Introduction

• All organisms:
– Are composed of one or more cells
– Carry out metabolism
– Transfer energy with ATP
– Encode hereditary information in DNA
• Tremendous diversity of life
– Bacteria-----whales----sequoia trees
• Biologists group organisms based on shared
characteristics
1
 Systematics
• Since fossil records are not complete,
scientists rely on other types of evidence to
establish the best hypothesis of
evolutionary relationships
• Systematics: the study of evolutionary
relationships
• Phylogeny: a hypothesis about patterns of
relationship among species

3
Classification
• What characters
are suitable for
classification
• Systematics
– Combination of
taxonomy & phylogeny
– Systematic approach to
understanding
evolutionary
relationships among
organisms
 Phylogeny
What is a phylogeny?
Branching diagram showing relationships between species (or higher taxa)
based on their shared common ancestors

Species: A B C D A
E
F B
E
Time

C
F
D
Time

A and B are most closely related because they share a common ancestor
( call the ancestor “E”) that C and D do not share

A+B+C are more closely related to each other than to D because they share
a common ancestor (“F”) that D does not share
 Phylogeny

Terminal nodes = contemporary taxa

Internal nodes =
ancestral taxa
Wittiker’s 5 Kingdom Classification
Scheme
 What is Systematics?
• Uses diverse – Molecular Biology
approaches: – Genetics
– Morphology – Physiology
– Anatomy – Ecology
– Palynology
– Evolution
– Microscopy
– Bioinformatics
– Biochemistry
 The Fossil Record

• The fossil record often provides clues to

evolutionary relationships
• It can not be read like a story book because
some fossil records are incomplete
• Systematic taxonomists consider other
evidence to confirm information contained
within the fossil record with other lines of
evidence, like…
 Morphology
• Taxonomists study an organism’s
morphology and compare it to
other living organisms.
– Homologous features are important
but it is important to separate features
that are truly homologous with those
the seem homologous but are actually
analogous.
– The more homologous features two
organisms share, the more closely
related they are thought to be.
 Embryological Patterns
of Development
• Early pattern in
embryological development
provide evidence of
phylogenetic relationships.
• They also provide means of
testing hypotheses about
relationships that have
developed from other lines
of evidence
 Chromosomes and Macromolecules

• Taxonomists use comparisons of

macromolecules such as DNA, RNA, and proteins
as a kind of “molecular clock”.
• Scientists compare amino acid sequences for
homologous protein molecules of different
species.
• The number of amino acid differences a clue to
how long ago two species diverged from a
shared evolutionary ancestor.
 Chromosomes and Macromolecules

• Biologists also compare the karyotypes or

patterns of chromosomes of two related
species.
• Regions of chromosomes that have the same
pattern of banding are clues to the relatedness
of organisms.
• The chromosomes of humans and chimpanzees
show a surprising degree of similarity (see fig
18-5,page345)
 Comparison of Karyotypes

• Human (HSA), chimpanzee (PPA), gorilla (GGO), and orangutan

(PPY) chromosomes are illustrated in a comparative karyotype
of the great apes.
• Photo courtesy of Dr. Mariano Rocchi, Institute of Genetics, Italy.
 Comparison of Karyotypes

• Human (HSA), chimpanzee (PPA), gorilla (GGO), and orangutan

(PPY) chromosomes are illustrated in a comparative karyotype
of the great apes.
• Photo courtesy of Dr. Mariano Rocchi, Institute of Genetics, Italy.
 Systematics

Phylogenies depict evolutionary relationships

20
 Pendekatan sistematik

• PHENETICS.

• CLADISTICS
 PHENETICS VS. CLADISTICS

 Before the 1950s, the ways in which individuals classified taxa

were not well defined.
 In the 1950s, two more precise approaches to systematics
arose: PHENETICS and CLADISTICS.
 Phenetics, also known as “numerical taxonomy”, relies on
overall similarity, utilizing as many features as possible, to
classify organisms (Michener and Sokal).
 Phenetics, as is the case with all phylogenetic approaches,
deals with characters and character states.

