1. Phylogenetic inference using molecular sequence 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 123456 1- 252- 35344- 4847079- 578616276- 67770687366-

12. Distance matrix 123456 1- 252- 35344- 4847079- 578616276- 67770687366-

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

14. Revised matrix 123456 1- 252- 35344- 4847079- 578616276- 67770687366-

15. Revised matrix 123456 1- 2323 52.5 - 44- 4847079- 578616276- 67770687366-

16. Revised matrix 123456 1- 2323 52.5- 4847079- 578616276- 67770687366-

17. Revised matrix 123456 1- 2323 52.5- 48474.5- 578616276- 67770687366-

18. Revised matrix 123456 1- 2323 52.5- 48474.5- 57861.576- 67770687366-

19. Revised matrix 123456 1- 2323 52.5- 48474.5- 57861.576- 677697366-

20. Revised matrix 123456 1- 2323 52.5- 48474.5- 57861.576- 677697366-

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

22. Revise the matrix again 12, 3456 1- 52.5- 48474.5- 57861.576- 677697366-

23. Revise the matrix again 1, 2, 3456 - 52.5- 48474.5- 57861.576- 677697366-

24. Revise the matrix again 1, 2, 3456 - 48474.5- 57861.576- 677697366-

25. Revise the matrix again 1, 2, 3456 - 479.25- 57861.576- 677697366-

26. Revise the matrix again 1, 2, 3456 - 479.25- 569.7576- 677697366-

27. Revise the matrix again 1, 2, 3456 - 479.25- 569.7576- 673 66-

28. Revise the matrix again 1, 2, 3456 - 479.25- 569.7576- 673 66-

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

30. Revise the matrix again 1, 2, 345, 6 1, 2, 3- 479.25- 5656 69.7576- 73 66-

31. Revise the matrix again 1, 2, 345, 6 1, 2, 3- 479.25- 5, 671.32576- 7366-

32. Revise the matrix again 1, 2, 345, 6 1, 2, 3- 479.25- 5, 671.32574.5- 66-

33. Revise the matrix again 1, 2, 345, 6 1, 2, 3- 479.25- 5, 671.32574.5-

34. Revise the matrix again 1, 2, 345, 6 1, 2, 3- 479.25- 5, 671.32574.5-

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

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

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