1. Evolutionary Analysis

2. Tree Mathematical structure Model evolutionary history

4. Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6

5. Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Sister taxa Outgroup Root Branch Node Tip Polytomy (more than one branch emerging from one node)

6. (a) The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. Camel Peccary Pig Hippo Whale Deer Cow Astragalus (ankle bone) ARTIODACTYLS Gain of pulley- shaped astragalus

7. (b) If whales are related to hippos, then two changes occurred in the astragalus. Camel Peccary Pig Hippo Whale Deer Cow ARTIODACTYLS Gain of pulley- shaped astragalus Loss of pulley- shaped astragalus

8. (a) The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. (b) If whales are related to hippos, then two changes occurred in the astragalus. Camel Peccary Pig Hippo Whale Deer Cow Camel Peccary Pig Hippo Whale Deer Cow (c) Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Cow Locus Deer Whale Hippo Pig Peccary Camel Astragalus (ankle bone) 1  gene present 0  gene absent ?  still undetermined Whales and hippos share four unique SINE genes (4, 5, 6, and 7) ARTIODACTYLS Gain of pulley- shaped astragalus Loss of pulley- shaped astragalus Gain of pulley- shaped astragalus

9. Phylogenetic Tree shows ancestor-descendent relationships among populations or species clarifies evolutionary relationships

10. Root Ancestor of all sequences on tree

11. Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Sister taxa Outgroup Root Branch Node Tip Polytomy (more than one branch emerging from one node)

12. Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Taxon 1 Taxon 3 Taxon 2 Taxon 4 Taxon 5 Taxon 6

13. (a)(b) (c) 123123 456456 165165 432432 245245 631631

14. (a)(b) (c) 123123 456456 165165 432432 245245 631631 =

15. Types of Trees Rooted Unrooted

16. Rooted Trees Node identified as root, from which all other nodes descend Have direction corresponding to evolutionary time

17. Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6 Sister taxa Outgroup Root Branch Node Tip Polytomy (more than one branch emerging from one node)

18. Unrooted Trees Lacks root Does not specify evolutionary relationships Nothing about ancestors and descendents

20. Unrooted Trees Lacks root Does not specify evolutionary relationships Nothing about ancestors and descendents Many tree-building programs generate unrooted trees!

21. Types of Trees Cladogram Phylogram

22. Cladogram

23. Relative recency of common ancestry

24. Cladogram

25. Relative recency of common ancestry Does not show amount of evolutionary change

26. Phylogram

27. Also contains branch lengths Numbers associated with branches Amount of evolutionary change

28. Phylogram

29. Cladogram Phylogram

31. Constructing a Tree Construct multiple sequence alignment Build Tree Evaluate Tree

32. So how do I build a tree?

33. http://www.phylogeny.fr/ http://expasy.org/tools/ http://evolution.genetics.washington.edu/ph ylip/software.html#methods

34. So how do I build a tree? http://www.phylogeny.fr/

36. Tree building programs

37. Tree drawing programs

39. FASTA alignment

42. Newick Format (((((((Prochlorococcus_marinus:0.499642,Synechococcus_BL107:0.212828) 0.961000:0.131562,Cyanobium_PCC7001:0.279338)0.984000:0.159534, Thiomicrospira_crunogena:0.805902)0.230000:0.067881, Allochromatium_vinosum:0.522452)0.974000:0.136543,(Bradyrhizobium_BTAi1:1.004711, Nitrobacter_hamburgensis:0.728510)0.596000:0.070606)0.895000:0.088934, Halothiobacillus_neapolitanus:0.624513)0.987000:0.172336, Acidimicrobium_ferrooxidans:0.338388,Acidithiobacillus_ferrooxidans:0.255268);

43. Tree drawing programs

48. File formats to save your tree

50. http://www.phylogeny.fr/

51. Evaluating Trees Do your results make sense?

52. Evaluating Trees Do your results make sense? resample your data

55. Bootstrap tree branch support values

56. Evaluating Trees Do your results make sense? resample your data ground-truth your data

57. www.ncbi.nlm.nih.gov http://rdp.cme.msu.edu/du/

58. www.ncbi.nlm.nih.gov

59. Organism Trees vs Gene Trees Don’t always match!

60. Homologs Orthologs separated by speciation Paralogs produced by gene duplication Xenologs result of horizontal gene transfer

61. Tree-building resources http://www.phylogeny.fr/ http://expasy.org/tools/ http://evolution.genetics.washington.edu/ph ylip/software.html#methods