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 molecular sequence data

Phylogenetic inference using molecularsequence data

Matt Herron

University of Arizona

Department of Ecology and Evolutionary Biology


Example bats

Example: bats

  • Megachiroptera (flying foxes)


Example bats1

Example: bats

  • Megachiroptera (flying foxes)

  • Microchiroptera (all others)


Example bats2

Example: bats

  • Megachiroptera (flying foxes)

  • Microchiroptera (all others)

  • Monophyly disputed


Example bats3

Example: bats

  • Megachiroptera (flying foxes)

  • Microchiroptera (all others)

  • Monophyly disputed

  • Close relatives:

    • Flying lemurs (colugos)?


Example bats4

Example: bats

  • Megachiroptera (flying foxes)

  • Microchiroptera (all others)

  • Monophyly disputed

  • Close relatives:

    • Flying lemurs (colugos)?

    • Primates?


Example bats5

Example: bats

  • Megachiroptera (flying foxes)

  • Microchiroptera (all others)

  • Monophyly disputed

  • Close relatives:

    • Flying lemurs (colugos)?

    • Primates?

    • Tree shrews?


What to do

What to do?

  • Download amino acid sequences from GenBank (NCBI)

  • Build a phylogenetic tree by neighbor-joining


Distance matrix

Distance matrix


Distance matrix1

Distance matrix


2 3 are sister

2 & 3 are sister

Roundleaf

bat

2

Little brown

bat

3


Revised matrix

Revised matrix


Revised matrix1

Revised matrix


Revised matrix2

Revised matrix


Revised matrix3

Revised matrix


Revised matrix4

Revised matrix


Revised matrix5

Revised matrix


Revised matrix6

Revised matrix


1 is sister to 2 3

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 again1

Revise the matrix again


Revise the matrix again2

Revise the matrix again


Revise the matrix again3

Revise the matrix again


Revise the matrix again4

Revise the matrix again


Revise the matrix again5

Revise the matrix again


Revise the matrix again6

Revise the matrix again


5 is sister to 6

5 is sister to 6

Roundleaf

bat

2

Little brown

bat

3

1

Flying fox

Mouse

lemur

6

5

Tree

shrew


Revise the matrix again7

Revise the matrix again


Revise the matrix again8

Revise the matrix again


Revise the matrix again9

Revise the matrix again


Revise the matrix again10

Revise the matrix again


Revise the matrix again11

Revise the matrix again


5 6 are sister to 1 2 3

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

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

Cape ground squirrel

  • Savannahs of southern Africa

  • Social

  • 1 premolar above and below

  • 2 pairs of mammae

  • 38 chromosomes


Mountain ground squirrel

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

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

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

Least chipmunk

  • Western United States, much of Canada

  • Solitary

  • 2 premolars above, 1 below

  • 4 pairs of mammae

  • 38 chromosomes


Black tailed prairie dog

Black-tailed prairie dog

  • Central United States

  • Social

  • 2 premolars above, 1 below

  • 4 pairs of mammae

  • 50 chromosomes


Woodchuck groundhog

Woodchuck / groundhog

  • Eastern United States, much of Canada

  • Solitary

  • 2 premolars above, 1 below

  • 4 pairs of mammae

  • 38 chromosomes


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