Phylogenetic inference using molecularsequence data
Matt Herron
University of Arizona
Department of Ecology and Evolutionary Biology
Example: bats
• Megachiroptera (flying foxes)
Example: bats
• Megachiroptera (flying foxes)
• Microchiroptera (all others)
Example: bats
• Megachiroptera (flying foxes)
• Microchiroptera (all others)
• Monophyly disputed
Example: bats
• Megachiroptera (flying foxes)
• Microchiroptera (all others)
• Monophyly disputed
• Close relatives:– Flying lemurs (colugos)?
Example: bats
• Megachiroptera (flying foxes)
• Microchiroptera (all others)
• Monophyly disputed
• Close relatives:– Flying lemurs (colugos)?– Primates?
Example: bats
• Megachiroptera (flying foxes)
• Microchiroptera (all others)
• Monophyly disputed
• Close relatives:– Flying lemurs (colugos)?– Primates?– Tree shrews?
What to do?
• Download amino acid sequences from GenBank (NCBI)
• Build a phylogenetic tree by neighbor-joining
Distance matrix
1 2 3 4 5 6
1 -
2 52 -
3 53 44 -
4 84 70 79 -
5 78 61 62 76 -
6 77 70 68 73 66 -
Distance matrix
1 2 3 4 5 6
1 -
2 52 -
3 53 44 -
4 84 70 79 -
5 78 61 62 76 -
6 77 70 68 73 66 -
2 & 3 are sister
2
3
Roundleafbat
Little brownbat
Revised matrix
1 2 3 4 5 6
1 -
2 52 -
3 53 44 -
4 84 70 79 -
5 78 61 62 76 -
6 77 70 68 73 66 -
Revised matrix
1 2 3 4 5 6
1 -
2
352.5
-
44 -
4 84 70 79 -
5 78 61 62 76 -
6 77 70 68 73 66 -
Revised matrix
1 2 3 4 5 6
1 -
2
352.5 -
4 84 70 79 -
5 78 61 62 76 -
6 77 70 68 73 66 -
Revised matrix
1 2 3 4 5 6
1 -
2
352.5 -
4 84 74.5 -
5 78 61 62 76 -
6 77 70 68 73 66 -
Revised matrix
1 2 3 4 5 6
1 -
2
352.5 -
4 84 74.5 -
5 78 61.5 76 -
6 77 70 68 73 66 -
Revised matrix
1 2 3 4 5 6
1 -
2
352.5 -
4 84 74.5 -
5 78 61.5 76 -
6 77 69 73 66 -
Revised matrix
1 2 3 4 5 6
1 -
2
352.5 -
4 84 74.5 -
5 78 61.5 76 -
6 77 69 73 66 -
1 is sister to 2 & 3
2
3
1 Flying fox
Roundleafbat
Little brownbat
Revise the matrix again
1 2, 3 4 5 6
1 -
2, 3 52.5 -
4 84 74.5 -
5 78 61.5 76 -
6 77 69 73 66 -
Revise the matrix again
1, 2, 3 4 5 6
1, 2, 3-
52.5 -
4 84 74.5 -
5 78 61.5 76 -
6 77 69 73 66 -
Revise the matrix again
1, 2, 3 4 5 6
1, 2, 3 -
4 84 74.5 -
5 78 61.5 76 -
6 77 69 73 66 -
Revise the matrix again
1, 2, 3 4 5 6
1, 2, 3 -
4 79.25 -
5 78 61.5 76 -
6 77 69 73 66 -
Revise the matrix again
1, 2, 3 4 5 6
1, 2, 3 -
4 79.25 -
5 69.75 76 -
6 77 69 73 66 -
Revise the matrix again
1, 2, 3 4 5 6
1, 2, 3 -
4 79.25 -
5 69.75 76 -
6 73 73 66 -
Revise the matrix again
1, 2, 3 4 5 6
1, 2, 3 -
4 79.25 -
5 69.75 76 -
6 73 73 66 -
5 is sister to 6
2
3
1
6
Flying fox
Roundleafbat
Little brownbat
Mouselemur
5 Treeshrew
Revise the matrix again
1, 2, 3 4 5, 6
1, 2, 3 -
4 79.25 -
5
6
69.75 76 -
73 73 66 -
Revise the matrix again
1, 2, 3 4 5, 6
1, 2, 3 -
4 79.25 -
5, 6 71.325 76 -
73 66 -
Revise the matrix again
1, 2, 3 4 5, 6
1, 2, 3 -
4 79.25 -
5, 6 71.325 74.5 -
66 -
Revise the matrix again
1, 2, 3 4 5, 6
1, 2, 3 -
4 79.25 -
5, 6 71.325 74.5 -
Revise the matrix again
1, 2, 3 4 5, 6
1, 2, 3 -
4 79.25 -
5, 6 71.325 74.5 -
5 & 6 are sister to 1, 2, & 3
2
3
1
6
Flying fox
Roundleafbat
Little brownbat
Mouselemur
5 Treeshrew
All that’s left is 4
4 Flyinglemur
2
3
1
6
Flying fox
Roundleafbat
Little brownbat
Mouselemur
5 Treeshrew
Cape ground squirrel
• Savannahs of southern Africa
• Social• 1 premolar above
and below• 2 pairs of mammae• 38 chromosomes
Mountain ground squirrel
• Mountains along the western coast of southern Africa
• Solitary• 1 premolar above
and below• 2 pairs of mammae• 38 chromosomes
Southern flying squirrel
• Eastern North America, parts of Central America
• Solitary• 2 premolars above,
1 below• 4 pairs of mammae• 48 chromosomes
Round-tailed ground squirrel
• Southwestern United States, northern Mexico
• Social• 2 premolars above,
1 below• 4 to 6 pairs of
mammae• 36 chromosomes
Least chipmunk
• Western United States, much of Canada
• Solitary• 2 premolars above,
1 below• 4 pairs of mammae• 38 chromosomes
Black-tailed prairie dog
• Central United States
• Social• 2 premolars above,
1 below• 4 pairs of mammae• 50 chromosomes
Woodchuck / groundhog
• Eastern United States, much of Canada
• Solitary• 2 premolars above,
1 below• 4 pairs of mammae• 38 chromosomes