population sizes are large. However, there may be considerable indirect selection for
mutational robustness and a correlated response to selection for robustness against non-genetic changes
(i.e. changes in the environment). The conditions under which selection could act to directly increase
mutational robustness are extremely restrictive, and for this reason, such selection is thought to be limited to
only a few viruses and other microbes having large population sizes. Mutational robustness is thought to be
one driver for theoretical viral quasispecies formation.
[edit] References
• Wagner, Andreas. 2005. Robustness and Evolvability in Living Systems (Princeton Studies in
Complexity). Princeton University Press. ISBN 0-691-12240-7


phenotype
Non-genetic
Developmental

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Evolution of sexual reproduction

(Redirected from Evolution of sex)
The evolution of sexual reproduction is currently described by several competing scientific
hypotheses. Many groups of organisms, notably the majority of animals and plants, reproduce sexually. The
evolution of sex contains two related, yet distinct, themes: its origin and its maintenance. However, since the
hypotheses for the origins of sex are difficult to test experimentally, most current work has been focused on
the maintenance of sexual reproduction.
It seems that a sexual cycle is maintained because it improves the quality of progeny (fitness),
despite reducing the overall number of offspring (the twofold cost of sex). In order for sex to be evolutionarily
advantageous, it must be associated with a significant increase in the fitness of offspring. One of the most
widely accepted explanations for the advantage of sex lies in the creation of genetic variation. Another
explanation is based on two molecular advantages. First is the advantage of recombinational DNA repair
(promoted during meiosis because homologous chromosomes pair at that time), and second is the
advantage of complementation (also known as hybrid vigor, heterosis or masking of mutations).
For the advantage due to creation of genetic variation, there are three possible reasons this might
happen. First, sexual reproduction can bring together mutations that are beneficial into the same individual
(sex aids in the spread of advantageous traits). Second, sex acts to bring together currently deleterious
mutations to create severely unfit individuals that are then eliminated from the population ( sex aids in the
removal of deleterious genes). Last, sex creates new gene combinations that may be more fit than previously
existing ones, or may simply lead to reduced competition among relatives.
For the advantage due to DNA repair, there is an immediate large benefit to removal of DNA damage
by recombinational DNA repair during meiosis, since this removal allows greater survival of progeny with
undamaged DNA. The advantage of complementation to each sexual partner is avoidance of the bad effects
of their deleterious recessive genes in progeny by the masking effect of normal dominant genes contributed
by the other partner.
The classes of hypotheses based on the creation of variation are further broken down below. It is
important to realise that any number of these hypotheses may be true in any given species (they are not
mutually exclusive), and that different hypotheses may apply in different species. However, a research
framework based on creation of variation has yet to be found that allows one to determine whether the
reason for sex is universal for all sexual species, and, if not, which mechanism is acting in each species.
On the other hand, the maintenance of sex based on DNA repair and complementation applies
widely to all sexual species. This explanation for the maintenance of sex is explored further in Section 6.2.
Contents
[hide]
• 1 Historical perspective
• 2 Two-fold cost of sex
• 3 Promotion of genetic variation
• 4 Spread of advantageous traits
• 4.1 Novel genotypes
• 4.2 Increased resistance to parasites
• 5 Deleterious mutation clearance
• 5.1 Maintenance of mutation-free individuals
• 5.2 Removal of deleterious genes
• 6 Other explanations
• 6.1 Speed of evolution
• 6.2 DNA repair and complementation
• 7 Origin of sexual reproduction
• 8 Mechanistic origin of sexual reproduction
• 8.1 Viral eukaryogenesis
• 8.2 Neomuran revolution
• 9 See also
• 10 References
[edit] Historical perspective
Modern philosophical-scientific thinking on the problem can be traced back to Erasmus Darwin in the
18th century; it also features in Aristotle's writings. The thread was later picked up by August Weismann in
1889, who understood that the purpose of sex was to generate genetic variation, as is detailed in the majority
of the explanations below. On the other hand, Charles Darwin, also in 1889, concluded that the effects of
hybrid vigor (complementation) “is amply sufficient to account for the ... genesis of the two sexes.” This is
consistent with the repair and complementation hypothesis, given below under “Other explanations.”
Several explanations have been suggested by biologists including W. D. Hamilton, Alexey
Kondrashov, George C. Williams, Harris Bernstein, Carol Bernstein, Michael M. Cox, Frederic A. Hopf and
Richard E. Michod to explain how sexual reproduction is maintained in a vast array of different living
organisms.
[edit] Two-fold cost of sex

This diagram illustrates the twofold cost of sex. If each individual were to contribute to the same
number of offspring (two), (a) the sexual population remains the same size each generation, where the (b)
asexual population doubles in size each generation.
In all multicellular sexual species, the population consists of two sexes, only one of which is capable
of bearing young (with the exception of simultaneous hermaphrodites). In an asexual species, each member
of the population is capable of bearing young. This implies that an asexual population has an intrinsic
capacity to grow more rapidly each generation. The cost was first described in mathematical terms by John
Maynard Smith.[1] He imagined an asexual mutant arising in a sexual population, half of which comprises
males that cannot themselves produce offspring. With female-only offspring, the asexual lineage doubles its
representation in the population each generation, all else being equal. Often all else is not equal, however, in
which case the realised fitness cost to sex may be much less than this intrinsic twofold cost of producing
males. For example, an asexual mutant arising in a sexual population occupies a niche frozen to that of its
parental genotype because the asexual descendants are genetically self-identical. Analysis of competitive
Lotka-Volterra equations suggests that the asexual lineage may never realise its full twofold advantage in
population growth capacity, if the broader niche of the sexual population confers even a small competitive
edge.[2]
An additional cost is that males and females must search for each other in order to mate, and sexual
selection often favours traits that reduce the survival of individuals.[1]
Evidence that the cost is not insurmountable comes from George C. Williams, who noted the
existence of species which are capable of both asexual and sexual reproduction. These species time their
sexual reproduction with periods of environmental uncertainty, and reproduce asexually when conditions are
more favourable. The important point is that these species are observed to reproduce sexually when they
could choose not to, implying that there is a selective advantage to sexual reproduction.[3]
Another disadvantage of sexual reproduction is that a sexually reproducing organism will only be
able to pass on 50% of its genes to each offspring. This is a consequence of the fact that gametes from
sexually reproducing species are haploid.[4]
[edit] Promotion of genetic variation

August Weismann proposed in 1889[5] an explanation for the evolution of sex, where the advantage
of sex is the creation of variation among siblings. It was then subsequently explained in genetics terms by
Fisher[6] and Muller[7] and has been recently summarised by Burt in 2000.[8]
George C. Williams gave an example based around the elm tree. In the forest of this example, empty
patches between trees can support one individual each. When a patch becomes available because of the
death of a tree, other trees' seeds will compete to fill the patch. Since the chance of a seed's success in
occupying the patch depends upon its genotype, and a parent cannot anticipate which genotype is most
successful, each parent will send many seeds, creating competition between siblings. Natural selection
therefore favours parents which can produce a variety of offspring.
A similar hypothesis is named the tangled bank hypothesis after a passage in Charles Darwin's The
Origin of Species:
"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds,
with birds singing on the bushes, with various insects flitting about, and with worms crawling through
the damp earth, and to reflect that these elaborately constructed forms, so different from each other,
and dependent on each other in so complex a manner, have all been produced by laws acting around
us."
The hypothesis, proposed by Michael Ghiselin in his 1974 book, The Economy of Nature and the
Evolution of Sex, suggests that a diverse set of siblings may be able to extract more food from its
environment than a clone, because each sibling uses a slightly different niche. One of the main proponents of
this hypothesis is Graham Bell of McGill University. The hypothesis has been criticised for failing to explain
how asexual species developed sexes. In his book, Evolution and Human Behavior (MIT Press, 2000), John
Cartwright comments:
"Although once popular, the tangled bank hypothesis now seems to face many problems, and
former adherents are falling away. The theory would predict a greater interest in sex among animals
that produce lots of small offspring that compete with each other. In fact, sex is invariably associated
with organisms that produce a few large offspring, whereas organisms producing small offspring
frequently engage in parthenogenesis [asexual reproduction]. In addition, the evidence from fossils
suggests that species go for vast periods of [geologic] time without changing much."
[edit] Spread of advantageous traits
[edit] Novel genotypes
This diagram illustrates how sex might create novel genotypes more rapidly. Two advantageous
alleles A and B occur at random. The two alleles are recombined rapidly in a sexual population (top), but in
an asexual population (bottom) the two alleles must independently arise because of clonal interference.
Sex could be a method by which novel genotypes are created. Since sex combines genes from two
individuals, sexually reproducing populations can more easily combine advantageous genes than can
asexual populations. If, in a sexual population, two different advantageous alleles arise at different loci on a
chromosome in different members of the population, a chromosome containing the two advantageous alleles
can be produced within a few generations by recombination. However, should the same two alleles arise in
different members of an asexual population, the only way that one chromosome can develop the other allele
is to independently gain the same mutation, which would take much longer.
Ronald Fisher also suggested that sex might facilitate the spread of advantageous genes by allowing
them to escape their genetic surroundings, if they should arise on a chromosome with deleterious genes.
But these explanations depend upon the rate of mutation. If favourable mutations are so rare that
each will become fixed in the population before the next arises (bearing in mind that mutation is a Poisson
process), then sexual and asexual populations would evolve at the same rate.
Additionally, these explanations depend upon group selection, which most theorists maintain is a
weak selective force relative to individual selection – sex is still disadvantageous to the individual due to the
twofold cost of sex. Therefore, these explanations do not explain why heterogonic species choose to adopt
sexual reproduction, as George C. Williams pointed out in his balance argument, and hence are insufficient
to explain the evolution of sex.
Supporters of these theories respond to the balance argument that the individuals produced by
sexual and asexual reproduction may differ in other respects too – which may influence the persistence of
sexuality. For example, in water fleas of the genus Cladocera, sexual offspring form eggs which are better
able to survive the winter.
[edit] Increased resistance to parasites

One of the most widely accepted theories to explain the persistence of sex is that it is maintained to
assist sexual individuals in resisting parasites, also known as the Red Queen's Hypothesis.[4][9][10]
When an environment changes, previously neutral or deleterious alleles can become favourable. If
the environment changed sufficiently rapidly (i.e. between generations), these changes in the environment
can make sex advantageous for the individual. Such rapid changes in environment are caused by the co-
evolution between hosts and parasites.
Imagine, for example that there is one gene in parasites with two alleles p and P conferring two types
of parasitic ability, and one gene in hosts with two alleles h and H, conferring two types of parasite
resistance, such that parasites with allele p can attach themselves to hosts with the allele h, and P to H. Such
a situation will lead to cyclic changes in allele frequency - as p increases in frequency, h will be disfavoured.
In reality, there will be several genes involved in the relationship between hosts and parasites. In an
asexual population of hosts, offspring will only have the different parasitic resistance if a mutation arises. In a
sexual population of hosts, however, offspring will have a new combination of parasitic resistance alleles.
In other words, like Lewis Carroll's Red Queen, sexual hosts are continually adapting in order to stay
ahead of their parasites.
Evidence for this explanation for the evolution of sex is provided by comparison of the rate of
molecular evolution of genes for kinases and immunoglobulins in the immune system with genes coding
other proteins. The genes coding for immune system proteins evolve considerably faster.[11][12]
Critics of the Red Queen hypothesis question whether the constantly-changing environment of hosts
and parasites is sufficiently common to explain the evolution of sex.
[edit] Deleterious mutation clearance

