2. time
morphospace

3. time
morphospace

4. Example: Feathers among vertebrate groups* A B C O
Shared, derived character
synapomorphy *
Example: Feathers among vertebrate groups

5. # A B C O *
Everyone has the character
It is ‘primitive’ in the phylogeny
Shared-primitive character
Symplesiomorphy
Example: The number of limbs in terrestrial vertebrates

6. A B C O *
How do you tell if a trait is
primitive or derived?
Outgroup

7. Principle of ParsimonyB C O *
Principle of Parsimony
Simpler explanation is more likely *
Parsimony -- topology that minimizes total evolutionary change

8. A B C O *
Vs. A B O C *

10. How to Construct Trees? Need characters morphological
mtDNA, cpDNA genera, species
nuclear DNA -- classes, families, orders, genera
rRNA -- kingdoms, phyla, classes
Need a method for using the characters

11. a’bc’de’fg a’b’cdefg’

12. a’bc’de’fg a’b’cdefg’
a’ is shared ancestral
a a’

13. a’bc’de’fg a’b’cdefg’
b b’
c c’
a’ is shared ancestral
b’ and c’ are shared derived
d’ e’ f’ and g’ are uninformative
a a’

16. v v

17. A B C B C A B A C 3 species -- 3 possible trees
3 known, plus 4th possible trees
3 known, plus ,137,824 possible trees
plus >>81023

18. How to find the “best” tree?
Sample 1000 trees find the best and search ‘near’ them
avoid characteristics of the worst trees
Break it up into smaller groups that can be searched, then
combine groups, forcing your search to areas that
maintain the branching you find in
Add one at a time
Algorithmic--searching for the best method for finding the tree

19. Maximum liklihood methods
Starts with a model of evolutionary change
e.g. All base pair changes equally likely
Transitions more likely than transversions
3rd base pair changes more likely than 1st base pair changes
Synonymous changes more likely than non-synonymous changes
Rules that imply probability
Calculate the probability that a particular change occurred
The tree that has the highest probability (i.e liklihood) is favored

20. 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

21. A B C C B A A B C
Phenomenon Phylogeny What it looks like
parallel
evolution
convergence
A B C D
A B C D A D B C
reversal
A B C B C A C B A

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

23. Consider 4 taxa, trait is one codon: 1. GAA 2. GAA 3. GAT 4. GAT
AGGGGGGG
GGGGGGAG
CCCCCCCC
TTTTTTCC
Ancestral state GGGGGGGG

24. Length of A + B + C
Length of D + E
D E
A C B

25. Types of characters
morphological
mtDNA, cpDNA genera, species
nuclear DNA -- families, orders, genera
rRNA -- phyla, classes
Considerations:
informative characters -- shared derived traits
direction of change -- outgroup
problems -- convergence, parallel evolution, reversal
Methods
parsimony
maximum likelihood, etc.

26. What is the relation of systematics to classification?
Monophyletic Paraphyletic Polyphyletic
all descendents of some, but not all, shared character
common ancestor descendents not present in
possess trait possess trait common ancestor

27. Classification that does not reflect
history is uninformative and misleading.
It may lead to mistakes--certainly
it is wrong

29. rates of evolutionary change -- Hawaiian honeycreepers
Uses of phylogenies
rates of evolutionary change -- Hawaiian honeycreepers
patterns of adaptive evolution -- hammerhead sharks
classify diversity
coevolution and cospeciation -- hosts and parasites
comparative method

34. 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

36. Using phylogenies to test for
cospeciation of host and
parasite:
Pocket gophers (Geomys spp.) and
their lice (Geomydoecus spp.;
Mallophaga)
Hafner et al 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

37. Gopher and louse phylogenies are significantly congruent
pocket gophers lice

38. The timing of diversification is significantly correlated in gophers and lice

39. Phylogenies congruent!!
but, are they?

41. Cyphomyrmex
Myrmecocrypta
Mycocepurus

42. A phylogeny represents the evolutionary history of a lineage in terms
in terms of when splits arose and how much descendant taxa
differ from the ancestor
Molecular sequence data have revolutionized the construction of
phylogenies because they provide large numbers of simple
characters
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 parsimonious
trees, especially if the number of taxa is large
Robust phylogenies based on molecular data enable evolutionary
biologists to address several types of questions