morphospace

tim

e

morphospace

tim

e

A BCO * * *

*

Shared, derived character

synapomorphy

Example: Feathers among vertebrate groups

A BCO * * *# # # #

Everyone has the character

It is ‘primitive’ in the phylogeny

Shared-primitive character

Symplesiomorphy

Example: The number of limbs in terrestrial vertebrates

A BCO * * *

How do you tell if a trait is primitive or derived?

Outgroup

A BCO * * *

*

Principle of Parsimony

Simpler explanation is more likely

Parsimony -- topology that minimizes total evolutionary change

A BCO * * *

Vs.

*

*

A BCO * * *

**

A BCO * * *

*

A BCO * * *

*

* *

*

A BOC * * *

*

How to Construct Trees?

Need characters morphologicalmtDNA, cpDNA -- genera, speciesnuclear DNA -- classes, families, orders, generarRNA -- kingdoms, phyla, classes

Need a method for using the characters

A B C D

a’bc’d’efg a’b’cdef’g a’bc’de’fg a’b’cdefg’

A B C D

A B C D

a’bc’d’efg a’b’cdef’g a’bc’de’fg a’b’cdefg’

A B C D

a a’

a’ is shared ancestral

A B C D

a’bc’d’efg a’b’cdef’g a’bc’de’fg a’b’cdefg’

A B C D

a a’

a’ is shared ancestralb’ and c’ are shared derivedd’ e’ f’ and g’ are uninformative

c c’b b’

vv

3 species -- 3 possible trees3 known, plus 4th -- 15 possible trees3 known, plus 10 -- 282,137,824 possible trees

plus 20 -- >>81023

A

A

B

B

C

C

A BC

How to find the “best” tree?

Sample 1000 trees find the best and search ‘near’ themavoid characteristics of the worst trees

Break it up into smaller groups that can be searched, then combine groups, forcing your search to areas thatmaintain the branching you find in

Add one at a time

Algorithmic--searching for the best method for finding the tree

Maximum liklihood methods

Starts with a model of evolutionary change

e.g. All base pair changes equally likely

Transitions more likely than transversions3rd base pair changes more likely than 1st base pair changesSynonymous changes more likely than non-synonymous changes

Rules that imply probability

Calculate the probability that a particular change occurredThe tree that has the highest probability (i.e liklihood) is favored

Using Molecular Data

Small number of character states (A,T, G, C)

Reversions A G A will be frequent

What do you do with mistakes?

Homoplasy

A B C C B A A B C

Phenomenon Phylogeny What it looks like

parallelevolution

convergence

A B C DA B C D A D B C

reversalA B C B C A C B A

How good is a method (e.g. parsimony) at uncovering the phylogeny?

Consider 4 taxa, trait is one codon:

1. GAA2. GAA3. GAT4. GAT

1. GAA 3. GAT

2. GAA 4. GAT

A T

AGGGGGGG GGGGGGAG

CCCCCCCC TTTTTTCC

Ancestral state GGGGGGGG

Length of A + B + C

Length

of

D +

E

D E

A CB

Types of charactersmorphologicalmtDNA, cpDNA -- genera, speciesnuclear DNA -- families, orders, generarRNA -- phyla, classes

Considerations:informative characters -- shared derived traitsdirection of change -- outgroupproblems -- convergence, parallel evolution, reversal

Methodsparsimonymaximum likelihood, etc.

Monophyletic Paraphyletic Polyphyletic

all descendents of some, but not all, shared character common ancestor descendents not present in possess trait possess trait common ancestor

What is the relation of systematics to classification?

Classification that does not reflecthistory is uninformative and misleading.It may lead to mistakes--certainlyit is wrong

Uses of phylogenies

rates of evolutionary change -- Hawaiian honeycreepers

patterns of adaptive evolution -- hammerhead sharks

classify diversity http://tolweb.org/tree/phylogeny.html

coevolution and cospeciation -- hosts and parasites

comparative method

Sequence of character change:

Evolution of hammerhead sharks

Two hypothesized functions: - bowplane to increase lift

while swimming - enhanced orientation and

prey detection

Martin 1997 Nature 364:494

921 bp mtDNA; eight hammerhead taxa plus outgroup

Using phylogenies to test for cospeciation of host and parasite:

Pocket gophers (Geomys spp.) and their lice (Geomydoecus spp.; Mallophaga)

Hafner et al. 1994 Science 265:1087

14 species of pocket gophers and associated lice species 379 bp of cytochrome oxidase I gene

134 polymorphic sites in gophers; 178 in lice

pocket gophers lice

Gopher and louse phylogenies are significantly congruent

The timing of diversification is significantly correlated in gophers and lice

Phylogenies congruent!!

but, are they?

Cyphomyrmex

Myrmecocrypta

Mycocepurus

A phylogeny represents the evolutionary history of a lineage in termsin terms of when splits arose and how much descendant taxadiffer from the ancestor

Molecular sequence data have revolutionized the construction of phylogenies because they provide large numbers of simplecharacters

Phylogenies are based on shared derived characters; ancestral vs.derived state is determined by comparison to an outgroup

Parsimony is the most frequently used method for constructing phylogenies, but it may produce multiple equally parsimonioustrees, especially if the number of taxa is large

Robust phylogenies based on molecular data enable evolutionary biologists to address several types of questions