Mutations can have many different effects upon an organism. It is generally believed that the majority
of non-neutral mutations are deleterious, which means that they will cause a decrease in the organism's
overall fitness.[13] If a mutation has a deleterious effect, it will then usually be removed from the population
by the process of natural selection. Sexual reproduction is believed to be more efficient than asexual
reproduction in removing those mutations from the genome.[14]
There are two main hypotheses which explain how sex may act to remove deleterious genes from
the genome.
[edit] Maintenance of mutation-free individuals

Main article: Muller's ratchet
In a finite asexual population under the pressure of deleterious mutations, the random loss of
individuals without such mutations is inevitable. This is known as Muller's ratchet. In a sexual population,
however, mutation-free genotypes can be restored by recombination of genotypes containing deleterious
mutations.
This comparison will only work for a small population - in a large population, random loss of the most
fit genotype becomes unlikely even in an asexual population.
[edit] Removal of deleterious genes
Diagram illustrating different relationships between numbers of mutations and fitness. Kondrashov's
model requires synergistic epistasis, which is represented by the blue line - each mutation has a
disproproportionately large effect on the organism's fitness.
This hypothesis was proposed by Alexey Kondrashov, and is sometimes known as the deterministic
mutation hypothesis.[14] It assumes that the majority of deleterious mutations are only slightly deleterious,
and affect the individual such that the introduction of each additional mutation has an increasingly large effect
on the fitness of the organism. This relationship between number of mutations and fitness is known as
synergistic epistasis.
By way of analogy, think of a car with several minor faults. Each is not sufficient alone to prevent the
car from running, but in combination, the faults combine to prevent the car from functioning.
Similarly, an organism may be able to cope with a few defects, but the presence of many mutations
could overwhelm its backup mechanisms.
Kondrashov argues that the slightly deleterious nature of mutations means that the population will
tend to be composed of individuals with a small number of mutations. Sex will act to recombine these
genotypes, creating some individuals with fewer deleterious mutations, and some with more. Because there
is a major selective disadvantage to individuals with more mutations, these individuals die out. In essence,
sex compartmentalises the deleterious mutations.
There has been much criticism of Kondrashov's theory, since it relies on two key restrictive
conditions. The first requires that the rate of deleterious mutation should exceed one per genome per
generation in order to provide a substantial advantage for sex. While there is some empirical evidence for it
(for example in Drosophila[15] and E. coli[16]), there is also strong evidence against it.[ citation needed]
Secondly, there should be strong interactions among loci (synergistic epistasis), a mutation-fitness relation
for which there is only limited evidence. Conversely, there is also the same amount of evidence that
mutations show no epistasis (purely additive model) or antagonistic interactions (each additional mutation
has a disproportionally small effect).
[edit] Other explanations

[edit] Speed of evolution
Ilan Eshel suggested that sex prevents rapid evolution. He suggests that recombination breaks up
favourable gene combinations more often than it creates them, and sex is maintained because it ensures
selection is longer-term than in asexual populations - so the population is less affected by short-term
changes.[citation needed] This explanation is not widely accepted, as its assumptions are very restrictive.
It has recently been shown in experiments with Chlamydomonas algae that sex can remove the
speed limit on evolution.[17]
[edit] DNA repair and complementation

As discussed in the earlier part of this article, sexual reproduction is conventionally explained as an
adaptation for producing genetic variation through allelic recombination. As acknowledged above, however,
serious problems with this explanation have led many biologists to conclude that the benefit of sex is a major
unsolved problem in evolutionary biology.
An alternative “informational” approach to this problem has led to the view that the two fundamental
aspects of sex, genetic recombination and outcrossing, are adaptive responses to the two major sources of
“noise” in transmitting genetic information. Genetic noise can occur as either physical damage to the genome
(e.g. chemically altered bases of DNA or breaks in the chromosome) or replication errors (mutations)[18][19]
[20] This alternative view is referred to as the repair and complementation hypothesis, to distinguish it from
the traditional variation hypothesis.
The repair and complementation hypothesis assumes that genetic recombination is fundamentally a
DNA repair process, and that when it occurs during meiosis it is an adaptation for repairing the genomic DNA
which is passed on to progeny. Recombinational repair is the only repair process known which can
accurately remove double-strand damages in DNA, and such damages are both common in nature and
ordinarily lethal if not repaired. Recombinational repair is prevalent from the simplest viruses to the most
complex multicellular eukaryotes. It is effective against many different types of genomic damage, and in
particular is highly efficient at overcoming double-strand damages. Studies of the mechanism of meiotic
recombination indicate that meiosis is an adaptation for repairing DNA.[21] These considerations form the
basis for the first part of the repair and complementation hypothesis.
In some lines of descent from the earliest organisms, the diploid stage of the sexual cycle, which was
at first transient, became the predominant stage, because it allowed complementation — the masking of
deleterious recessive mutations (i.e. hybrid vigor or heterosis). Outcrossing, the second fundamental aspect
of sex, is maintained by the advantage of masking mutations and the disadvantage of inbreeding (mating
with a close relative) which allows expression of recessive mutations (commonly observed as inbreeding
depression). This is in accord with Charles Darwin,[22] who concluded that the adaptive advantage of sex is
hybrid vigor; or as he put it, “the offspring of two individuals, especially if their progenitors have been
subjected to very different conditions, have a great advantage in height, weight, constitutional vigor and
fertility over the self fertilised offspring from either one of the same parents.”
However, outcrossing may be abandoned in favor of parthogenesis or selfing (which retain the
advantage of meiotic recombinational repair) under conditions in which the costs of mating are very high. For
instance, costs of mating are high when individuals are rare in a geographic area, such as when there has
been a forest fire and the individuals entering the burned area are the initial ones to arrive. At such times
mates are hard to find, and this favors parthenogenic species.
In the view of the repair and complementation hypothesis, the removal of DNA damage by
recombinational repair produces a new, less deleterious form of informational noise, allelic recombination, as
a by-product. This lesser informational noise generates genetic variation, viewed by some as the major effect
of sex, as discussed in the earlier parts of this article.
[edit] Origin of sexual reproduction

All sexually reproducing organisms derive from a common ancestor which was a single celled
eukaryotic species[citation needed]. Many protists reproduce sexually, as do the multicellular plants, animals,
and fungi. There are a few species which have secondarily lost this feature, such as Bdelloidea and some
parthenocarpic plants.
Organisms need to replicate their genetic material in an efficient and reliable manner. The necessity
to repair genetic damage is one of the leading theories explaining the origin of sexual reproduction. Diploid
individuals can repair a mutated section of its DNA via homologous recombination, since there are two
copies of the gene in the cell and one copy is presumed to be undamaged. A mutation in an haploid
individual, on the other hand, is more likely to become resident, as the DNA repair machinery has no way of
knowing what the original undamaged sequence was.[18] The most primitive form of sex may have been one
organism with damaged DNA replicating an undamaged strand from a similar organism in order to repair
itself.[23]
Another theory is that sexual reproduction originated from selfish parasitic genetic elements that
exchange genetic material (that is: copies of their own genome) for their transmission and propagation. In
some organisms, sexual reproduction has been shown to enhance the spread of parasitic genetic elements
(e.g.: yeast, filamentous fungi).[24] Bacterial conjugation, a form of genetic exchange that some sources
describe as sex, is not a form of reproduction, but rather an example of horizontal gene transfer. However, it
does support the selfish genetic element theory, as it is propagated through such a "selfish gene", the F-
plasmid.[23] Similarly, it has been proposed that sexual reproduction evolved from ancient haloarchaea
through a combination of jumping genes, and swapping plasmids.[25]
A third theory is that sex evolved as a form of cannibalism. One primitive organism ate another one,
but rather than completely digesting it, some of the 'eaten' organism's DNA was incorporated into the 'eater'
organism.[23]
Sex may also be derived from prokaryotic processes. A comprehensive 'origin of sex as vaccination'
theory proposes that eukaryan sex-as-syngamy (fusion sex) arose from prokaryan unilateral sex-as-infection
when infected hosts began swapping nuclearised genomes containing coevolved, vertically transmitted
symbionts that provided protection against horizontal superinfection by more virulent symbionts. Sex-as-
meiosis (fission sex) then evolved as a host strategy to uncouple (and thereby emasculate) the acquired
symbiont genomes.[26]
[edit] Mechanistic origin of sexual reproduction

Though theories positing benefits that lead to the origin of sex are often problematic, several credible
theories on the evolution of the mechanisms of sexual reproduction have been proposed.
[edit] Viral eukaryogenesis

The viral eukaryogenesis (VE) theory proposes that eukaryotic cells arose from a combination of a
lysogenic virus, an archaeon and a bacterium. This model suggests that the nucleus originated when the
lysogenic virus incorporated genetic material from the archaeon and the bacterium and took over the role of
information storage for the amalgam. The archaeal host transferred much of its functional genome to the
virus during the evolution of cytoplasm but retained the function of gene translation and general metabolism.
The bacterium transferred most of its functional genome to the virus as it transitioned into a mitochondrion.
[27]
For these transformations to lead to the eukaryotic cell cycle, the VE hypothesis specifies a pox-like
virus as the lysogenic virus. A pox-like virus is a likely ancestor because of its fundamental similarities with
eukaryotic nuclei. These include a double stranded DNA genome, a linear chromosome with short telomeric
repeats, a complex membrane bound capsid, the ability to produce capped mRNA, and the ability to export
the capped mRNA across the viral membrane into the cytoplasm. The presence of a lysogenic pox-like virus
ancestor explains the development of meiotic division, an essential component of sexual reproduction.[28]
Meiotic division in the VE hypothesis arose because of the evolutionary pressures placed on the
lysogenic virus as a result of its inability to enter into the lytic cycle. This selective pressure resulted in the
development of processes allowing the viruses to spread horizontally throughout the population. The
outcome of this selection was cell-to-cell fusion. (This is distinct from the conjugation methods used by
bacterial plasmids under evolutionary pressure, with important consequences.)[27] The possibility of this kind
of fusion is supported by the presence of fusion proteins in the envelopes of the pox viruses that allow them
to fuse with host membranes. These proteins could have been transferred to the cell membrane during viral
reproduction, enabling cell-to-cell fusion between the virus host and an uninfected cell. The theory proposes
meiosis originated from the fusion between two cells infected with related but different viruses which
recognised each other as uninfected. After the fusion of the two cells, incompatibilities between the two
viruses result in a meiotic-like cell division.[28]
The two viruses established in the cell would initiate replication in response to signals from the host
cell. A mitosis-like cell cycle would proceed until the viral membranes dissolved, at which point linear
chromosomes would be bound together with centromeres. The homologous nature of the two viral
centromeres would incite the grouping of both sets into tetrads. It is speculated that this grouping may be the
origin of crossing over, characteristic of the first division in modern meiosis. The partitioning apparatus of the
mitotic-like cell cycle the cells used to replicate independently would then pull each set of chromosomes to
one side of the cell, still bound by centromeres. These centromeres would prevent their replication in
subsequent division, resulting in four daughter cells with one copy of one of the two original pox-like viruses.
The process resulting from combination of two similar pox viruses within the same host closely mimics
meiosis.[28]
[edit] Neomuran revolution
An alternative theory, proposed by Thomas Cavalier-Smith, was labeled the Neomuran revolution.
The designation "Neomuran revolution" refers to the appearances of the common ancestors of eukaryotes
and archaea. Cavalier-Smith proposes that the first neomurans emerged 850 million years ago. Other
molecular biologists assume that this group appeared much earlier, but Cavalier-Smith dismisses these
claims because they are based on the "theoretically and empirically" unsound model of molecular clocks.
Cavalier-Smith's theory of the Neomuran revolution has implications for the evolutionary history of the cellular
machinery for recombination and sex. It suggests that this machinery evolved in two distinct bouts separated
by a long period of stasis; first the appearance of recombination machinery in a bacterial ancestor which was
maintained for 3 Gy, until the neomuran revolution when the mechanics were adapted to the presence of
nucleosomes. The archaeal products of the revolution maintained recombination machinery that was
essentially bacterial, whereas the eukaryotic products broke with this bacterial continuity. They introduced
cell fusion and ploidy cycles into cell life histories. Cavalier-Smith argues that both bouts of mechanical
evolution were motivated by similar selective forces: the need for accurate DNA replication without loss of
viability.[29]
[edit] See also

