Phylogenetic inference using molecular sequence 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

Distance matrix

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

Revised matrix

Revised matrix

Revised matrix

Revised matrix

Revised matrix

Revised matrix

Revised matrix

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

Revise the matrix again 12,

Revise the matrix again 1, 2,

Revise the matrix again 1, 2,

Revise the matrix again 1, 2,

Revise the matrix again 1, 2,

Revise the matrix again 1, 2,

Revise the matrix again 1, 2,

5 is sister to Flying fox Roundleaf bat Little brown bat Mouse lemur 5 Tree shrew

Revise the matrix again 1, 2, 345, 6 1, 2,

Revise the matrix again 1, 2, 345, 6 1, 2, ,

Revise the matrix again 1, 2, 345, 6 1, 2, ,

Revise the matrix again 1, 2, 345, 6 1, 2, ,

Revise the matrix again 1, 2, 345, 6 1, 2, ,

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

All that’s left is 4 4 Flying lemur Flying fox Roundleaf bat Little brown bat Mouse lemur 5 Tree shrew

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