Study Area 3

Prepared by Raajeswari
Rajendran

This chapter describes how biologists trace phylogeny

The evolutionary history and relationships of a species or
group of related species.
The phylogeny of a group of organisms can be described by
the pattern of branching depicting their evolutionary
relationships a branching diagram called a phylogenetic
tree or cladogram.
The phylogenetic tree (the pattern of relationships) can also
be the basis for hypothesizing how organisms evolved (the
process of evolution).

To determine phylogeny, scientists use a branch of science

known as systematics a scientific discipline focused on
classifying organisms and determining their evolutionary
relationships.
Biologists use systematics
As an analytical approach to understanding the diversity and
relationships of organisms, both present-day and extinct.
Phylogenies are based on common ancestries inferred from
fossil, morphological, and molecular evidence.

Currently,
systematists use
Morphological,
biochemical,
and molecular
comparisons to
infer
evolutionary
relationships

Involves the study of body form and shape.

Information about phylogeny can be obtained through:
1. Embryology
2. Study of vestigial organs
3. The fossil record

If the early stages of development in vertebrates are compared,

gill slits are observed to form in all embryos, even though they
do not persist in adults, other than in fishes.
The striking similarity of the embryos of fishes, frogs, lizards,
birds and mammals has led biologists to hypothesize that these
organisms had a single line of descent and are all classified as
vertebrates.
This similarity indicates that all vertebrates share a
fundamental step in their developmental programs and it is the
modification of the later stages of development which
accounts for the great diversity of form within the vertebrates.
E.g. birds develop feathers and humans have a brain larger
than that of other primates.

Striking similarity between the embryos of vertebrates, from

fishes to mammals

Vestigial organs are rudimentary organs with no apparent

function, but are also clues to evolutionary relationships when
comparing organisms.
E.g. humans have a vestigial tail (coccyx) similar to the
prehensile tail of monkeys; an adult baleen whale lacks teeth
but develops them as an embryo.
The best explanation of vestigial organs is that they were
functional and present in ancestral species and therefore are
indicators of phylogeny.

Biologists draw on the fossil record

Which provides information about ancient organisms
Sedimentary rocks
Are the richest source of fossils
Are deposited into layers called strata

1 Rivers carry sediment to the

ocean. Sedimentary rock layers
containing fossils form on the
ocean floor.
2 Over time, new strata are
deposited, containing fossils
from each time period.
3 As sea levels change and the seafloor
is pushed upward, sedimentary rocks are
exposed. Erosion reveals strata and fossils.

Younger stratum
with more recent
fossils
Older stratum
with older fossils

The fossil record

Is based on the sequence in which fossils have accumulated in such
strata.
Fossils reveal
Ancestral characteristics that may have been lost over time.
Fossils can also be compared with living organisms and included in
phylogenetic trees, although only the hard parts of organims such as
bones, teeth and wood, are preserved and available for comparative
study.
Fossil records supply evidence of both the forms of life in the past and
their geological ages.
However, there is no way of knowing whether a fossil is a direct
ancestor of a more recent species or represents a related line of descent
(lineage) that became extinct. Also the fossil may not be complete.

Though sedimentary fossils are the most common

Paleontologists study a wide variety of fossils

(c) Leaf fossil, about 40 million years old

(b) Petrified tree in Arizona, about

190 million years old

(a) Dinosaur bones being excavated

from sandstone

(d) Casts of ammonites,

about 375 million
years old

(f) Insects
preserved
whole in
amber

(g) Tusks of a 23,000-year-old mammoth,

frozen whole in Siberian ice

(e) Boy standing in a 150-million-year-old

dinosaur track in Colorado

Evolutionary theory
Provides a cohesive explanation for many kinds of
observations.
Charles Darwin, who came up with the Theory of Natural
Selection, observed that evolution is a process of descent with
modification where characteristics present in an ancestral
organism are altered by natural selection in its descendants
over time as they face different environmental conditions.
As a result, related species can have characteristics with an
underlying similarity even though they may have very
different functions.
Such similarity resulting from common ancestry is known as
homology.

Three types of evolution have been noted:

Divergent evolution
2. Convergent evolution
3. Parallel evolution
1.