Book:Sex

• Asexual reproduction
• Biological reproduction
• Epistasis
• Genetic recombination
• Mutation
• Sexual reproduction
[edit] References
1. ^ a b John Maynard Smith The Evolution of Sex 1978.
2. ^ Doncaster, C. P. et al.; Pound, GE; Cox, SJ (2000). "The ecological cost of sex". Nature
404 (6775): 281–285. doi:10.1038/35005078. PMID 10749210.
3. ^ George C. Williams Sex and Evolution 1975, Princeton University Press, ISBN 0-691-
08152-2
4. ^ a b Matt Ridley 1995 The Red Queen: Sex and the Evolution of Human Nature 1995
Penguin.
5. ^ Weismann, A. 1889. Essays on heredity and kindred biological subjects. Oxford Univ.
Press, Oxford, UK
6. ^ Fisher, R. A. 1930. The genetical theory of natural selection. Clarendon Press, Oxford, UK
7. ^ Muller, H. J. (1932). "Some genetic aspects of sex". Am. Nat. 8: 118–138.
8. ^ Burt, A. (2000). "Perspective: sex, recombination, and the efficacy of selection—was
Weismann right?". Evolution 54 (2): 337–351. PMID 10937212.
9. ^ Van Valen, L. (1973). "A New Evolutionary Law". Evolutionary Theory 1: 1–30.
10.^ Hamilton, W. D. et al. (1990). "Sexual reproduction as an adaptation to resist parasites".
Proceedings of the National Academy of Sciences 87: 3566–3573. doi:10.1073/pnas.87.9.3566.
11.^ Kuma, K.; Iwabe, N.; Miyata, T. (1995). "Functional constraints against variations on
molecules from the tissue-level - slowly evolving brain-specific genes demonstrated by protein-
kinase and immunoglobulin supergene families". Molecular Biology and Evolution 12 (1): 123–130.
PMID 7877487.
12.^ Wolfe KH & Sharp PM. 1993. Mammalian gene evolution - nucleotide-sequence divergence
between mouse and rat. Journal of molecular evolution 37 (4): 441-456 OCT 1993
13.^ Griffiths et al. 1999. Gene mutations, p197-234, in Modern Genetic Analysis, New York,
W.H. Freeman and Company.
14.^ a b Kondrashov, A. S. (1988). "Deleterious mutations and the evolution of sexual
reproduction". Nature 336: 435–440. doi:10.1038/336435a0.
15.^ Whitlock, M. C.; Bourget, D. (2000). "Factors affecting the genetic load in Drosophila:
synergistic epistasis and correlations among fitness components". Evolution 54 (5): 1654–1660.
PMID 11108592.
16.^ Elena, S. F.; Lenski, R. E. (1997). "Test of synergistic interactions among deleterious
mutations in bacteria". Nature 390 (6658): 395–398. doi:10.1038/37108. PMID 9389477.
17.^ Colegrave, N. (2002). "Sex releases the speed limit on evolution". Nature 420 (6916): 664–
666. doi:10.1038/nature01191. PMID 12478292.
18.^ a b Bernstein H, Byerly HC, Hopf FA, Michod RE (1984). "Origin of sex". J. Theor. Biol. 110
(3): 323–51. doi:10.1016/S0022-5193(84)80178-2. PMID 6209512.
19.^ Bernstein H, Byerly HC, Hopf FA, Michod RE (1985). "Genetic damage, mutation, and the
evolution of sex". Science 229 (4719): 1277–81. doi:10.1126/science.3898363. PMID 3898363.
20.^ Bernstein H, Hopf FA, Michod RE (1987). "The molecular basis of the evolution of sex".
Adv. Genet. 24: 323–70. doi:10.1016/S0065-2660(08)60012-7. PMID 3324702.
21.^ Cox MM (2001). "Historical overview: searching for replication help in all of the rec places".
22.^ Darwin C. 1889. The effects of cross and self fertilisation in the vegetable kingdom.
Chapter XII. General Results pp. 436-463. D. Appleton and Company, New York
23.^ a b c Olivia Judson (2002). Dr. Tatiana's sex advice to all creation. New York: Metropolitan
Books. pp. 233–4. ISBN 0-8050-6331-5.
24.^ Hickey D (1982). "Selfish DNA: a sexually-transmitted nuclear parasite". Genetics 101 (3-
4): 519–31. PMID 6293914.
25.^ DasSarma, Shiladitya (2007). "Extreme Microbes". American Scientist. 95. pp. 224–231
26.^ Sterrer W (2002). "On the origin of sex as vaccination". Journal of Theoretical Biology 216
(4): 387–396. doi:10.1006/jtbi.2002.3008. PMID 12151256.
27.^ a b PJ Bell (2001). "Viral eukaryogenesis: was the ancestor of the nucleus a complex DNA
virus?". J Molec Biol 53 (3): 251–6.
28.^ a b c PJ Bell (2006). "Sex and the eukaryotic cell cycle is consistent with a viral ancestry for
the eukaryotic nucleus". J Theor Biol 243 (1): 54–63. doi:10.1016/j.jtbi.2006.05.015. PMID 16846615.
29.^ Cavalier-Smith, Thomas (2006). "Cell evolution and Earth history: stasis and revolution".
Royal Society of Biol Sci 361 (1470): 969–1006. doi:10.1098/rstb.2006.1842. PMID 16754610.

• Bell, Graham (1982). The masterpiece of nature: the evolution and genetics of sexuality.
Berkeley: University of California Press. ISBN 0-520-04583-1.
• Bernstein, Harris; Carol Bernstein (1991). Aging, sex, and DNA repair. Boston: Academic
Press. ISBN 0-12-092860-4.
• Hurst, L.D.; J.R. Peck (1996). "Recent advances in the understanding of the evolution and
maintenance of sex". Trends in Ecology and Evolution 11: 46–52. doi:10.1016/0169-5347(96)81041-
X.
• Levin, Bruce R.; Richard E. Michod (1988). The Evolution of sex: an examination of current
ideas. Sunderland, Mass: Sinauer Associates. ISBN 0-87893-459-6.
• Maynard Smith, John (1978). The evolution of sex. Cambridge, UK: Cambridge University
Press. ISBN 0-521-21887-X.
• Michod, Richard E. (1995). Eros and evolution: a natural philosophy of sex. Reading, Mass:
Addison-Wesley Pub. Co. ISBN 0-201-40754-X.
• "Scientists put sex origin mystery to bed, Wild strawberry research provides evidence on
when gender emerges". MSNBC. http://www.msnbc.msn.com/id/27927661/. Retrieved 2008-11-25.
• Ridley, Mark (1993). Evolution. Oxford: Blackwell Scientific. ISBN 0-632-03481-5.
• Ridley, Mark (2000). Mendel's demon: gene justice and the complexity of life . London:
• Ridley, Matt (1995). The Red Queen: sex and the evolution of human nature . New York:
Penguin Books. ISBN 0-14-024548-0.
• Szathmáry, Eörs; John Maynard Smith (1995). The Major Transitions in Evolution. Oxford:
W.H. Freeman Spektrum. ISBN 0-7167-4525-9.
• Taylor, Timothy (1996). The prehistory of sex: four million years of human sexual culture .
New York: Bantam Books. ISBN 0-553-09694-X.
• Williams, George (1975). Sex and evolution. Princeton, N.J: Princeton University Press.
ISBN 0-691-08147-6.

• The Origin of Sex: Cosmic Solution to an Ancient Mystery
• Why Sex is Good
• An essay summarising the different theories , dating from around 2001


phenotype
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Retrieved from "http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction"
Categories: Evolutionary biology | Sex

W000
Conrad Hal Waddington


Conrad Hal Waddington
8 November 1905
Born
Evesham, Worcestershire, England
26 September 1975
Died
Edinburgh, Scotland
Residence UK
Citizenship UK
Fields Developmental biology, Genetics, Paleontology
Cambridge University, Christ's College

Institutions University of Edinburgh
Wesleyan University
Alma mater Cambridge University
Known for Epigenetic landscape, canalisation, homeorhesis, genetic assimilation, chreod
Influences Alfred North Whitehead
Influenced Jean Piaget, Sanford Kwinter, Gregory Bateson, Margaret Mead