 Character: a feature that is thought to vary independently of

other features and to be homologous in closely related taxa.
 Character state: one of the alternative conditions of a character.
HOW TO DRAW A TREE USING A PHENETIC APPROACH

1. Score characters in your taxa.

HOW TO DRAW A TREE USING A PHENETIC APPROACH

1. Score characters in your taxa.

2. Create a distance matrix based on
overall similarity.
HOW TO DRAW A TREE USING A PHENETIC APPROACH

1. Score characters in your taxa.

2. Create a distance matrix based on
overall similarity.
HOW TO DRAW A TREE USING A PHENETIC APPROACH

1. Score characters in your taxa.

2. Create a distance matrix based on
overall similarity.
3. Link the two species with the
greatest similarity.
HOW TO DRAW A TREE USING A PHENETIC APPROACH

1. Score characters in your taxa.

2. Create a distance matrix based on
overall similarity.
3. Link the two species with the
greatest similarity.
4. Link the species with the greatest
average similarity to the first
grouping. For B, it’s (6+4)/2 = 5.
 THE RESULT OF PHENETIC ANALYSIS IS A PHENOGRAM

 A phenogram represents overall similarity, not necessarily

evolutionary relationships.
 Why not?!?
 Species may have similar character states for 3 reasons:

• They share a DERIVED character state that originated in a

common ancestor.
• They share an ANCESTRAL character state -- humans and
iguanas each have five toes, whereas a horse has one, but
we’re still closer to horses.
• They share a feature that is not HOMOLOGOUS.
Independent evolution of the same character in two
separate lineages is called HOMOPLASY.

 If there were no homoplasy, and all lineages evolved at about the

same rate, then overall similarity would work.
 Cladistics
• Derived characteristic: similarity that is
inherited from the most recent common
ancestor of an entire group
• Ancestral: similarity that arose prior to the
common ancestor of the group
• In cladistics, only shared derived characters are
considered informative about evolutionary
relationships
• To use the cladistic method character variation
must be identified as ancestral or derived

29
 Cladistics
• Characters can be any aspect of the phenotype
– Morphology - Physiology
– Behavior - DNA
• Characters should exist in recognizable
character states
– Example: Teeth in amniote vertebrates has two
states, present in most mammals and reptiles and
absence in birds and turtles

30
 Cladistics
Examples of ancestral versus derived characters
• Presence of hair is a shared derived feature of
mammals
• Presence of lungs in mammals is an ancestral
feature; also present in amphibians and reptiles

31
 Cladistics
• Determination of ancestral versus derived
– First step in a manual cladistic analysis is to polarize
the characters (are they ancestral or derived)
• Example: polarize “teeth” means to determine presence
or absence in the most recent common ancestor

32
 Cladistics
– Outgroup comparison is used to assign character
polarity
• A species or group of species not a member of the
group under study is designated as the outgroup
– Outgroup species do not always exhibit the
ancestral condition

33
 Cladistics
• Following the character state-outgroup
method
– Presence of teeth in mammals and reptiles is
ancestral
– Absence of teeth in birds and turtles is derived

34
 Cladistics
Construction of a cladogram
• Polarize characteristics
• Clade: species that share a common ancestor
as indicated by the possession of shared
derived characters
• Clades are evolutionary units and refer to a
common ancestor and all descendants
• Synapomorphy: a derived character shared by
clade members
35
 Cladistics
• A simple cladogram is a nested set of clades
• Plesiomorphies: ancestral states
• Symplesiomorphies: shared ancestral states,
not informative about phylogenetics.

36
 THE COMPETING APPROACH: CLADISTICS

Proposed by Willi Hennig in 1950.

He proposed a new method for reconstructing phylogenies.
He also offered the opinion that patterns of classification should reflect
only monophyletic groups.
These two proposals together have come to be known as CLADISTICS.
Followers of this tradition are known as CLADISTS.
Their diagrams of evolutionary relationships are sometimes referred to
as CLADOGRAMS.
Monophyletic groups are known as CLADES.
Phylogeny and classification
Classification

Note that taxa are nested

on the basis of shared
common ancestors

e.g., All tetrapods share

a common ancestor with
legs, but other chordates
outside of Tetrapoda do
not share this common
ancestor

The traits mapped onto

the phylogeny are
synapomorphies – we
will return to them later
 Phylogeny and classification
Monophyletic group Paraphyletic group
Includes an ancestor Includes ancestor and
all of its descendants some, but not all of its
descendants
Polyphyletic group
Includes two convergent
descendants but not their
common ancestor

A B C D A B C D A B C D

How could this happen? Taxon A is highly derived Taxon A and C share
and looks very different similar traits through
from B, C, and ancestor convergent evolution

