Phylogeny

Campbell Chapter 26
Organizing life: binomial nomenclature

Turdus migratorius Acer rubrum

Carolus Linnaeus
Organizing life:
Hierarchical classification
Organizing life
Taxonomy is the ordered division and naming of organisms
In18th century, Carolus Linnaeus published a system of taxonomy based on
resemblances
Two key features of his system remain useful today
two-part names for species (binomial)
The first part of the name is the genus
Second part, called specific epithet, is unique for each species within genus
First letter of the genus is capitalized, and the entire species name is italicized
Both parts together name the species (not the specific epithet alon
hierarchical classification
Linnaean classification- grouping species in increasingly broad categories
Commonly used taxonomic groups (taxon): domain, kingdom, phylum, class, order, family,
genus, and species
A taxonomic unit at any level of hierarchy is called a taxon
 Phylogeny
Discipline of systematics classifies
organisms and determines their
evolutionary relationships
Systematists illustrate hypotheses
of evolutionary relationships with
phylogenetic trees
To infer evolutionary relationships
systematists use
Fossils
Molecular data
Genetic data
Building a phylogeny

Vertebral column
Hinged jaws
+ +

Four walking legs
Amnion
Hair

List of measurable
Ingroup Outgroup
characters
Building a phylogeny
Building a phylogeny
The taxa being classified form the ingroup
An outgroup is a taxa tha is known to have diverged before the the members of
the ingroup have started to diverged.
The outgroup acts as a reference point. Systematists compare each ingroup
members with the outgroup to differentiate between shared derived and
shared ancestral characteristics.
Shared ancestral characters are shared by the outgroup and ingroup
Shared derived characters are shared only by some members of the ingroup
Character can be both ancestral and derived, depending on the context. For
instance, when classifying vertebrates, the presence of hair is considered a
shared derived characters of mammals but when classifying only mammals, the
presence of hair is considered a shared ancestral characters.
 Anatomy of a Tree
Phylogenetic tree a hypothesis about
evolutionary relationships
Each branch point represents the
divergence of two species
Sister taxa are groups that share an
immediate common ancestor
Rooted tree includes branch to
represent last common ancestor of all
taxa
Basal taxon diverges early in history of
a group and originates near common
ancestor of group
Polytomy is a branch from which more
than two groups emerge and is used to
illustrate uncertainty in relationship
Linking Classification & Phylogeny

Like the linnean classification, a

phylogeny is hierarchal system
Systematists recognizes only
groups (taxa) that include a
common ancestor and all its
descendants
Linnaean classification and
phylogeny can differ from each
other because linnean
classification does not necessary
reflect evolutionary relationships
Linking Classification & Phylogeny: Cladistic
 Evo Edu Outreach (2008) 1:121137

Which statement is true?

tendency to place humans or some other preferred taxon at
the top or right of every tree appears to be an unshakable
A) Birds and turtles are equally related to kangoroo
habit among many phylogeneticists, although there is no
B) Lizards are more closely related to alligators than they are to birds
objective reason for doing so). As indicated in Fig. 5, even
C) Turtles are equally related to lizards and kangoroo
on cladograms, in which the lengths of the branches are not

en
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Linking Classification & Phylogeny: Cladistic
Cladistics groups organisms by common descent
Clade- group of species that includes an ancestral species and all its
descendants
Clades can be nested in larger clades, but not all groupings of organisms
qualify as clades
A valid clade is monophyletic, signifying that it consists of the ancestor
species and all its descendants
A paraphyletic grouping consists of an ancestral species and some, but not
all, of the descendants
A polyphyletic grouping consists of various species with different ancestors
What We Can and Cannot Learn from
Phylogenetic Trees
Phylogenetic trees show patterns of descent, not phenotypic
similarity
Phylogenetic trees do not indicate when species evolved or how
much change occurred in a lineage
It should not be assumed that a taxon evolved from the taxon next
to it
Reading a Tree: Relatedness among taxa
132