Conrad Hal Waddington FRS FRSE (1905–1975) was a developmental biologist, paleontologist,
geneticist, embryologist and philosopher who laid the foundations for systems biology. He had wide interests
that included poetry and painting, as well as left-wing political leanings.[ citation needed]
Contents
[hide]
• 1 Life
• 2 Epigenetic landscape
• 3 Waddington as an organiser
• 4 References
• 5 Selected works
• 5.1 Books
• 5.2 Papers
[edit] Life
Waddington, known as "Wad" to his friends and "Con" to family, was born to Hal and Mary Ellen
(Warner) Waddington, 8 November 1905. Until nearly three years of age, Waddington lived with his parents
in India, where his father worked on a tea estate in the Wayanad district. In 1910, at the age of four, he was
sent to live with family in England including his aunt, uncle, and Quaker grandmother. His parents remained
in India until 1928. During his childhood, he was particularly attached to a local druggist and distant relation,
Dr. Doeg. Doeg, who Waddington called "Grandpa", introduced Waddington to a wide range of sciences from
chemistry to geology.[1] During the year following the completion of his entrance exams to university,
Waddington received an intense course in chemistry from E. J. Holmyard. Aside from being "something of a
genius of a [chemistry] teacher," Holmyard introduced Waddington to the "Alexandrian Gnostics" and the
"Arabic Alchemists." From these lessons in metaphysics, Waddington first gained an appreciation for
interconnected holistic systems. Waddington reflected that this early education prepared him for Alfred North
Whitehead's philosophy in the 1920s and 30s and the cybernetics of Norbert Wiener and others in the 1940s.
[2]
He attended Clifton College and Sidney Sussex College, Cambridge University. He took the Natural
Sciences Tripos, earning a First in Part II in geology in 1926.[3] He took up a Lecturership in Zoology and
was a Fellow of Christ's College until 1942. His friends included Gregory Bateson, Walter Gropius, C. P.
Snow, Solly Zuckerman, Joseph Needham, and J. D. Bernal.[4][5] His interests began with palaeontology but
moved on to the heredity and development of living things. He also studied philosophy.
During World War II he was involved in operational research with the Royal Air Force and became
scientific advisor to the Commander in Chief of Coastal Command from 1944 to 1945. After the war he
became Professor of Animal Genetics at the University of Edinburgh. He would stay at Edinburgh for the rest
of life with the exception of one year (1960–1961) when he was a Fellow on the faculty in the Center for
Advanced Studies at Wesleyan University in Middletown, Connecticut.[6] His personal papers are largely
kept at the University of Edinburgh library.
Waddington was married twice. His first marriage produced a son, C. Jake Waddington, professor of
physics at the University of Minnesota, but ended in 1936. He then married Justin Blanco White, daughter of
the writer Amber Reeves, with whom he had two daughters, mathematician Dusa McDuff and anthropologist
Caroline Humphrey.[7]
In the early 1930s, Waddington and many other embryologists looked for the molecules that would
induce the amphibian neural tube. The search was, of course, beyond the technology of that time, and most
embryologists moved away from such deep problems. Waddington, however, came to the view that the
answers to embryology lay in genetics, and in 1935 went to Thomas Hunt Morgan's Drosophila laboratory in
California, even though this was a time when most embryologists felt that genes were unimportant and just
played a role in minor phenomena such as eye colour.
In the late 30's, Waddington produced formal models about how gene regulatory products could
generate developmental phenomena, showed how the mechanisms underpinning Drosophila development
could be studied through a systematic analysis of mutations that affected the development of the Drosophila
wing (this was the essence of the approach that won the 1995 Nobel prize in medicine for Christiane
Nüsslein-Volhard and Eric F. Wieschaus). In a period of great creativity at the end of the 1930s, he also
discovered mutations that affected cell phenotypes and wrote his first textbook of developmental epigenetics,
a term that then meant the external manifestation of genetic activity.
Waddington also coined other essential concepts, such as canalisation, which refers to the ability of
an organism to produce the same phenotype despite variation in genotype or environment. He also identified
a mechanism called genetic assimilation which would allow an animal’s response to an environmental stress
to become a fixed part of its developmental repertoire, and then went on to show that the mechanism would
work. He thus demonstrated that the ideas of inheritance put forward by Jean-Baptiste Lamarck could, in
principle at least, occur.
In 1972, Waddington founded the Centre for Human Ecology.
[edit] Epigenetic landscape

Waddington's epigenetic landscape is a metaphor for how gene regulation modulates development.
[8] One is asked to imagine a number of marbles rolling down a hill towards a wall. The marbles will compete
for the grooves on the slope, and come to rest at the lowest points. These points represent the eventual cell
fates, that is, tissue types. Waddington coined the term Chreode to represent this cellular developmental
process. This idea was actually based on experiment: Waddington found that one effect of mutation (which
could modulate the epigenetic landscape) was to affect how cells differentiated. He also showed how
mutation could affect the landscape and used this metaphor in his discussions on evolution—he was the first
person to emphasise that evolution mainly occurred through mutations that affected developmental anatomy.
[edit] Waddington as an organiser

Waddington was very active in advancing biology as a discipline. He contributed to a book on the
role of the sciences in times of war, and helped set up several professional bodies representing biology as a
discipline.[9]
A remarkable number of his contemporary colleagues in Edinburgh became Fellows of the Royal
Society during his time there, or shortly thereafter.[10]
Waddington was an old-fashioned intellectual who lived in both the arts and science milieus of the
1950s and wrote widely. His 1960 book "Behind Appearance; a Study Of The Relations Between Painting
And The Natural Sciences In This Century" (MIT press) not only has wonderful pictures but is still worth
reading.
Waddington was, without doubt, the most original and important thinker about developmental biology
of the pre-molecular age and the medal of the British Society for Developmental Biology is named after him.
[edit] References
1. ^ Robertson, Alan. 1977. "Conrad Hal Waddington. 8 November 1905–26 September 1975."
Biographical Memoirs of Fellows of the Royal Society 23, 575-622. Pp. 575-76.
2. ^ Waddington, C. H. 1975. The Evolution of an Evolutionist . Ithica, NY: Cornell University
Press. Pg. 2.
3. ^ Robertson, Alan. 1977. "Conrad Hal Waddington. 8 November 1905 — 26 September
1975." Biographical Memoirs of Fellows of the Royal Society 23, 575-622. Pg 577.
4. ^ Robertson, Alan. 1977. "Conrad Hal Waddington. 8 November 1905 — 26 September
1975." Biographical Memoirs of Fellows of the Royal Society 23, 575-622. Pp. 579-580.
5. ^ Yoxen, Edward. 1986. "Form and Strategy in Biology: Reflections on the Career of C. H.
Waddington." In A History of Embryology, edited by T. J Horder, J. A Witkowski, and C. C Wylie.
Cambridge: Cambridge University Press. Pp. 310-11.
6. ^ "Guide to the Center for Advanced Studies Records, 1958 - 1969". Wesleyan.edu.
http://www.wesleyan.edu/libr/schome/FAs/ce1000-137.html. Retrieved 2010-04-04.
7. ^ Robertson, Alan. 1977. Conrad Hal Waddington. 8 November 1905 — 26 September 1975.
Biographical Memoirs of Fellows of the Royal Society 23, 575-622. P. 578
8. ^ Goldberg, A. D., Allis, C. D., & Bernstein, E. (2007). Epigenetics: A landscape takes shape.
Cell, 128, 635-638.
9. ^ [1] Hall BK. 2004. In search of evolutionary developmental mechanisms: the 30-year gap
between 1944 and 1974. J Exp Zool B Mol Dev Evol. 2004 Jan 15;302(1):5-18.
10.^ Robertson, Alan. 1977. Conrad Hal Waddington. 8 November 1905 — 26 September 1975.
Biographical Memoirs of Fellows of the Royal Society 23, 575-622. P. 585.
[edit] Selected works
[edit] Books
• Waddington, C. H. (1940). Organisers & genes. Cambridge: Cambridge University Press.
• Waddington, C. H. (1941). The Scientific Attitude, Pelican Books
• Waddington, C. H. (1946). How animals develop. London : George Allen & Unwin Ltd.
• Waddington, C. H. (1953). The Epigenetics of birds. Cambridge : Cambridge University
Press.
• Waddington, C. H. (1956). Principles of Embryology. London : George Allen & Unwin.
• Waddington, C. H. (1957). The Strategy of the Genes. London : George Allen & Unwin.
• Waddington, C. H. (1959). Biological organisation cellular and subcellular : proceedings of a
Symposium. London: Pergamon Press.
• Waddington, C. H. (1960). The ethical animal. London : George Allen & Unwin.
• Waddington, C. H. (1961). The human evolutionary system. In: Michael Banton (Ed.),
Darwinism and the Study of Society. London: Tavistock.
• Waddington, C. H. (1966). Principles of development and differentiation . New York:
Macmillan Company.
• Waddington, C. H. (1966). New patterns in genetics and development . New York: Columbia
University Press.
• Waddington, C. H., ed. (1968–72). Towards a Theoretical Biology. 4 vols. Edinburgh:
Edinburgh University Press.
• Waddington, C. H., Kenny, A., Longuet-Higgins, H.C., Lucas, J.R. (1972). The Nature of
Mind, Edinburgh: Edinburgh University Press (1971-3 Gifford Lectures in Edinburgh, online)
• Waddington, C. H., Kenny, A., Longuet-Higgins, H.C., Lucas, J.R. (1973). The Development
of Mind, Edinburgh: Edinburgh University Press (1971-3 Gifford Lectures in Edinburgh, online)
• Waddington, C. H. (1977) (published posthumously). Tools for Thought. London: Jonathan
Cape Ltd.
[edit] Papers
• Waddington, C. H. 1953. Genetic assimilation of an acquired character. Evolution 7: 118-
126.
• Waddington, C. H. 1956. Genetic assimilation of the bithorax phenotype. Evolution 10: 1-13.
• Waddington, C. H. 1961. Genetic assimilation. Advances Genet. 10: 257-290.
• Waddington, C. H. 1974. A Catastrophe Theory of Evolution. Annals of the New York
Academy of Sciences 231: 32-42.

• NAHSTE Project Record of C.H. Waddington
• Induction and the Origin of Developmental Genetics - works by Salome Gluecksohn-
Schoenhimer and Conrad Hal Waddington
• Epigenetics News
W000
Richard Lewontin

Richard Lewontin
29 March 1929 (1929-03-29) (age 81)

Born
New York
Nationality United States
Fields Genetics, Evolutionary biology, Population genetics
Institutions Harvard
Alma mater Columbia University
Doctoral advisor Theodosius Dobzhansky
Known for Evolutionary biology, Population genetics

Richard Charles "Dick" Lewontin (born March 29, 1929) is an American evolutionary biologist,
geneticist and social commentator. A leader in developing the mathematical basis of population genetics and
evolutionary theory, he pioneered the notion of using techniques from molecular biology such as gel
electrophoresis to apply to questions of genetic variation and evolution.
In a pair of 1966 papers co-authored with J.L. Hubby in the journal Genetics, Lewontin helped set the
stage for the modern field of molecular evolution.
In 1979 he and Stephen Jay Gould introduced the term "spandrel" into evolutionary theory. A
spandrel is an evolved biological feature which arises as the result of the modification of another trait.
Lewontin strongly opposes genetic determinism, especially as allegedly expressed by sociobiology
and evolutionary psychology.
Contents
[hide]
• 1 Biography
• 2 Work in population genetics
• 3 Work on human genetic diversity
• 4 Critique of orthodox evolutionary biology
• 4.1 Sociobiology and evolutionary psychology
• 4.2 Agribusiness
• 5 Recognition
• 6 Bibliography
• 7 Footnotes
• 8 References
[edit] Biography
Lewontin was born in New York City to Jewish parents. Lewontin attended Forest Hills High School
and the École Libre des Hautes Études in New York. In 1951, he obtained a bachelor's degree in biology
from Harvard University. In 1952, he received a master's degree in mathematical statistics followed by a
doctorate in zoology in 1954, both from Columbia University where he was a student of Theodosius
Dobzhansky. Lewontin held faculty positions at North Carolina State University, the University of Rochester,
and the University of Chicago. In 1973 Lewontin served as Alexander Agassiz Professor of Zoology and
Professor of Biology at Harvard until 1998, and as of 2003 was the Alexander Agassiz Research Professor at
Harvard. Lewontin has worked with and had great influence on many philosophers of biology, including
William C. Wimsatt, Elliott Sober, Philip Kitcher, Elisabeth Lloyd, Peter Godfrey-Smith, and Robert Brandon,
often inviting them to work in his lab.
[edit] Work in population genetics

