Phylogenetic inference using molecular sequence data

1. Phylogenetic inference using molecularsequence data Matt Herron University of Arizona Department of Ecology and Evolutionary Biology

2. Example: bats • Megachiroptera (flying foxes)

3. Example: bats • Megachiroptera (flying foxes) • Microchiroptera (all others)

4. Example: bats • Megachiroptera (flying foxes) • Microchiroptera (all others) • Monophyly disputed

5. Example: bats • Megachiroptera (flying foxes) • Microchiroptera (all others) • Monophyly disputed • Close relatives: • Flying lemurs (colugos)?

6. Example: bats • Megachiroptera (flying foxes) • Microchiroptera (all others) • Monophyly disputed • Close relatives: • Flying lemurs (colugos)? • Primates?

7. Example: bats • Megachiroptera (flying foxes) • Microchiroptera (all others) • Monophyly disputed • Close relatives: • Flying lemurs (colugos)? • Primates? • Tree shrews?

8. What to do? • Download amino acid sequences from GenBank (NCBI) • Build a phylogenetic tree by neighbor-joining

11. Distance matrix

12. Distance matrix

13. 2 & 3 are sister Roundleaf bat 2 Little brown bat 3

14. Revised matrix

15. Revised matrix

16. Revised matrix

17. Revised matrix

18. Revised matrix

19. Revised matrix

20. Revised matrix

21. 1 is sister to 2 & 3 Roundleaf bat 2 Little brown bat 3 1 Flying fox

22. Revise the matrix again

23. Revise the matrix again

24. Revise the matrix again

25. Revise the matrix again

26. Revise the matrix again

27. Revise the matrix again

28. Revise the matrix again

29. 5 is sister to 6 Roundleaf bat 2 Little brown bat 3 1 Flying fox Mouse lemur 6 5 Tree shrew

30. Revise the matrix again

31. Revise the matrix again

32. Revise the matrix again

33. Revise the matrix again

34. Revise the matrix again

35. 5 & 6 are sister to 1, 2, & 3 Roundleaf bat 2 Little brown bat 3 1 Flying fox Mouse lemur 6 5 Tree shrew

36. All that’s left is 4 Roundleaf bat 2 Little brown bat 3 1 Flying fox Mouse lemur 6 5 Tree shrew 4 Flying lemur

37. Cape ground squirrel • Savannahs of southern Africa • Social • 1 premolar above and below • 2 pairs of mammae • 38 chromosomes

38. Mountain ground squirrel • Mountains along the western coast of southern Africa • Solitary • 1 premolar above and below • 2 pairs of mammae • 38 chromosomes

39. Southern flying squirrel • Eastern North America, parts of Central America • Solitary • 2 premolars above, 1 below • 4 pairs of mammae • 48 chromosomes

40. Round-tailed ground squirrel • Southwestern United States, northern Mexico • Social • 2 premolars above, 1 below • 4 to 6 pairs of mammae • 36 chromosomes

41. Least chipmunk • Western United States, much of Canada • Solitary • 2 premolars above, 1 below • 4 pairs of mammae • 38 chromosomes

42. Black-tailed prairie dog • Central United States • Social • 2 premolars above, 1 below • 4 pairs of mammae • 50 chromosomes

43. Woodchuck / groundhog • Eastern United States, much of Canada • Solitary • 2 premolars above, 1 below • 4 pairs of mammae • 38 chromosomes