Comparative morphology focuses on the basic similarity of

organisms as evidence of how they diverged during evolution
and departed from a common ancestral form divergent
evolution.
E.g. the flightless emu and a sparrow are different in many
ways but both have feathers, indicating they are related as
birds. Likewise, the comparative study of bones reveals that
the flipper of a whale has the same basic structure as the front
leg of a frog or crocodile and the wing of a bird or bat.
Structures that have the same basic plan but not necessarily
the same function are known as homologous structures that
indicate divergent evolution.
Homologous structures indicate common inheritance a
common ancestor.

Homologous structures between organisms

Are anatomical resemblances that represent variations on a structural theme that was present in a common ancestor.

Homologous structures indicates that birds, frogs, crocodiles, bats and whales are related as tetrapods; mammalian forelimbs are

homologous structures that indicate humans, cats, whales and bats descended from a common ancestor.

Human

Cat

Whale

Bat

In convergent evolution, organisms from different,

unrelated or distantly related lineages come to resemble
one another superficially.
Structures that have a similar function as a result of
convergence are called analogous structures.
E.g. plants of the families Cactaceae in the New World
and Euphorbiceae in the Old World look remarkably
similar with their succulent, leafless stems; both groups
of plants are adapted to arid environments and their
succulence is an analogous feature that serves as a store
of water.

Convergent evolution occurs when similar environmental pressures and

natural selection produce similar (analogous) adaptations in organisms
from different evolutionary lineages.
E.g. a forest-dwelling Australian marsupial called the sugar glider is
superficially very similar to flying squirrels which are gliding eutherians
that live in North American forests the ability to glide through the air
evolved independently in these two distantly related groups of mammals.
Another example shown below is the similarity between the marsupial
mole and the mole which is eutherian.

Marsupial mole

Mole

In Australia, convergent evolution

Has resulted in a diversity of marsupials that resemble eutherians in
other parts of the world
Marsupial mammals
Plantigale

Eutherian mammals
Deer mouse

Mole

Marsupial mole

Sugar
glider

Flying squirrel

Wombat
Woodchuck

Tasmanian devil

Kangaroo

Wolverine

Patagonian cavy

Prepared by Raajeswari
Rajendran

Closely related organisms also independently evolve similar

features termed parallel evolution.
E.g. within the plant genus Banksia, the ability to resprout and
regenerate vegetatively appears to have evolved a number of
times and is not a feature of all Banksia species.
Convergent and parallel evolution result in features that are so
similar that we could be misled in our search for phylogeny if
other features did not indicate that the organisms are
unrelated.

In addition to fossil organisms

Phylogenetic history can be inferred from certain morphological and
molecular similarities among living organisms
In general, organisms that share very similar morphologies or similar DNA
sequences
Are likely to be more closely related than organisms with vastly
different structures or sequences
Systematists use computer programs and mathematical tools
When analyzing comparable DNA segments from different organisms
With the development of techniques for sequencing amino acids in
proteins and nucleotides in DNA, it is now possible to compare
organisms at the most basic level.


1.
2.
3.
4.
5.

There are several ways to study homologies in molecules:

Study of amino acid sequences
Study of nucleotide sequences
Study of mitochondrial DNA sequences
Study of ribosomal RNA
DNA-DNA hybridization a technique where single strands of DNA from
two organisms are combined to form hybrid double helices. The melting
point of this hybrid DNA is directly related to how closely the nucleotide
sequences match and gives an overall measure of the genetic similarity of a
pair of organisms; the lower the melting point the greater the difference
between the two strands while the higher the melting point, the closer the
similarity between the two strands.

Phylogenetic systematics connects classification with evolutionary history

Taxonomy
Is the ordered division of organisms into categories based on a set of
characteristics used to assess similarities and differences.
Binomial nomenclature
Is the two-part format of the scientific name of an organism
Was developed by Carolus Linnaeus.
The binomial name of an organism or scientific epithet
Is latinized
Is the genus and species

Linnaeus also introduced a system

For grouping species in increasingly broad categories
Species

Panthera

Genus

Felidae

Family

Carnivora

Order

Class

Phylum

Kingdom
Domain

Panthera
pardus

Mammalia

Chordata
Animalia

Eukarya

Species

Panthera

Family

Panthera
Mephitis
Canis
Canis
Lutra lutra
pardus
mephitis
familiaris
lupus
(European
(leopard) (striped skunk)
otter) (domestic dog) (wolf)

Genus

Systematists depict evolutionary relationships

In branching phylogenetic trees.