Lewontin has worked in both theoretical and experimental population genetics. A hallmark of his work
has been an interest in new technology. He was the first person to do a computer simulation of the behavior
of a single locus (previous simulation work having been of models with multiple loci). In 1960 he and Ken-Ichi
Kojima were the first population geneticists to give the equations for change of haplotype frequencies with
interacting natural selection at two loci.[1] This set off a wave of theoretical work on two-locus selection in the
1960s and 1970s. Their paper gave a theoretical derivation of the equilibria expected, and also investigated
the dynamics of the model by computer iteration. Lewontin later introduced the D' measure of linkage
disequilibrium.[2] (An achievement that he would be less happy to claim is that he introduced the name
"linkage disequilibrium" itself, one about which many population geneticists have been unenthusiastic).
In 1966, he and Jack Hubby published a paper that revolutionized population genetics.[3] They used
protein gel electrophoresis to survey dozens of loci in Drosophila pseudoobscura, and reported that a large
fraction of the loci were polymorphic, and that at the average locus there was about a 15% chance that the
individual was heterozygous. (Harry Harris reported similar results for humans at about the same time).[4]
Previous work with gel electrophoresis had been reports of variation in single loci and did not give any sense
of how common variation was.
Lewontin and Hubby's paper also discussed the possible explanation of the high levels of variability
by either balancing selection or neutral mutation. Although they did not commit themselves to advocating
neutrality, this was the first clear statement of the neutral theory for levels of variability within species.
Lewontin and Hubby's paper had great impact—the discovery of high levels of molecular variability gave
population geneticists ample material to work on, and gave them access to variation at single loci. The
possible theoretical explanations of this rampant polymorphism became the focus of most population
genetics work thereafter. Martin Kreitman was later to do a pioneering survey of population-level variability in
DNA sequences while a Ph.D. student in Lewontin's lab.[5]
[edit] Work on human genetic diversity

In a landmark paper, Richard Lewontin identified that most of the variation (80-85%) within human
populations is found within local geographic groups and differences attributable to traditional "race" groups
are a minor part of human genetic variability (1-15%).[6] In a 2003 paper, A.W.F. Edwards criticized
Lewontin's conclusion, that because the probability of racial misclassification of an individual based on
variation in a single genetic locus is approximately 30%, race is an invalid taxonomic construct, terming it
Lewontin's Fallacy.
[edit] Critique of orthodox evolutionary biology

In 1975, when E. O. Wilson's book Sociobiology proposed evolutionary explanations for human
social behaviors, a number of biologists responded negatively, including Lewontin, S.J. Gould, Ruth
Hubbard, and others.[7]
Lewontin and his late Harvard colleague Stephen Jay Gould introduced the term spandrel to
evolutionary biology, inspired by the architectural term "spandrel", in an influential 1979 paper "The spandrels
of San Marco and the Panglossian paradigm: a critique of the adaptationist programme." "Spandrels" were
described as features of an organism that exist as a necessary consequence of other (perhaps adaptive)
features, but do not directly improve fitness (and thus are not necessarily adaptive).[8] The relative frequency
of spandrels versus adaptations continues to stir controversy in evolutionary biology.
Lewontin was an early proponent of a hierarchy of levels of selection in his article "The Units of
Selection". He has been a major influence on philosophers of biology, notably William C. Wimsatt (who
taught with Lewontin and Richard Levins at the University of Chicago), Robert Brandon and Elisabeth Lloyd
(who studied with Lewontin as graduate students), Philip Kitcher, and Elliot Sober. Lewontin briefly argued for
the historical nature of biological causality in "Is Nature Probable or Capricious?"
In "Organism and Environment" in Scientia, and in more popular form in the last chapter of Biology
as Ideology, Lewontin argued that while traditional Darwinism has portrayed the organism as passive
recipient of environmental influences, a correct understanding should emphasize the organism as an active
constructor of its own environment. Niches are not pre-formed, empty receptacles into which organisms are
inserted, but are defined and created by organisms. The organism-environment relationship is reciprocal and
dialectical. M.W. Feldman, K.N. Laland, and F.J. Odling-Smee among others have developed Lewontin's
conception in more detailed models.
Lewontin has long been a critic of traditional neo-Darwinian approaches to adaptation. In his article
"Adaptation" in the Italian Encyclopedia Einaudi, and in a toned-down version in Scientific American, he
emphasized the need to give an engineering characterization of adaptation separate from measurement of
number of offspring, rather than simply assuming organs or organisms are at adaptive optima.[9] Lewontin
has claimed that his more general, technical criticism of adaptationism grew out of his recognition that the
fallacies of sociobiology reflect fundamentally flawed assumptions of adaptiveness of all traits in much of the
modern evolutionary synthesis.
Lewontin accused neo-Darwinists of telling “Just So” stories when they try to show how natural
selection explains such novelties as long-necked giraffes.[10]
[edit] Sociobiology and evolutionary psychology

Along with others, such as Gould, Lewontin has been a persistent critic of some themes in neo-
Darwinism; specifically, he has criticised proponents of sociobiology and evolutionary psychology such as
Edward O. Wilson and Richard Dawkins, who attempt to explain animal behaviour and social structures in
terms of evolutionary advantage or strategy—this has been controversial when applied to humans, because
some see it as genetic determinism. Lewontin, in his writing, calls for what he considers a more nuanced
view of evolution, which he claims requires a more careful understanding of the context of the whole
organism as well as the environment.
Such concerns about what he views as the oversimplification of genetics led Lewontin to be a
frequent commentator in debates, and he has lectured widely to promote his views on evolutionary biology
and science. In books such as Not in Our Genes (co-authored with Steven Rose and Leon J. Kamin) and
numerous articles, Lewontin has questioned much of the claimed heritability of human behavioral traits such
as intelligence as measured by IQ tests, promoted by books such as The Bell Curve.
Lewontin has been criticized by some academics for a rejection of sociobiology for non-scientific
reasons. Some credit this rejection to political beliefs (Wilson 1995). Lewontin has at times identified himself
as Marxist or at least left-leaning (Levins and Lewontin 1985). Others (Kitcher 1985) have countered that
Lewontin's criticisms of sociobiology are genuine scientific concerns about the discipline and claim that
attacking Lewontin's motives amount to an ad hominem argument.
[edit] Agribusiness
Lewontin has also written on the economics of agribusiness. He has contended that hybrid corn was
developed and propagated not because of its superior quality, but because it allowed agribusiness
corporations to force farmers to buy new seed each year rather than plant seed produced by their previous
crop of corn. Lewontin testified in an unsuccessful suit in California challenging the state's financing of
research to develop automatic tomato pickers, favoring the profits of agribusiness over the employment of
farm workers.
[edit] Recognition
• 1961: Fulbright Fellowship
• 1961: National Science Foundation Senior Postdoctoral Fellow
• 1970s: Membership of the National Academy of Sciences (later resigned)
• 1994: Sewall Wright Award from the American Society of Naturalists
[edit] Bibliography
• Lewontin, R. C.; K. Kojima (1960). "The evolutionary dynamics of complex polymorphisms".
Evolution (Evolution, Vol. 14, No. 4) 14 (4): 458–472. doi:10.2307/2405995.
• Lewontin, R. C. (1966). "Is Nature Probable or Capricious?". Bio Science 16: 25–27.
• Lewontin, R. C.; J. L. Hubby (1966). "A molecular approach to the study of genic
heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural
populations of Drosophila pseudoobscura". Genetics 54 (2): 595–609. PMID 5968643.
• Lewontin, R. C. (1970). "The Units of Selection". Annual Reviews of Ecology and
Systematics 1: 1–18. doi:10.1146/annurev.es.01.110170.000245.
• "The Apportionment of Human Diversity," Evolutionary Biology, vol. 6 (1972) pp. 391–398.
• Lewontin, R. C. (1974). The genetic basis of evolutionary change. New York: Columbia
• "Adattamento," Enciclopedia Einaudi, (1977) vol. 1, 198-214.
• "Adaptation," Scientific American, vol. 239, (1978) 212-228.
• Gould, S.J., and Richard Lewontin (1979). "The spandrels of San Marco and the Panglossion
paradigm: a critique of the adaptationist programme". Proc R Soc Lond B 205 (1161): 581–598.
doi:10.1098/rspb.1979.0086. PMID 42062.
• Lewontin, R. C. (1995). Human diversity (2nd ed.). New York: Scientific American Library.
ISBN 0-7167-6013-4.
• "The Organism as Subject and Object of Evolution," Scientia vol. 188 (1983) 65-82.
• Not in Our Genes: Biology, Ideology and Human Nature (with Steven Rose and Leon J.
Kamin) (1984) ISBN 0-394-72888-2
• The Dialectical Biologist (with Richard Levins), Harvard University Press (1985) ISBN 0-674-
20283-X
• Biology as Ideology: The Doctrine of DNA (1991) ISBN 0-06-097519-9
• The Triple Helix: Gene, Organism, and Environment , Harvard University Press (2000) ISBN
0-674-00159-1
• It Ain't Necessarily So: The Dream of the Human Genome and Other Illusions , New York
Review of Books (2000)
• Biology Under The Influence: Dialectical Essays on the Coevolution of Nature and Society
(with Richard Levins), (2007)
[edit] Footnotes
1. ^ Lewontin, R. C. and K. Kojima (1960). "The evolutionary dynamics of complex
polymorphisms". Evolution 14: 458-472.
2. ^ Lewontin, R. C. (1964). "The interaction of selection and linkage. I. General considerations;
heterotic models". Genetics 49: 49-67.
3. ^ Lewontin, R. C.; J. L. Hubby (1966). "A molecular approach to the study of genic
heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural
populations of Drosophila pseudoobscura". Genetics 54: 595-609.
4. ^ Harris, H. (1966) "Enzyme polymorphisms in man". Proceedings of the Royal Society of
London, Series B, Biological Sciences. 164 (955): 298-310.
5. ^ Kreitman, M. (1983) "Nucleotide polymorphism at the Alcohol dehydrogenase locus of.
Drosophila melanogaster", Nature 304: 412–417.
6. ^ Lewontin, R (1972). "The Apportionment of Human Diversity". Evolutionary Biology 6: 391–
398.
7. ^ Elizabeth Allen et al., 1975, "Against 'Sociobiology'", The New York Review of Books,
http://www.nybooks.com/articles/archives/1975/nov/13/against-sociobiology/.
8. ^ Gould SJ, Lewontin RC (1979). "The spandrels of San Marco and the Panglossian
paradigm: a critique of the adaptationist programme". Proc. R. Soc. Lond., B, Biol. Sci. 205 (1161):
581–98. doi:10.1098/rspb.1979.0086. PMID 42062.
9. ^ Lewontin RC (1978). "Adaptation". Sci. Am. 239 (3): 212–8, 220, 222 passim.
doi:10.1038/scientificamerican0978-212. PMID 705323.
10.^ "Science Contra Darwin", Newsweek, April 8, 1985, p.80
[edit] References
• Philip Kitcher (1985). Vaulting Ambition : Sociobiology and the Quest for Human Nature . MIT
Press. ISBN 0-262-11109-8.
• Steven Pinker (2002). The Blank Slate: The Denial of Human Nature in Modern Intellectual
Life. Penguin Press.
• Rama S. Singh, Costas Krimbas, Diane Paul, and John Beatty (2001). Thinking about
Evolution. Cambridge University Press. - a two volume Festschrift for Lewontin with a full
bibliography
• Edward O. Wilson (1995). "Science and ideology". Academic Questions 8.
• Richard Lewontin (2004). The Triple Helix: Gene, Organism and Environment. MIT Press.

