Phylogeny & Cladistics

Objectives
The basics of phylogenetic trees
How phylogenetic trees are constructed.
How phylogenies can address questions
about evolution.

Phylogeny and Classification

Our classifications
will come to be, as
far as they can be
so made, genealogies.
- Charles Darwin, 1859

Systematics is the study of biological diversity

in an evolutionary context. It includes
speciation
taxonomy
**phylogeny

How to classify life

Phenetic classification
Based on overall similarity
Those organisms most similar are classified
more closely together.

Taxonomy is the branch of systematics concerned

with naming and classification.

Scientific names are binomials

Carolus Linnaeus
Example: Acer saccharum
1707-1778
- Acer is the genus name - it is a Latin noun
- saccharum is the specific epithet - it is a Latin
adjective

Biological
classifications are
hierarchical: each
taxonomic group is
nested within a
more inclusive
higher order group.

(Note that only the genus name

and specific epithet are italicized.)

Phylogeny and classification

Hierarchy

All taxonomic classifications are hierarchical how does phylogeny differ?

Class

Order

Order

Family
Genus
Species 1
Species 2
Species 3
Species 4
Genus
Species 1
Species 2
Species 3

Family
Genus
Species 1
Species 2

Family
Genus
Species 1
Species 2
Species 3
Species 4
Species 5
Species 6
Species 7
Species 8
Species 9

Genus
Species 1
Species 2
Genus
Species 1

Genus
Species 1
Species 2
Species 3

Problem with phenetic classification:

Can be arbitrary,
e.g., classify these:

Phylogenetic classification
Based on known (inferred) evolutionary
history.
Advantage:
Classification reflects pattern of evolution
Classification not ambiguous

Phylogeny is the study of the

pattern of divergence history.
(as opposed to speciation, which
addresses process.)
Assembling a phylogeny
using cladistics, taxa are
associated on the
basis of shared evolutionary
innovations.

Willi Hennig, 1913 - 1976

Founder of Phylogenetic
Systematics
(also called cladistics)

Phylogeny and classification

Hierarchy
Phylogenetic (cladistic) classification reflects evolutionary history
The only objective form of classification organisms share a true evolutionary
history regardless of our arbitrary decisions of how to classify them
Phylogeny

Classification
Genus
Family
Genus
Order
Genus
Family
Genus

Class

Genus
Family
Genus
Order
Genus
Family
Genus

Phylogeny
Phylogenetics: the study of ancestor descendent
relationships. The objective of phylogeneticists is
to construct phylogenies
Phylogeny: A hypothesis of ancestor descendent
relationships.
Phylogenetic tree: a graphical summary of a
phylogeny

Phylogeny
ALL life forms are related by common ancestry and
descent. The construction of phylogenies provides
explanations of the diversity seen in the natural world.
Phylogenies can be based on morphological data,
physiological data, molecular data or all three.

Today, phylogenies are usually constructed using

DNA sequence data

Phylogenetic Characters
We use characters to construct phylogenies. A character
is any attribute of an organism that can provide us with
insights into history (shared ancestry).
In molecular phylogenies, characters are typically
nucleotide positions in homologous gene sequence, and
each position can possess four CHARACTER
STATES: A,C, G, or T
Cladograms are constructed based on the similarities of
homogolous DNA sequences
Mutations in the ancestral gene results in all descendant
possessing the new (derived) trait

Phylogenetic Trees
TAXA

TIME
speciation

Cladogram or Phylogenetic Tree

The point at which branching occurs (node) signifies a

speciation event from a common ancestral population

Fig. 26-5

Branch
point
(node)

Taxon A
Taxon B
Taxon C

ANCESTRAL
LINEAGE

Taxon D
Taxon E
Taxon F

Common ancestor of
taxa AF

Polytomy
(ancestral group
splits into more
than two Taxa

Sister
taxa (B &
C more
related to
each
other
than to A)

Apomorphy (derived trait)

= a new, derived feature

E.g., for this evolutionary transformation
scales
-------->
feathers
(ancestral feature)
(derived feature)

Presence of feathers is an apomorphy

for birds.

Taxa are grouped by apomorphies

Apomorphies are the result of evolution.

Taxa sharing apomorphies

underwent same evolutionary history
should be grouped together.

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

Polyphyletic group

Includes an ancestor
all of its descendants

Includes ancestor and

some, but not all of its
descendants

Includes two convergent

descendants but not their
common ancestor

How could this happen?

