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Phylogenetic inference using molecular sequence data

This study explores phylogenetic inference using molecular sequence data, focusing on bats, particularly the Megachiroptera (flying foxes) and Microchiroptera (other bats). It discusses monophyly disputes and close relatives such as flying lemurs and primates. The process includes downloading amino acid sequences from GenBank, building phylogenetic trees through neighbor-joining, and revising distance matrices to clarify evolutionary relationships among species like roundleaf bats, little brown bats, and various rodents. This analysis enhances our understanding of evolutionary connections and biodiversity.

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Phylogenetic inference using molecular sequence data

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  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

  9. Distance matrix

  10. Distance matrix

  11. 2 & 3 are sister Roundleaf bat 2 Little brown bat 3

  12. Revised matrix

  13. Revised matrix

  14. Revised matrix

  15. Revised matrix

  16. Revised matrix

  17. Revised matrix

  18. Revised matrix

  19. 1 is sister to 2 & 3 Roundleaf bat 2 Little brown bat 3 1 Flying fox

  20. Revise the matrix again

  21. Revise the matrix again

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

  28. Revise the matrix again

  29. Revise the matrix again

  30. Revise the matrix again

  31. Revise the matrix again

  32. Revise the matrix again

  33. 5 & 6 are sister to 1, 2, & 3 Roundleaf bat 2 Little brown bat 3 1 Flying fox Mouse lemur 6 5 Tree shrew

  34. 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

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

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

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

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

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

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

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

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