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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