Only monophyletic groups (clades) are recognized in cladistic classification

 Classifying Proper Clades
A clade consists of an ancestral This is missing
species plus all descendant descendant species
species

Here is a missed The goal of systematics is to define

ancestor species monophyletic taxa (a.k.a., clades)
 All descendants
(of the shown set, i.e., of D, E, G, H, J, and K)
Monophyletic

A correct
grouping

A clade

Ancestor
 Convergent evolution?
Polyphyletic

This is a
mistake

Polyphylies
happen when
species are
included in
“clades” that they
don’t belong in
 This is an
analogy
Analogies

This is a
polyphyletic
grouping

This is the
true clade
Paraphyletic

This is a
mistake

But one made for

“legitimate” reasons
 Phylogeny and classification
Monophyly
Each of the colored lineages
in this echinoderm phylogeny
is a good monophyletic group

Asteroidea

Ophiuroidea

Echinoidea

Holothuroidea

Crinoidea

Each group shares a common

ancestor that is not shared by any
members of another group
 Paraphyletic groups
Foxes Paraphyly
“Foxes” are paraphyletic with respect
to dogs, wolves, jackals, coyotes, etc.

This is a trivial example because

“fox” and “dog” are not formal
taxonomic units, but it does show
that a dog or a wolf is just a derived
fox in the phylogenetic sense

Lindblad-Toh et al. (2005) Nature 438: 803-819

 Paraphyletic groups
Canids

Monophyly
Note that canids are still a good
monophyletic clade within Mammalia

Each of the colored lineages within

canids is also a monophyletic clade

Lindblad-Toh et al. (2005) Nature 438: 803-819

 Paraphyletic groups

Lizards Paraphyly
“Lizards” (Sauria) are
paraphyletic with respect
to snakes (Serpentes)

Serpentes is a monophyletic
clade within lizards

Squamata (lizards + snakes)

is a monophyletic clade
sister to sphenodontida

Snakes are just derived,

limbless lizards

Fry et al. (2006) Nature 439: 584-588

 Paraphyletic groups
Reptilia
Paraphyly
Birds are more closely related
to crocodilians than to other
extant vertebrates

Archosauria = Birds + Crocs

We think of reptiles as turtles,

lizards, snakes, and crocodiles

But Reptilia is a paraphyletic

group unless it includes Aves
 What does this mean?
It means that No, it means
“reptiles” don’t that you’re one
exist! of us!

What it means is that “reptile” is only a Reptilia

valid clade if it includes birds Turtles
Aves
Crocodiles
Birds are still birds, but Aves cannot be (birds)
considered a “Class” equivalent to Lizards and snakes
Class Reptilia because it is evolutionarily
nested within Reptilia Tuataras
 Reconstructing evolutionary history

Cladistic methods (Willi Hennig 1966)

Based on shared, derived characters = synapomorphies
Similarity is not enough – requires similarity reflecting descent with modification
Requires characters that can be assigned a particular character state

Characters and character states

Character: eye color Character states: blue, brown, green
mammary glands present, absent
number of legs 0, 2, 4, 6, 8, etc.

Molecular
Characters nucleotide bases A, C, T, G

amino acid codons ACC, CGT, GAT, etc.

PHYLOGENETICLY INFORMATIVE CHARACTERS IN CLADISTICS

 SYNAPOMORPHIES: Shared derived characters are the most useful

characters for assessing phylogenetic relationships. They are
homologous characters that reflect descent from a common ancestor.

 AUTAPOMORPHIES: Characters that are unique to a single taxon are

uninformative for assessing the phylogenetic relationships among
groups.

 PLEISIOMORPHIES, SYMPLESIOMORPHIES: Shared primitive

characters are useless for reconstructing the phylogenetic
relationships among taxa.
TIME Autapomorphies can become synapomorphies over time…

“Autapomorphies”
“Synapomorphies”
 Terminology
Plesiomorphy Character state found in ancestor of group
Apomorphy Derived character state in descendants of group
Symplesiomorphy Shared, ancestral character state
Synapomorphy Shared, derived character state (indicates homology)

