Phylogenetic inference using molecular sequence data
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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.

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Phylogenetic inference using molecular sequence data

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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


Distance matrix


2 & 3 are sister

Roundleaf

bat

2

Little brown

bat

3


Revised matrix


Revised matrix


Revised matrix


Revised matrix


Revised matrix


Revised matrix


Revised matrix


1 is sister to 2 & 3

Roundleaf

bat

2

Little brown

bat

3

1

Flying fox


Revise the matrix again


Revise the matrix again


Revise the matrix again


Revise the matrix again


Revise the matrix again


Revise the matrix again


Revise the matrix again


5 is sister to 6

Roundleaf

bat

2

Little brown

bat

3

1

Flying fox

Mouse

lemur

6

5

Tree

shrew


Revise the matrix again


Revise the matrix again


Revise the matrix again


Revise the matrix again


Revise the matrix again


5 & 6 are sister to 1, 2, & 3

Roundleaf

bat

2

Little brown

bat

3

1

Flying fox

Mouse

lemur

6

5

Tree

shrew


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


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


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