morphospace

2. time morphospace

3. time morphospace

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

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

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

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

8. A A A B B B C C C O O O * * * * * * * * * * * * Vs. A B C O * * * * * * * * * * * * * O A B 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’ a’bc’d’efg a’b’cdef’g A B C D A B C D

12. a’bc’de’fg a’b’cdefg’ a’bc’d’efg a’b’cdef’g A B C D A B C D a’is shared ancestral a a’

13. a’bc’de’fg a’b’cdefg’ a’bc’d’efg a’b’cdef’g A B C D A B C D 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 C B A C A B 3 species -- 3 possible trees 3 known, plus 4th -- 15 possible trees 3 known, plus 10 -- 282,137,824 possible trees plus 20 -- >>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. Phenomenon Phylogeny What it looks like A B C C B A A B C parallel evolution A B C D A B C D A D B C convergence A B C B C A C BA reversal

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

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

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

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. 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

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. 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

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