Polarity Distinguishing ancestral (0) from derived (1) = assigning polarity

- polarity can be assessed by outgroup comparison

A B C D
“Blue” and “square” are plesiomorphic

“Small size” is an apomorphy for A

“Red” is a synapomorphy for A + B
“Circle” is a synapomorphy for A + B + C
…but a symplesiomorphy for A + B
 PHYLOGENETICLY INFORMATIVE CHARACTERS

Amphioxus Cartilaginous Fish Bony fish Amphibians Squamates Birds

FEATHERS

CARTILAGE LUNGS
SKELETON LIMBS

BONY
SKELETON

PAIRED SENSE ORGANS

JAWS
VERTEBRAE

NOTOCHORD
Synapomorphy
Synapomorphy

Each character shown in

pink is a synapomorphy

Shared - by all descendants

in the clade
e.g., all chordates share a
notochord

Derived – not present in

ancestral taxa
e.g., ancestral deuterostome
lacks a notochord

Any clade must share at

least one synapomorphy
Synapomorphy

How can we tell how well

a clade is supported?

In part, by the number of

synapomorphies

Few synapomorphies = weaker support

Many synapomorphies = stronger support

 Homoplasy
Homoplasy
Taxa share a character, but not by descent from a common ancestor
Equivalent to analogy, homoplasy is a product of convergent evolution
Homoplasy gives the impression of homology (synapomorphy) and therefore
misleads phylogenetic analyses by supporting polyphyletic taxa

Recovered
phylogeny

True phylogeny
 True phylogeny:
Homoplasy Malawi cichlids
monophyletic

Lake Tanganyika Lake Malawi

Homoplasies that look like
homologies:
Stripes
Spotted caudal fin
Yellow color

Recovered
phylogeny
 Morphological characters
Examples
Skull structure in cetaceans Genitalia in ants
 Morphological characters
Constructing a character matrix
Suppose we want to know the phylogeny of cichlids A, B, C using an Outgroup
First, we need characters that are variable within this group

Character: Pattern Caudal Caudal Forehead

Pattern Shape Bulge?
Out
Striped Spot Round No
A Synapomorphies
Barred None Forked No

B
Barred None Forked No
C
Apomorphy
Barred None Round Yes
 Parsimony
How do we decide the “best” phylogeny?
Parsimony – the simplest explanation is preferred (Occam’s razor)
A trivial example (much more complicated with real datasets)

Most parsimonious:
Requires 5 steps Requires only 4 steps

Round  forked tail

Round  forked tail

Round  forked tail

Stripe  barred
Spot  plain tail
Stripe  barred
Spot  plain tail
No bump  forehead bump No bump  forehead bump
 Molecular characters
Outgroup AAGCTTCATA Invariable sites

Species A GAGCTTCACA These are not useful

Species B GTGCTTCACG phylogenetic characters

Species C GTGCTTCACG
Out
Out

A
A

B
B

C
 Molecular characters
Outgroup AAGCTTCATA Synapomorphies
supporting A+B+C
Species A GAGCTTCACA
Species B GTGCTTCACG
Species C GTGCTTCACG
Out
Out

A
A

B
B
AG TC

C Any mutations at
this time would affect
A, B and C because they
have not yet diverged C
 Molecular characters
Outgroup AAGCTTCATA Synapomorphies
supporting A+B+C
Species A GAGCTTCACA
Synapomorphies
Species B GTGCTTCACG supporting B+C
Species C GTGCCTCACG Apomorphy for C

Out
Out

A
A

B
B
AG TC

C
AT AG
C
Any mutations at this time would only affect C TC
 Molecular characters
Homoplasy is still a problem
There are only 4 possible character states for nucleotides: A G C T
Homoplasy arises when nucleotide mutates back to ancestral state: ATA

Out
AAGCTTCATA
GAGCTTCACA
GTGCTTCACG A
GTGCTTCACG AAGCTTCATA
GAGCTTCACA B
GTGCTTCACG AAGCTTCATA
AG TC GTGCTTCACG GAGCTTCACA
GTGCTTCACG
GAGCTTCACG
AT AG
Back-mutation “erases” C
synapomorphy and TA
produces homoplasy
 Molecular characters
Homoplasy is still a problem
There are only 4 possible character states for nucleotides: A G C T
Homoplasy arises when nucleotide mutates back to ancestral state: ATA

Out
AAGCTTCATA
GAGCTTCACA CA
GTGCTTCACG A
GTGCTTCACG AAGCTTCATA
GAGCTTCACA B
GTGCTTCACG AAGCTTCATA Homoplasy
AG TC GTGCTTCACG can also reflect
GAGCTTAACA
convergent
GTGCTTCACG mutations
GAGCTTAACG
AT AG
Back-mutation “erases” C
synapomorphy and TA CA
produces homoplasy
 Morphology vs molecules
Morphology Nucleotides
Homoplasy can be assessed from Homoplasy can’t be assessed directly
structure, development, etc. PRO (an “A” is an “A”) CON

Characters may be subject to selection Characters may or may not be subject

= convergence = homoplasy CON to selection – depends on the site ?