Wikiquote has a collection of quotations related to: Richard Lewontin
• an interview given at Berkeley in 2003

• a profile and bibliography
• Gene, Organism and Environment: Bad Metaphors and Good Biology - RealAudio stream of
Hitchcock lecture on UCTV
• The Concept of Race: The Confusion of Social and Biological Reality - RealAudio stream of
Hitchcock lecture on UCTV
• Internalism and Externalism in Biology , lecture delivered at Harvard university on December
13, 2007.


phenotype
Non-genetic
Developmental

W000
Nature versus nurture


The nature versus nurture debate concerns the relative importance of an individual's innate qualities
("nature," i.e. nativism, or innatism) versus personal experiences ("nurture," i.e. empiricism or behaviorism) in
determining or causing individual differences in physical and behavioral traits.
"Nature versus nurture" in its modern sense was coined[1][2][3] by the English Victorian polymath
Francis Galton in discussion of the influence of heredity and environment on social advancement, although
the terms had been contrasted previously, for example by Shakespeare (in his play, The Tempest: 4.1).
Galton was influenced[4] by the book On the Origin of Species written by his cousin, Charles Darwin. The
concept embodied in the phrase has been criticized[3][4] for its binary simplification of two tightly interwoven
parameters, as for example an environment of wealth, education and social privilege are often historically
passed to genetic offspring.
The view that humans acquire all or almost all their behavioral traits from "nurture" is known as
tabula rasa ("blank slate"). This question was once considered to be an appropriate division of developmental
influences, but since both types of factors are known to play such interacting roles in development, many
modern psychologists consider the question naive—representing an outdated state of knowledge.[5][6][6][7][8]
Psychologist Donald Hebb is said to have once answered a journalist's question of "which, nature or nurture,
contributes more to personality?" by asking in response, "Which contributes more to the area of a rectangle,
its length or its width?"[9][10][11][12] That is, the idea that either nature or nurture explains a creature's
behavior is a sort of single cause fallacy.
In the social and political sciences, the nature versus nurture debate may be contrasted with the
structure versus agency debate (i.e. socialization versus individual autonomy). For a discussion of nature
versus nurture in language and other human universals, see also psychological nativism.
Contents
[hide]
• 1 Scientific approach
• 2 Heritability estimates
• 3 Interaction of genes and environment
• 4 IQ debate
• 5 Personality traits
• 5.1 Advanced techniques
• 6 Philosophical difficulties
• 6.1 Are the traits real?
• 6.2 Biological determinism
• 6.3 Is the problem real?
• 7 Myths about identity
• 8 History of the nature versus nurture debate
• 9 See also
• 10 References
[edit] Scientific approach

To disentangle the effects of genes and environment, behavioral geneticists perform adoption and
twin studies. Behavioral geneticists do not generally use the term "nurture" to explain that portion of the
variance for a given trait (such as IQ or the Big Five personality traits) that can be attributed to environmental
effects. Instead, two different types of environmental effects are distinguished: shared family factors (i.e.,
those shared by siblings, making them more similar) and nonshared factors (i.e., those that uniquely affect
individuals, making siblings different). To express the portion of the variance due to the "nature" component,
behavioral geneticists generally refer to the heritability of a trait.
With regard to the Big Five personality traits as well as adult IQ in the general U.S. population, the
portion of the overall variance that can be attributed to shared family effects is often negligible.[13] On the
other hand, most traits are thought to be at least partially heritable. In this context, the "nature" component of
the variance is generally thought to be more important than that ascribed to the influence of family
upbringing.
In her Pulitzer Prize-nominated book The Nurture Assumption, author Judith Harris argues that
"nurture," as traditionally defined in terms of family upbringing does not effectively explain the variance for
most traits (such as adult IQ and the Big Five personality traits) in the general population of the United
States. On the contrary, Harris suggests that either peer groups or random environmental factors (i.e., those
that are independent of family upbringing) are more important than family environmental effects.[14][15]
Although "nurture" has historically been referred to as the care given to children by the parents, with
the mother playing a role of particular importance, this term is now regarded by some as any environmental
(not genetic) factor in the contemporary nature versus nurture debate. Thus the definition of "nurture" has
expanded to include influences on development arising from prenatal, parental, extended family, and peer
experiences, and extending to influences such as media, marketing, and socio-economic status. Indeed, a
substantial source of environmental input to human nature may arise from stochastic variations in prenatal
development.[16][17]
[edit] Heritability estimates
This chart illustrates three patterns one might see when studying the influence of genes and
environment on traits in individuals. Trait A shows a high sibling correlation, but little heritability (i.e. high
shared environmental variance c2; low heritability h2). Trait B shows a high heritability since correlation of
trait rises sharply with degree of genetic similarity. Trait C shows low heritability, but also low correlations
generally; this means Trait C has a high nonshared environmental variance e2. In other words, the degree to
which individuals display Trait C has little to do with either genes or broadly predictable environmental factors
—roughly, the outcome approaches random for an individual. Notice also that even identical twins raised in a
common family rarely show 100% trait correlation.
While there are many examples of single-gene-locus traits, current thinking in biology discredits the
notion that genes alone can determine most complex traits. At the molecular level, DNA interacts with signals
from other genes and from the environment. At the level of individuals, particular genes influence the
development of a trait in the context of a particular environment. Thus, measurements of the degree to which
a trait is influenced by genes versus environment will depend on the particular environment and genes
examined. In many cases, it has been found that genes may have a substantial contribution, including
psychological traits such as intelligence and personality.[18] Yet these traits may be largely influenced by
environment in other circumstances, such as environmental deprivation.
A researcher seeking to quantify the influence of genes or environment on a trait needs to be able to
separate the effects of one factor away from that of another. This kind of research often begins with attempts
to calculate the heritability of a trait. Heritability quantifies the extent to which variation among individuals in a
trait is due to variation in the genes those individuals carry. In animals where breeding and environments can
be controlled experimentally, heritability can be determined relatively easily. Such experiments would be
unethical for human research. This problem can be overcome by finding existing populations of humans that
reflect the experimental setting the researcher wishes to create.
One way to determine the contribution of genes and environment to a trait is to study twins. In one
kind of study, identical twins reared apart are compared to randomly selected pairs of people. The twins
share identical genes, but different family environments. In another kind of twin study, identical twins reared
together (who share family environment and genes) are compared to fraternal twins reared together (who
also share family environment but only share half their genes). Another condition that permits the
disassociation of genes and environment is adoption. In one kind of adoption study, biological siblings reared
together (who share the same family environment and half their genes) are compared to adoptive siblings
(who share their family environment but none of their genes).
Some have pointed out that environmental inputs affect the expression of genes (see the article on
epigenetics). This is one explanation of how environment can influence the extent to which a genetic
disposition will actually manifest.[citation needed] The interactions of genes with environment, called gene–
environment interactions, are another component of the nature–nurture debate. A classic example of gene–
environment interaction is the ability of a diet low in the amino acid phenylalanine to partially suppress the
genetic disease phenylketonuria. Yet another complication to the nature–nurture debate is the existence of
gene-environment correlations. These correlations indicate that individuals with certain genotypes are more
likely to find themselves in certain environments. Thus, it appears that genes can shape (the selection or
creation of) environments. Even using experiments like those described above, it can be very difficult to
determine convincingly the relative contribution of genes and environment.
[edit] Interaction of genes and environment

may be challenged and removed. (June 2008)
In only very few cases is it fair to say that a trait is due almost entirely to nature, or almost entirely to
nurture.[citation needed] In the case of most diseases now strictly identified as genetic, such as Huntington's
disease, there is a better than 99.9% correlation between having the identified gene and the disease and a
similar correlation for not having either. On the other hand, Huntington's animal models live much longer or
shorter lives depending on how they are cared for (animal husbandry).
At the other extreme, traits such as native language are environmentally determined: linguists have
found that any child (if capable of learning a language at all) can learn any human language with equal
facility. With virtually all biological and psychological traits, however, genes and environment work in concert,
communicating back and forth to create the individual.
But even in the most clear-cut cases, extreme genetic or environmental conditions can overrule the
other—if a child is born mute due to a genetic mutation, it will not learn to speak any language regardless of
the environment; similarly, someone who is practically certain to eventually develop Huntington's disease
according to their genotype may die in an unrelated accident (an environmental event) long before the
disease will manifest itself.
Examples of environmental, interactional, and genetic traits are:
Predominantly Environmental Interactional Predominantly Genetic
Specific language Height Blood type
Specific religion Weight Eye color
Skin color
The "two buckets" view of heritability.
More realistic "homogenous mudpie" view of heritability.

Steven Pinker (2004) likewise described several examples:
concrete behavioral traits that patently depend on content provided by the home or culture—
which language one speaks, which religion one practices, which political party one supports—are not
heritable at all. But traits that reflect the underlying talents and temperaments—how proficient with
language a person is, how religious, how liberal or conservative—are partially heritable.
When traits are determined by a complex interaction of genotype and environment it is possible to
measure the heritability of a trait within a population. However, many non-scientists who encounter a report
of a trait having a certain percentage heritability imagine non-interactional, additive contributions of genes
and environment to the trait. As an analogy, some laypeople may think of the degree of a trait being made up
of two "buckets," genes and environment, each able to hold a certain capacity of the trait. But even for
intermediate heritabilities, a trait is always shaped by both genetic dispositions and the environments in
which people develop, merely with greater and lesser plasticities associated with these heritability measures.
Heritability measures always refer to the degree of variation between individuals in a population .
These statistics cannot be applied at the level of the individual. It is incorrect to say that since the heritability
index of personality is about 0.6, you got 60% of your personality from your parents and 40% from the
environment. To help to understand this, imagine that all humans were genetic clones. The heritability index
for all traits would be zero (all variability between clonal individuals must be due to environmental factors).
And, contrary to erroneous interpretations of the heritibility index, as societies become more egalitarian
(everyone has more similar experiences) the heritability index goes up (as environments become more
similar, variability between individuals is due more to genetic factors).
A highly genetically loaded trait (such as eye color) still assumes environmental input within normal
limits (a certain range of temperature, oxygen in the atmosphere, etc.). A more useful distinction than "nature
vs. nurture" is "obligate vs. facultative"—under typical environmental ranges, what traits are more "obligate"
(e.g., the nose—everyone has a nose) or more "facultative" (sensitive to environmental variations, such as
specific language learned during infancy). Another useful distinction is between traits that are likely to be
adaptations (such as the nose) and those that are byproducts of adaptations (such the white color of bones),
or are due to random variation (non-adaptive variation in, say, nose shape or size).
[edit] IQ debate
Main article: Heritability of IQ
Evidence suggests that family environmental factors may have an effect upon childhood IQ,
accounting for up to a quarter of the variance. On the other hand, by late adolescence this correlation
disappears, such that adoptive siblings are no more similar in IQ than strangers.[19]
Moreover, adoption studies indicate that, by adulthood, adoptive siblings are no more similar in IQ
than strangers (IQ correlation near zero), while full siblings show an IQ correlation of 0.6. Twin studies
reinforce this pattern: monozygotic (identical) twins raised separately are highly similar in IQ (0.74), more so
than dizygotic (fraternal) twins raised together (0.6) and much more than adoptive siblings (~0.0).[20]
[edit] Personality traits

