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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

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




2 3 are sister
2 & 3 are sister

Roundleaf

bat

2

Little brown

bat

3









1 is sister to 2 3
1 is sister to 2 & 3

Roundleaf

bat

2

Little brown

bat

3

1

Flying fox









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







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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