1. GENE 3000 Fall 2013 slides 127-159

3. wiki. wiki. wiki.

5. 4 species can be related to each other in only 3 ways

6. A B C

7. evolution - story of gain and loss when and how were complex eyes evolved? in what species are they lost? are the genes required to develop eyes still there? can they be expressed in different ways? how frequently are genes gained and lost? how often is there lateral gene transfer between hosts and pathogens, or microbes? why are there more A/T bases in parts of the mitochondrion?

8. Nature, June 2012

9. all starts with this

10. terms phylogeny: visual representation of the evolutionary history of populations, genes, species tips: terminal ends of a phylogeny, representing the populations, genes, species branches: lineages evolving through time node: where lineages split; the common ancestor to descendants clade: a group all descended from one ancestor

11. terms phylogeny: visual representation of the evolutionary history of populations, genes, species tips: terminal ends of a phylogeny, representing the populations, genes, species branches: lineages evolving through time node: where lineages split; the common ancestor to descendants clade: a group all descended from one ancestor discovermagazine.com

14. organisms are related through descent from ancestors progression of generations

19. more than 2 million identified and classified species extant

20. taxonomy (systematics) groups defined on previous slides are clades group comprised of one organism and all its descendants (mono- phyly) indication of homology

22. Archosaurs

23. how do we know? inference, reconstruction characters are heritable traits that can be compared (an A in position 117; body hair) careful evaluation of homology assume that having more things in common indicates more recent common ancestor (longer shared history)

24. homology and homoplasy similarity without shared descent is homoplasy - convergent evolution (wings) or evolutionary reversal (snakes don’t have legs) homology may require full evidence, e.g. development of insect wings very different from development of bird wings

25. phylogeny inference morphological characters (presence, absence, quality) DNA-based characters work the same (idea is there may be more independence, and more of them)

26. our data matrix Text? in NEXUS format

27. parsimony analysis assume each state evolved only once (not necessarily true) principle of parsimony: the simplest explanation is the most likely we can identify how often this assumption is violated

28. one character tentacular forelimbs might be able to split into 2 clades, but cannot fully resolve tree

29. parsimony is a CRITERION our assumption of parsimony does not find the tree, it is a score given to a tree trees are searched algorithmically for all possible topologies (or all possible better than score X) a parsimony phylogeny analysis returns the set of most-parsimonious trees

30. our tree

31. eyeless

32. “presence of 2 eyes” - obviously negatively correlated with “eyeless”

33. tail

34. digits

35. dark stripes hmmm correlated with digits!?

36. wings

37. circular tail fin “forked” tail fin

38. “protruding body”

39. 2 digits - an autapomorphy

40. our tree parsimony tree(s) from class data matrix which characters exhibit HOMOPLASY remember: homoplasy may be evolutionary convergence/reversal, may also reflect our own uncertainty about the character and how it develops! see Box 1 (chapter 4) for another example

41. molecular data we will come to this later how it is analyzed, but we see the problems of highly correlated, non-independent characters hard to identify very many characters thus not a fully resolved phylogeny (but good!) if you sequence a single gene region, might have 100 characters that are unbiased by the person collecting the data

42. example of carnivores define “carnivore” please...

43. why study phylogeny of carnivores? lets ask a simple question: did aquatic pinnipeds evolve only once, or were there multiple transitions to the sea?

44. 12 characters, 10 carnivores

45. synapomorphies

46. 13 13

47. 20 characters, 3 equally parsimonious trees our result is robust to this uncertainty: one origin of pinnipeds (consensus at left)

48. parsimony simple assumption, simple model - may lead to several ‘equally parsimonious’ results more data will not always solve the problem more complex models evaluate the non-independence of data, the empirical patterns of DNA substitution, and probability theory