Personality is a frequently cited example of a heritable trait that has been studied in twins and
adoptions. Identical twins reared apart are far more similar in personality than randomly selected pairs of
people. Likewise, identical twins are more similar than fraternal twins. Also, biological siblings are more
similar in personality than adoptive siblings. Each observation suggests that personality is heritable to a
certain extent. However, these same study designs allow for the examination of environment as well as
genes. Adoption studies also directly measure the strength of shared family effects. Adopted siblings share
only family environment. Unexpectedly, some adoption studies indicate that by adulthood the personalities of
adopted siblings are no more similar than random pairs of strangers. This would mean that shared family
effects on personality are zero by adulthood. As is the case with personality, non-shared environmental
effects are often found to out-weigh shared environmental effects. That is, environmental effects that are
typically thought to be life-shaping (such as family life) may have less of an impact than non-shared effects,
which are harder to identify. One possible source of non-shared effects is the environment of pre-natal
development. Random variations in the genetic program of development may be a substantial source of non-
shared environment. These results suggest that "nurture" may not be the predominant factor in
"environment."[citation needed]
[edit] Advanced techniques

The power of quantitative studies of heritable traits has been expanded by the development of new
techniques. Developmental genetic analysis examines the effects of genes over the course of a human
lifespan. For example, early studies of intelligence, which mostly examined young children, found that
heritability measures 40–50%. Subsequent developmental genetic analyses found that variance attributable
to additive environmental effects is less apparent in older individuals,[21][22][23] with estimated heritability of
IQ being higher than that in adulthood. However, the high IQ heritability estimates are derived with
questionable methodologies, according to work by Peter Schönemann.[24]
Another advanced technique, multivariate genetic analysis, examines the genetic contribution to
several traits that vary together. For example, multivariate genetic analysis has demonstrated that the genetic
determinants of all specific cognitive abilities (e.g., memory, spatial reasoning, processing speed) overlap
greatly, such that the genes associated with any specific cognitive ability will affect all others. Similarly,
multivariate genetic analysis has found that genes that affect scholastic achievement completely overlap with
the genes that affect cognitive ability.
Extremes analysis, examines the link between normal and pathological traits. For example, it is
hypothesized that a given behavioral disorder may represent an extreme of a continuous distribution of a
normal behavior and hence an extreme of a continuous distribution of genetic and environmental variation.
Depression, phobias, and reading disabilities have been examined in this context.
For a few highly heritable traits, some studies have identified loci associated with variance in that trait
in some individuals. For example, research groups have identified loci that are associated with schizophrenia
(Harrison and Owen, 2003) in subsets of patients with that diagnosis.
[edit] Philosophical difficulties
[edit] Are the traits real?
It is sometimes a question whether the "trait" being measured is even a real thing. As an example,
much energy has been devoted to calculating the heritability of intelligence (usually the I.Q., or intelligence
quotient), but there is still some disagreement as to what exactly "intelligence" is.
[edit] Biological determinism

If genes do contribute substantially to the development of personal characteristics such as
intelligence and personality, then many wonder if this implies that genes determine who we are. See Genetic
determinism and Biological determinism.
[edit] Is the problem real?

Many scientists feel that the very question opposing nature to nurture is a fallacy. Already in 1951,
Calvin Hall in his seminal chapter[25] remarked that the discussion opposing nature and nurture was
fruitless. If an environment is changed fundamentally, then the heritability of a character changes, too.
Conversely, if the genetic composition of a population changes, then heritability will also change. As an
example, we may use phenylketonuria (PKU), which causes brain damage and progressive mental
retardation. PKU can be treated by the elimination of phenylalanine from the diet. Hence, a character (PKU)
that used to have a virtually perfect heritability is not heritable any more if modern medicine is available (the
actual allele causing PKU would still be inherited, but the phenotype PKU would not be expressed anymore).
Similarly, within, say, an inbred strain of mice, no genetic variation is present and every character will have a
zero heritability. If the complications of gene–environment interactions and correlations (see above) are
added, then it appears to many that heritability, the epitome of the nature–nurture opposition, is "a station
passed."[26]
[edit] Myths about identity

Within the debates surrounding cloning, for example, is the far-fetched contention that a Jesus or a
Hitler could be "re-created" through genetic cloning. Current thinking finds this largely inaccurate, and
discounts the possibility that the clone of anyone would grow up to be the same individual due to
environmental variation. For example, like clones, identical twins are genetically identical, and unlike the
hypothetical clones share the same family environment, yet they are not identical in personality and other
traits.
[edit] History of the nature versus nurture debate

Further information: Empiricism and Tabula rasa
Traditionally, human nature has been thought of as not only inherited but divinely ordained.[ citation
needed] Whole ethnic groups were considered to be, by nature, superior or inferior. Since the late Middle
Ages, intellectuals increasingly attributed differences among races, classes and genders to socialization
(nurture), rather than to innate qualities (nature).[ citation needed] In the 20th century, the Nazis pursued an
agenda based on the concept of human nature as defined by one's race. The Communists, on the other
hand, largely followed Marx's lead in defining the human identity as subject to social structures, not nature. In
scientific circles, this conflict led to ongoing controversy of sociobiology and evolutionary psychology.[citation
needed]
[edit] See also
Look up nurture in Wiktionary, the free dictionary.
• Behavioural genetics
• Communibiology
• Diathesis–stress model
• Differential susceptibility hypothesis
• Epigenetic theory
• Genetic determinism
• The Nurture Assumption (book)
• Race and crime in the United States
• David Reimer
• Social determinism
• Structure and agency
[edit] References
1. ^ http://books.google.com/books?id=_uE-
bpGo2N4C&pg=PA227&dq=Nature+versus+nurture+galton&lr=&as_drrb_is=b&as_minm_is=1&as_
miny_is=1800&as_maxm_is=1&as_maxy_is=1900&as_brr=0&cd=6#v=onepage&q&f=false
2. ^ http://books.google.com/books?
id=CCepY1AJYNQC&pg=PA9&dq=Nature+versus+nurture+galton&lr=&as_drrb_is=b&as_minm_is=
1&as_miny_is=1800&as_maxm_is=1&as_maxy_is=1900&as_brr=0&cd=2#v=onepage&q&f=false
3. ^ a b http://books.google.com/books?
id=GkMJDdcL7QUC&pg=PA35&dq=Nature+versus+nurture+galton&lr=&as_drrb_is=q&as_minm_is
=1&as_miny_is=1800&as_maxm_is=1&as_maxy_is=1900&as_brr=0&cd=7#v=onepage&q&f=false
4. ^ a b http://books.google.com/books?
id=RUVAHbzAeAkC&pg=PA35&dq=Nature+versus+nurture+galton&lr=&as_drrb_is=q&as_minm_is
=1&as_miny_is=1800&as_maxm_is=1&as_maxy_is=1900&as_brr=0&cd=4#v=onepage&q&f=false
5. ^ Dusheck, Jennie, The Interpretation of Genes. Natural History, October 2002.
6. ^ a b Carlson, N.R. et al.. (2005) Psychology: the science of behaviour (3rd Canadian ed)
Pearson Ed. ISBN 0-205-45769-X
7. ^ Ridley, M. (2003) Nature via Nurture: Genes, Experience, & What Makes Us Human .
Harper Collins. ISBN 0-00-200663-4
8. ^ Westen, D. (2002) Psychology: Brain, Behavior & Culture . Wiley & Sons. ISBN 0-471-
38754-1
9. ^ Scott, A. (1995). Stairway to the mind: The controversial new science of consciousness.
Springer. ISBN 0387943811
10.^ Michael J. Meaney (2001) Nature, nurture, and the disunity of knowledge. Annals of the
New York Academy of Sciences 935:50–61.
11.^ Herschkowitz, N & Herschkowitz, EC (2002) A good start in life: Understanding your child's
brain and behavior. Joseph Henry Press. ISBN 0309076390
12.^ Meaney M. (2004) The nature of nurture: maternal effects and chromatin remodelling, in
Essays in Social Neuroscience, Cacioppo, JT & Berntson, GG eds. MIT press. ISBN 0262033232
13.^ DeFries, J.C., McGuffin, P., McClearn, G.E., Plomin, R. (2000) Behavioral Genetics 4th Ed.
W H Freeman & Co.
14.^ Website for "The Nurture Assumption."
15.^ The Edge Annual Question-2006
16.^ Rice DS, Tang Q, Williams RW, Harris BS, Davisson MT, Goldowitz D (September 1997).
"Decreased retinal ganglion cell number and misdirected axon growth associated with fissure defects
in Bst/+ mutant mice". Invest. Ophthalmol. Vis. Sci. 38 (10): 2112–24. PMID 9331275.
http://www.iovs.org/cgi/reprint/38/10/2112. Retrieved 2009-04-14.
17.^ Stetter M, Lang EW, Müller A (1993). "Emergence of orientation selective simple cells
simulated in deterministic and stochastic neural networks". Biol. Cybern. 68 (5): 465–76.
doi:10.1007/BF00198779. PMID 8476987. http://www.springerlink.com/content/x271j1542j02r4v0/.
18.^ Plomin, R., DeFries, J.C., McClearn, G.E., & McGuffin, P. 2001. Behavioral Genetics. (4th
Edition). New York: Worth Publishers.
19.^ Plomin, R., DeFries, J. C., McClearn, G. E. and McGuffin, P. (2001). Behavioral Genetics
(4th Ed.). New York: Freeman. ISBN 0-7167-5159-3.
20.^ Bouchard TJ Jr. Genetic and environmental influences on adult intelligence and special
mental abilities. Hum Biol. 1998 Apr; 70(2): 257–79
21.^ Plomin, R.; Spinath, F.M. (2004). "Intelligence: genetics, genes, and genomics". Journal of
Personality and Social Psychology 86 (1): 112–129. doi:10.1037/0022-3514.86.1.112.
PMID 14717631.
22.^ M. McGue, T.J. Bouchard Jr., W.G. Iacono, & D.T. Lykken (1993) Behavioral Genetics of
Cognitive Ability: A Life-Span Perspective, in Nature, Nurture, and Psychology, by R. Plomin & G.E.
McClearn (Eds.) Washington, DC: American Psychological Association
23.^ Plomin, R.; Fulker, D.W.; Corley, R.; DeFries, J.C. (1997). "Nature, Nurture and Cognitive
Development from 1 to 16 years: A Parent-Offspring Adoption Study". Psychological Science 8: 442–
447. doi:10.1111/j.1467-9280.1997.tb00458.x.
24.^ Schönemann, P. Models and muddles of heritability. Genetica, 99, 97–108
25.^ C.S. Hall (1951) The Genetics of Behavior, in Handbook of Experimental Psychology, by
S.S. Stevens (Ed.) New York, NY, USA: John Wiley and Sons, pp. 304–329
26.^ Crusio, W.E. (1990). "Estimating heritabilities in quantitative behavior genetics: A station
passed". Behavioral and Brain Sciences 13: 127–128.
Notes
• Alarcon, M.; Plomin, R.; Fulker, D.W.; Corley, R.; DeFries, J.C. (1998). "Multivariate path
analysis of specific cognitive abilities: data at 12 years of age in the Colorado Adoption Project".
Behavior Genetics 28 (4): 255–264. doi:10.1023/A:1021667213066. PMID 9803018.
• Riemann, A.; Jang, K.L.; McCrae, R.R.; Angleitner, R.; Livesley, W.J. (1998). "Heritability of
facet-level traits in a cross-cultural twin sample: support for a hierarchical model of personality".
Journal of Personality and Social Psychology 74 (6): 1556–1565. doi:10.1037/0022-3514.74.6.1556.
PMID 9654759.
• Joseph, J. (2004) The Gene Illusion: Genetic Research in Psychiatry and Psychology Under
the Microscope. New York: Algora. (2003 United Kingdom Edition by PCCS Books)
• Joseph, J. (2006). The Missing Gene: Psychiatry, Heredity, and the Fruitless Search for
Genes. New York: Algora.
• Harrison PJ, Owen MJ. (2003) Genes for schizophrenia? Recent findings and their
pathophysiological implications. Lancet, 361(9355), 417–9.
• Neill, J.T. (2004). Nature vs nurture in intelligence. Wilderdom.
• Pinker, S. (2004) Why nature & nurture won't go away. Dædalus.
• Plomin, R.; Fulker, D.W.; Corley, R.; DeFries, J.C. (1997). "Nature, nurture and cognitive
development from 1 to 16 years: a parent-offspring adoption study". Psychological Science 8: 442–
447. doi:10.1111/j.1467-9280.1997.tb00458.x.
• Plomin, R., DeFries, J.C., McClearn, G.E. and McGuffin, P. (2001). Behavioral Genetics (4th
Ed.). New York: Freeman. ISBN 0-7167-5159-3.
• Ridley, M. (2003). Nature Via Nurture: Genes, Experience, and What Makes Us Human.
HarperCollins. ISBN 0-06-000678-1. (republished under the title The Agile Gene: How Nature Turns
on Nurture)
• Rowe, D.C. (1994). The limits of family influence: Genes, experience, and behavior. New
York: Guilford Press.
• Wahlsten, D. (1997). "Leilani Muir versus the Philosopher King: eugenics on trial in Alberta".
Genetica 99 (2–3): 185–198. doi:10.1007/BF02259522. PMID 9463073.
• At least two Science Fiction novels have plots that bear on this debate (in very different ways
from each other): Cyteen by C.J. Cherryh (1988) and The Coming of the Quantum Cats by Frederik
Pohl (1986).
[hide]v · d · eHuman group differences
Gender/Se Gender differences | Biology of gender | Biology and sexual orientation | Sex
x and intelligence | Gender and crime | Sex and spatial cognition | Gender and suicide |
Sex and emotion | Sex and illness | Sex differences in humans
Population groups in biomedicine | Ancestry and health | Ethnicity and health
Race (United States) | Race and crime (US, UK)| Race and intelligence | Race and face
perception | Race and genetics | Race and absolute pitch
Nations and intelligence | Neuroscience and intelligence | Religiosity and