Relatedness between two groups is

determined based on the number of R
SHARED common ancestors (not
based from the number of nodes
between the two taxa)
for instance, in this tree, Human and
chimps share 6 common ancestors
(Z,Y,X,W, V, U). Chimps are and gorillas
share 5 common ancestors (Z,Y,X,W,
V). Chimps are thus more closely
related to humans than to gorillas.
Human and chimps are equally
related to gorillas because they both
share 5 common ancestors with
gorillas (Z,Y,X,W, V).
 How many ancestors are shared
between turtles and lizards in this tree?
131

Fig. 13 Evolutionary relatedness and physical similarity are not

necessarily linked. The rates at which physical features change can
differ among lineages (Fig. 8), and superficially similar morphologies
can evolve independently in more than one lineage. As a result, close
 ative
exam

Reading a tree: The style does not matter, corre

tions

only the branching order

126 Evo Edu Outreach (2008) 1:121137 teach
interr
can

126 Evosents
Edu
in the peer-reviewed scientific literature, often with signif- think
icant implications for the conclusions drawn from compar-
in the peer-reviewed scientific liter
ative analyses (see Crisp and icantCook 2005 for
implications for several Misc
the conclusio
examples). The following sections describe (see
ative analyses and seek
Crisptoand C
correct ten of the most commonly encountered
examples). misconcep-sections
The following Notio
tions about evolutionary trees. correctSeveral
ten of theof most
thesecommonly
are (scale
interrelated and therefore overlap tions toaboutan extent, but eachtrees.
evolutionary cases
can be illustrated using distinct examples.
interrelated andLearning
therefore(and lowe
overlap
teaching students) to avoid these can misunderstandings
be illustrated usingrepre- Arist
distinct ex
sents a key step toward the development of adequate
teaching students) to avoidtreethese m
thinking skills. sents a key step toward the develo
thinking skills.
Misconception #1: Higher and Lower
Misconception #1: Higher and Low
Notions of a Great Chain of Being or scala naturae
(scales of nature), in which livingNotionsspecies
of a (and,
GreatinChain
some of Be
Fig.cases, nonlivingtrees
4 Evolutionary matter and/or
can be the indivine)
(scales
presented aof areof ranked
nature),
variety from living
in which
ways. This
 are exactly equa
ancestor (recall

Reading a tree: the order of the tips does not third, more dista
A more rapi

reflect the pattern of relationship

internal nodes w
shown in Fig. 1
sister to cats and
sister to amnio
130 Evo Edu Outreach (2008) 1:121137 tetrapods. This s
therefore equall
included in a clade with humans before fishes canin other
words, because frogs and humans share a common ancestor
that is not shared with fishesfrogs are more closely
related to humans than to fishes. Indeed, frogs and humans
are exactly equally related to fishes through this common
ancestor (recall that two cousins are equally related to a

=
third, more distant relative).
A more rapid approach is to mentally rotate a few
internal nodes with no effect on the topology of the tree, as
shown in Fig. 11b. In this modified tree, humans are still
sister to cats and birds are sister to lizards, frogs are then
sister to amniotes, and fishes are the outgroup to the
tetrapods. This second tree is identical in topology and is
Fig. 11 The
therefore equally order ofas
accurate terminal nodestree.
the first is meaningless.
However, Oneitof the most
common misconceptions about evolutionary trees is that the order of
the terminal nodes provides information about their relatedness. Only
branching order (i.e., the sequence of internal nodes) provides this
Frogs and human share a common ancestor that is not shared with
information; because all internal nodes can be rotated without
affecting the topology (Fig. 6), the order of the tips is meaningless.
fish. Thus frogs are more closely related to humans than to fish.
Nevertheless, there is a strong tendency for readers to take the tree in a
as indicating that frogs are more closely related to fishes than humans
Reading a tree: the order of the tips does not
reflect the pattern of relationship
Evo Edu Outreach (2008) 1:121137

to one of branching
the result (e.g., OHa

Misconception #2: M

Although it is clea
evolution as tree-like

Fig. 6 All internal nodes can be rotated without changing the

topology. Although they may look quite different, the four trees
of the American Association for the Advancement of Science

