Phylogenetic inference using molecular sequence data
description
Transcript of Phylogenetic inference using molecular sequence data
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