Other intelligence | Heritability of IQ | Fertility and intelligence | Height and intelligence |
dynamics Health and intelligence | Longevity and intelligence | Blood type | Human genetic
variation | Human genetic clustering | Y-DNA haplogroups


phenotype
Non-genetic
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Nature_versus_nurture"
Categories: Personality theories | Human behavior

W000
Morphogenetic field

A.G.Gurwitsch analysed the embryonic development of the sea-urchin as a vector-field, as if the
proliferation of cells into organs were brought about by putative external forces.
This article is about the mainstream developmental biology concept. For Rupert Sheldrake's
concept of the same name see the corresponding section of Morphic field.
In developmental biology, a morphogenetic field is a group of cells able to respond to discrete,
localized biochemical signals leading to the development of specific morphological structures or organs.[1][2]
The spatial and temporal extent of the embryonic fields are dynamic, and within the field is a collection of
interacting cells out of which a particular organ is formed.[3] As a group, the cells within a given
morphogenetic field are constrained — i.e. cells in a limb field will become a limb tissue, those in a cardiac
field will become heart tissue.[4] Importantly, however, the specific cellular programming of individual cells in
a field is flexible: an individual cell in a cardiac field can be redirected via cell-to-cell signaling to replace
specific damaged or missing cells.[4] Imaginal discs in insect larvae are examples of morphogenetic fields.[5]
Contents
[hide]
• 1 Historical development
• 2 See also
• 3 References
• 3.1 Further reading

The concept of the morphogenetic field, fundamental in the early twentieth century to the study of
embryological development, was first introduced in 1910 by Alexander G. Gurwitsch.[6] Experimental support
was provided by Ross Granville Harrison's experiments transplanting fragments of a newt embryo into
different locations.[7]
Harrison was able to identify "fields" of cells producing organs such as limbs, tail and gills and to
show that these fields could be fragmented or have undifferentiated cells added and a complete normal final
structure would still result. It was thus considered that it was the "field" of cells, rather than individual cells,
that were patterned for subsequent development of particular organs. The field concept was developed
further by Harrison's friend Hans Spemann, and then by Paul Weiss and others.[3]
By the 1930s, however, the work of geneticists, especially Thomas Hunt Morgan, revealed the
importance of chromosomes and genes for controlling development, and the rise of the new synthesis in
evolutionary biology lessened the perceived importance of the field hypothesis. Morgan was a particularly
harsh critic of fields since the gene and the field were perceived as competitors for recognition as the basic
unit of ontogeny.[3] With the discovery and mapping of master control genes, such as the homeobox genes
the pre-eminence of genes seemed assured. But in the late twentieth century the field concept was
"rediscovered" as a useful part of developmental biology. It was found, for example, that different mutations
could cause the same malformations, suggesting that the mutations were affecting a complex of structures
as a unit, a unit that might correspond to the field of early 20th century embryology.
Scott Gilbert proposes that the morphogenetic field is a middle ground between genes and evolution.
[3] That is, genes act upon fields, which then act upon the developing organism.[3] Jessica Bolker describes
morphogenetic fields not merely as incipient structures or organs, but as dynamic entities with their own
localized development processes, which are central to the emerging field of evolutionary development ("evo-
devo").[8]
[edit] See also

• Morphogenesis
• Evolutionary developmental biology
[edit] References
1. ^ Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Universal Mechanisms
of Animal Development. in: Molecular Biology of the Cell (4th ed.). Garland. ISBN 0815332181.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?&rid=mboc4.section.3792.
2. ^ Jacobson AG, Sater AK (1 November 1988). "Features of embryonic induction".
Development 104 (3): 341–59. PMID 3076860. http://dev.biologists.org/cgi/reprint/104/3/341.
3. ^ a b c d e Gilbert SF, Opitz JM, Raff RA (1996). "Resynthesizing evolutionary and
developmental biology". Dev. Biol. 173 (2): 357–72. doi:10.1006/dbio.1996.0032. PMID 8605997.
4. ^ a b Gilbert SF (2003). Developmental biology (7th ed.). Sunderland, Mass: Sinauer
Associates. pp. 65–6. ISBN 0-87893-258-5.
5. ^ Alberts B, et al. (2002). Organogenesis and the Patterning of Appendages. in: Molecular
Biology of the Cell (4th ed.). Garland. ISBN 0815332181. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?
rid=mboc4.figgrp.3898.
6. ^ Beloussov, LV (1997). "Life of Alexander G. Gurwitsch and his relevant contribution to the
theory of morphogenetic fields". International Journal of Developmental Biology 41 (6): 771–779.
http://www.ijdb.ehu.es/web/contents.php?vol=41&issue=6&doi=9449452. , with comment by SF
Gilbert and JM Optiz.
7. ^ de Robertis, EM; Morita, EA; Cho, KWY (1991). "Gradient fields and homeobox genes".
Development 112: 669–678. http://dev.biologists.org/cgi/reprint/112/3/669.pdf.
8. ^ Bolker, JA (2000). "Modularity in Development and Why It Matters to Evo-Devo". American
Zoologist 40: 770–776. doi:10.1668/0003-1569(2000)040[0770:MIDAWI]2.0.CO;2.
• Davidson EH (1 July 1993). "Later embryogenesis: regulatory circuitry in morphogenetic
fields". Development 118 (3): 665–90. PMID 7915668. http://dev.biologists.org/cgi/reprint/118/3/665.
• Gilbert SF (2006). "The "Re-discovery" of Morphogenic Fields. in: DevBio: a companion to
Developmental Biology, 8th ed.". Sinauer Associates. http://8e.devbio.com/article.php?ch=3&id=18.

See a morphogenetic field model and simulation at: Lahoz-Beltra, R., Selem Mojica, N., Perales-
Gravan, C., Navarro, J., Marijuan, P.C., 2008. Towards a Morphogenetic Field Theory.
http://bioinformatica.net/mf-project/index.html


phenotype
Non-genetic Epigenetics · Maternal effect · Dual inheritance theory

influences
Developmental
Retrieved from "http://en.wikipedia.org/wiki/Morphogenetic_field"
Categories: Developmental biology

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[edit] Domains are units of protein structure

[edit] Tertiary structure of domains

[edit] Domains have limits on size

[edit] Domains and quaternary structure

[edit] Domains as evolutionary modules

[edit] Multidomain proteins

[edit] Types of organisation

[edit] Domains are autonomous folding units

[edit] Advantage of domains in protein folding

[edit] Domains and protein flexibility

[edit] Hinges by secondary structures

[edit] Helical to extended conformation

[edit] Shear motions

[edit] Domain motion and functional dynamics in enzymes

[edit] Domain definition from structural co-ordinates

[edit] Example domains

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[edit] Structural domain databases

[edit] Sequence domain databases

[hide]v · d · eProtein domains

General Structural domain · Protein folding · Structure determination methods

All-β folds: Immunoglobulin domain · Beta barrel · Beta-propeller

α+β folds: DNA clamp · Ferredoxin fold · Ribonuclease A · SH2-like fold

Processes Protein biosynthesis · Posttranslational modification · Protein folding · Protein

Structures Protein structure · Protein structural domains · Proteasome

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[edit] Molecular biology

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[edit] Cellular memory

[edit] Inherited epigenetic memory

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[edit] Animal behavior

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Intelligent design movement

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[edit] History of the movement

Pandas was followed in 1991 by Darwin on Trial, a neo-creationist polemic by University of

[edit] The Wedge strategy

[edit] Kansas evolution hearings

[edit] Reception by the scientific community

– Phillip Johnson, The Evolution Debate Can Be Won[23]

[edit] The Center for Science and Culture

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[edit] Higher education

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[edit] Two-fold cost of sex