Taxon A is highly derived

and looks very different
from B, C, and ancestor

Taxon A and C share

similar traits through
convergent evolution

Only monophyletic groups (aka clades) are recognized in cladistic

classification

Phylogeny and classification

Monophyly
Each of the colored lineages
in this echinoderm phylogeny
is a good monophyletic group (clade)

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
reptiles dont
exist!

No, it means
that youre one
of us!

What it means is that reptile is only a

valid clade if it includes birds
Birds are still birds, but Aves cannot be
considered a Class equivalent to
Class Reptilia because it is evolutionarily
nested within Reptilia

Reptilia
Aves
(birds)

Turtles
Crocodiles
Lizards and snakes
Tuataras

Review:
Introduction
to
Phylogenetic
Trees

Cladisitc Character State Definitions

Plesiomorphy: refers to the ancestral character state
Apomorphy: a character state different than the ancestral
state, also called a DERIVED STATE
Derived does not mean better or advanced (as the
mutations that create them can be deleterious, neutral or
beneficial)
Synapomorphy: a derived character state (apomorphy)
that is SHARED by two or more taxa due to inheritance
from a common ancestor: these character states are
phylogenetically informative using the parsimony or
cladistic criterion

Autapomorphy: a uniquely derived character state

Constructing Phylogenetic Trees

We use homologous characters (synapomorphies)
to construct phylogenetic trees and to identify
groups that are monophyletic; synapomorphies are
phylogenetically informative.
We want to avoid using homoplasious characters
to construct phylogenies

Character States

we will return
to this

After Page and Holmes 1998

More Synapomorphies

shared
shared

Homology and Homoplasy

A character state that is shared between two
DNA sequences or taxa may be so because
they inherited it from a common ancestor, or it
is HOMOLOGOUS (a homology/
synapomorphy)
Alternatively, the shared character might occur
because they were evolved independently, in
which case they are called a HOMOPLASY

Why can Homoplasy Occur?

After Page and Holmes1998

Homoplasy and Polyphyly

Homoplasy results in erroneous, polyphyletic groupings

such as vultures

A Vulture

Vultures are a polyphyletic group. New world and old world

vultures provide an example of homoplasy resulting from convergent
evolution.

Analogy (non homology): The fins of a whale and

the fins of a shark are another example of homoplasy
due to convergence, the independent acquisition of a
character in different lineages

Reversals & Phylogeny

Parsimony (also known as cladistics)

The Principle of Parsimony: simple explanations
are preferred over more complicated ones.
In terms of phylogenetic trees, less evolutionary
steps are better than more steps to explain
relationships. The tree with the least number of
steps is the most parsimonious.
The parsimony method minimizes the total number of
evolutionary changes required to explain relationships

Constructing Trees with Parsimony

Outgroup: When constructing a phylogeny for a
group of organisms, we need to employ an
outgroup, which is not part of the group of interest
(the ingroup), but also not too distantly related to
it.
The outgroup is used to polarize the character
states, or infer change. The character state
possessed by the outgroup is defined a priori as
ancestral (pleisiomorphic)

Whale Evolution

Ambulocetus

The Artiodactyla
The artiodactyla are a group of hoofed mammals
that possess an even number of toes, and includes
camels, pigs, peccaries, deer, the hippopotamus,
cattle and giraffes. The perissodactyla are hoofed
mammals that possess an odd number of toes (e.g.
horses, rhinos, tapirs).
Are whales really a member of the artiodactyla?

Selecting Phylogenetic Trees with

Parsimony

Whales early

Figure 4.8, pg. 121

Whales late

Parsimony
using
morphology
Figure 14.5, pg. 558

Outgroup is a Perissodactyl

Parsimony
using
molecular
characters
Figure 14.6, pg. 559

Site 142 is plesiomorphic (uninformative)

Site 192 is a autapomorphic (uninformative)
Sites 162, 166 & 177 are synapomorphies (informative)

What do the informative sites tell us

about whale phylogeny?
Site 162 & 166
conflict with site 177
Hence there is
homoplasy in the data
set.
What is the most
parsimonious tree
looking at all
characters?
Whales early 47 nt
changes
Whales late 41 nt
changes

Whales late has less evolutionary steps to explain relationships: the

most parsimonious explanation