Order

Felidae

Mephitis

Lutra

Mustelidae

Carnivora

Canis

Canidae

Each branch point

Represents the divergence of two species

Leopard

Domestic cat

Common ancestor

Deeper branch points

Represent progressively greater amounts of divergence

Wolf

Leopard

Common ancestor

Domestic cat

Phylogenetic systematics informs the construction of phylogenetic trees based

on shared characteristics
A cladogram
Is a depiction of patterns of shared characteristics among taxa
A clade within a cladogram
Is defined as a group of species that includes an ancestral species and all its
descendants
Cladistics
Is the study of resemblances among clades
Clades
Can be nested within larger clades, but not all groupings or organisms
qualify as clades

In cladistic analysis
Clades are defined by their evolutionary novelties.
A shared primitive character
Is a homologous structure that predates the branching of a particular clade
from other members of that clade
Is shared beyond the taxon we are trying to define
A shared derived character
Is an evolutionary novelty unique to a particular clade

Systematists use a method called outgroup comparison

To differentiate between shared derived and shared primitive
characteristics.
As a basis of comparison we need to designate an outgroup
which is a species or group of species that is closely related to the
ingroup, the various species we are studying
Outgroup comparison
Is based on the assumption that homologies present in both the
outgroup and ingroup must be primitive characters that predate the
divergence of both groups from a common ancestor

The outgroup comparison

Enables us to focus on just those characters that were derived at the
various branch points in the evolution of a clade

Lamprey

Tuna

Salamander

Turtle

Leopard

TAXA

Lancelet
(outgroup)
CHARACTERS

Hair

Amniotic (shelled) egg

Four walking legs

Hinged jaws

Vertebral column (backbone)

Turtle
Salamander
Tuna
Lamprey
Lancelet (outgroup)

(a) Character table. A 0 indicates that a character is absent; a 1

indicates that a character is present.

Leopard
Hair

Amniotic egg
Four walking legs
Hinged jaws

Vertebral column

(b) Cladogram. Analyzing the distribution of these

derived characters can provide insight into vertebrate
phylogeny.

Lancelet
(outgroup)

CHARACTERS

Lancelet
(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

TAXA

Lamprey

Bass

Vertebral
column
(backbone)
Hinged jaws

Four walking
legs

Amnion

Hair

Vertebral
column

Frog

Hinged jaws
Turtle

Four walking legs

Amnion

Leopard
Hair

(a) Character table

(b) Phylogenetic tree

Lancelet
(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

CHARACTERS

TAXA

Vertebral
column
(backbone)

Hinged jaws

Four walking
legs

Amnion

Hair

(a) Character table

Lancelet
(outgroup)
Lamprey

Bass
Vertebral
column

Frog

Hinged jaws
Turtle

Four walking legs

Amnion

Leopard
Hair

(b) Phylogenetic tree

An outgroup is a species or group of species that is

closely related to the ingroup, the various species being
studied
The outgroup is a group that has diverged before the
ingroup
Systematists compare each ingroup species with the
outgroup to differentiate between shared derived and
shared ancestral characteristics

Any chronology represented by the branching pattern of a phylogenetic

tree
Is relative rather than absolute in terms of representing the timing of
divergences

The best hypotheses for phylogenetic trees

Are those that fit the most data: morphological, molecular, and fossil.
Much of an organisms evolutionary history is documented in its genome
Comparing nucleic acids or other molecules to infer relatedness
Is a valuable tool for tracing organisms evolutionary history

The tree of life

Bacteria

The early history of these

domains is not yet clear

Billion years ago

Is divided into three great

clades called domains:
Bacteria, Archaea, and
Eukarya

Eukarya Archaea

Symbiosis of
chloroplast
ancestor with
ancestor of green
plants

Symbiosis of
mitochondrial
ancestor with
ancestor of
eukaryotes

Possible fusion
of bacterium
and archaean,
yielding
ancestor of
eukaryotic cells

Last common
ancestor of all
living things

2
3
1
4

Origin of life