Takes lots of time to identify and code Sequencing yields lots of characters
characters for analysis CON if gene is sufficiently variable PRO

Requires parsimony analysis ? Can use either parsimony or likelihood

analysis – stronger inference PRO

Only someone familiar with taxon can Any idiot can get sequence data
identify good characters PRO & CON PRO & CON

With either approach, it all comes down to successfully identifying

synapomorphies and distinguishing them from homoplasies
APPLICATIONS OF PHYLOGENETIC ANALYSIS:

I) Forensic Studies
 TRACING THE SOURCE OF HIV INFECTION

 In 1990, the CDC determined that a young woman, Kimberly Bergalis,

was most likely infected with HIV by her dentist in Florida. She had no
risk factors for HIV - no sex, no drugs, no blood transfusion.

 The dentist, Dr. David Acer, then requested that the CDC test his other
patients.

 Among approximately 1100 former patients tested, the CDC identified

seven that tested positive for HIV.

 To establish the source of the infection, the CDC sequenced viral

genes isolated from the dentist, the HIV-positive patients, and a control
group of 35 local HIV-positive people.
 Patients had no
known risk factors

 Tracking the
origin of HIV
infection in
dental patients
by
reconstructing LC = “local control”
a phylogeny of
HIV isolates
Known risk factors

From Ou et al. (1992)

 HIV FROM THE DENTIST -- FOLLOW-UP

 Kimberly Bergalis died in 1991 at the age of 23.

 Dr. David Acer died in 1990.
 Two of his infected patients were still alive as of 2001 -- one is in
mid-forties, other is in mid-twenties.
 Still not clear how the dentist transmitted HIV to his patients, but all
patients underwent invasive procedures like root canals or tooth
extraction.
 No other examples of a dentist transmitting HIV to patients -- we
can still go to the dentist.
Tracing the origin of
commercial whale
meat

JE93 was a hybrid Fin/Blue whale

from the north Atlantic born in 1965,
tagged in 1986, harpooned in 1989,
and illegally sold in the meat markets
of Japan in 1993.

FROM: Cipriano & Palumbi. 1999. Nature 397:307-308

APPLICATIONS OF PHYLOGENETIC ANALYSIS:

II) Ancient DNA Studies

INSECTS IN AMBER
What are the relationships between extinct flightless birds and
modern bird groups???

13 ft.

Dinornis giganteus
 Complete mitochondrial genome sequences of two extinct moas (and
partial sequence of the extinct Elephant Bird: Mullerornis) clarify ratite
evolution:

FROM: Cooper et al. 2001. Nature 409:704-707

APPLICATIONS OF PHYLOGENETIC ANALYSIS:

III) Origins of Domesticated Species

MULTIPLE AND ANCIENT ORIGINS OF THE DOMESTIC DOG

FROM:Vila et al. 1997. Science 276:1687-1689

APPLICATIONS OF PHYLOGENETIC ANALYSIS:

IV) Character Evolution

ESTIMATING THE HISTORY OF CHARACTER EVOLUTION

 Estimate a phylogeny for species with the character of interest.

 Map the characters on the phylogeny.
 Use the principle of parsimony to infer the character states in the
ancestral groups.
 EXAMPLE: THE EVOLUTION OF EUSOCIALITY

 Eusocial species possess three traits:

• Individuals cooperate in caring for the young.

• There is reproductive division of labor, with non-reproducing
workers helping more fecund individuals.
• Generations overlap, so that offspring help their parents.
 dragonflies

termites.
roaches

Eusociality
evolved once in
termites

grasshoppers

walking sticks

lice and bugs

beetles

wasps, bees, ants

Eusociality

flies and fleas

evolved at least
a dozen times in
the Hymenoptera.

caddisflies, moths