As a means of correcting this misinterpretation, one may

There is no line of progress in a tree

As a means of correcting this misinterpretation,
take the timeone
take the time to identify the clades(Baum
depicted
to may
et inal.the
identify the clades depicted in the tree
tree Humans, cats, and their common
2005).
(Baum et al. 2005). Humans, cats,mammalian
and their common
ancestor represent one clade, as do birds,
mammalian ancestor represent onelizards,
clade, and
as their
do birds,
common ancestor. These lineages together
lizards, and their common ancestor. These lineages together

=
Fig. 10 There are no main lines or side tracks in evolution.
Undoubtedly, many readers will consider the tree depicted in a to
reflect a main line of evolutionary progress from a primitive ancestor
to an advanced species like humans, with other groups such as
Long branches do not imply no change.
 Evo Edu Outreach (2008) 1:121137

Which statement is true?

tendency to place humans or some other preferred taxon at
the top or right of every tree appears to be an unshakable
A) Birds and turtles are equally related to kangoroo
habit among many phylogeneticists, although there is no
B) Lizards are more closely related to alligators than they are to birds
objective reason for doing so). As indicated in Fig. 5, even
C) Turtles are equally related to lizards and kangoroo
on cladograms, in which the lengths of the branches are not

en
cal
hat
ot.
ate
unt
ore
Phylograms
Cladograms depict evolutionary relationships (only branch order
important)
Phylogram- length of branch reflects number of genetic changes that
took place in particular DNA sequence in that lineage
Phylograms
Branch length can
represent chronological
time, and branching
points determined from
fossil record and/or
molecular clock
calculations
 Applying Phylogeny

2010 Cholera outbreak in Haiti

How did the bacterium got to Haiti?
Molecular clock
Molecular clock
Molecular clock uses constant rates of evolution in some genes to
estimate absolute time of evolutionary change
In orthologous genes, nucleotide substitutions are proportional to
time since they last shared a common ancestor
Molecular clocks are calibrated against branches whose dates are
known from the fossil record
Individual genes vary in how clocklike they are
 Paralogous and Orthologous genes

Orthologous genes are found in a single copy in Paralogous genes result from gene duplication,
genome and are homologous between species find more than one copy in genome
They can diverge only after speciation occurs Can diverge within clade that carries them and
evolve new functions
Neutral Theory and Molecular Clock
Neutral theory states much evolutionary change in genes and proteins
has no effect on fitness and is not influenced by natural selection
It states that rate of molecular change in these genes and proteins should
be regular like a clock
Molecular clock does not run as smoothly as neutral theory predicts
Irregularities result from natural selection in which some DNA changes are
favoured over others
Estimates of evolutionary divergences older than fossil record have high
degree of uncertainty
Use of multiple genes may improve estimates
Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that
HIV is descended from viruses that
infect chimpanzees and other
primates
Comparison of HIV samples shows
that the virus evolved in a very
clocklike way
Application of a molecular clock to
one strain of HIV suggests that that
strain spread to humans during the
1930s
The tree of life: from two domains to three
kingdoms
The tree of life: from two domains to three
kingdoms
Early taxonomists classified all species as either plants or animals
Later, five kingdoms were recognized: Monera (prokaryotes), Protista,
Plantae, Fungi, and Animalia
More recently, three-domain system adopted: Bacteria, Archaea, and
Eukarya
Three-domain system supported by data from many sequenced
genomes
The Tree of Life

Ribosomes are present in all living cells (prokaryotic and eukaryotic)

and serve the same conserved translation function
DNA coding for rRNA changes relatively slowly and useful for
investigating branching points hundreds of millions of years ago
The tree of life is based largely on rRNA genes, as these have evolved
slowly
Tree of life suggests that eukaryotes and archaea are more closely
related to each other than to bacteria
The tree of life?
There have been substantial
interchanges of genes between
organisms in different domains
Horizontal gene transfer is the
movement of genes from one
genome to another
Horizontal gene transfer occurs by
exchange of transposable elements
and plasmids, viral infection, and
fusion of organisms
Horizontal gene transfer challenges
the notion of a tree of life
The tree of life?

Some researchers suggest

that eukaryotes arose as a
fusion between a bacterium
and archaean
If so, early evolutionary
relationships might be better
depicted by a ring of life
instead of a tree of life