Phylogeny & Cladistics

Objectives

The basics of phylogenetic trees

How phylogenetic trees are constructed.

How phylogenies can address questions

about evolution.

Our classifications

will come to be, as

far as they can be

so made, genealogies.

- Charles Darwin, 1859

Phylogeny and Classification

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

Example: Acer saccharum

- Acer is the genus name - it is a Latin noun

- saccharum is the specific epithet - it is a Latin

adjective

Carolus Linnaeus

1707-1778

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

Family Family

Genus

Species 1

Species 2

Species 3

Species 4

Species 1

Species 2

Species 3

Genus

Genus

Species 1

Species 2

Order

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

Species 1

Genus

Species 1

Species 2

Species 3

Genus

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)

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 and classification

Class

Order

Order

Family

Family

Family

Genus

Genus

Genus

Genus

Genus

Genus

FamilyGenus

Genus

PhylogenyClassification

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 anddescent. 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 characteris any attribute of an organism that can provide us withinsights into history (shared ancestry).

In molecular phylogenies, characters are typicallynucleotide positions in homologous gene sequence, andeach position can possess four CHARACTERSTATES: A,C, G, or T

Cladograms are constructed based on the similarities ofhomogolous DNA sequences

Mutations in the ancestral gene results in all descendantpossessing the new (derived) trait

A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

TAXA

Phylogenetic Trees

The point at which branching occurs (node) signifies a speciation event from a common ancestral population

Fig. 26-5

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

ANCESTRAL LINEAGE

Taxon A

Polytomy (ancestral group

splits into more

than two Taxa

Common ancestor of

taxa AF

Branch point

(node)

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

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

Includes an ancestor

all of its descendants

A B C D

Paraphyletic group

Includes ancestor and

some, but not all of its

descendants

A B C D

Polyphyletic group

Includes two convergent

descendants but not their

common ancestor

A B C D

Taxon A is highly derived

and looks very different

from B, C, and ancestor

How could this happen? 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

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

Paraphyletic groups

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

Foxes

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

Paraphyletic groups

Monophyly

Note that canids are still a good

monophyletic clade within Mammalia

Each of the colored lineages within

canids is also a monophyletic clade

Canids

Paraphyletic groups

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

Paraphyly

Lizards (Sauria) areparaphyletic 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

Lizards

Paraphyletic groups

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

Reptilia

What does this mean?

It means that

reptiles dontexist!

No, it means

that youre oneof 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 toClass 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

After Page and Holmes 1998

we will return

to this

More Synapomorphies

sharedshared

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

Figure 4.8, pg. 121

Whales early Whales late

Parsimony

using

morphologyFigure 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