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

1 2 3 4 5 6

1 -

2 52 -

3 53 44 -

4 84 70 79 -

5 78 61 62 76 -

6 77 70 68 73 66 -

Distance matrix

1 2 3 4 5 6

1 -

2 52 -

3 53 44 -

4 84 70 79 -

5 78 61 62 76 -

6 77 70 68 73 66 -

2 & 3 are sister

2

3

Roundleafbat

Little brownbat

Revised matrix

1 2 3 4 5 6

1 -

2 52 -

3 53 44 -

4 84 70 79 -

5 78 61 62 76 -

6 77 70 68 73 66 -

Revised matrix

1 2 3 4 5 6

1 -

2

352.5

-

44 -

4 84 70 79 -

5 78 61 62 76 -

6 77 70 68 73 66 -

Revised matrix

1 2 3 4 5 6

1 -

2

352.5 -

4 84 70 79 -

5 78 61 62 76 -

6 77 70 68 73 66 -

Revised matrix

1 2 3 4 5 6

1 -

2

352.5 -

4 84 74.5 -

5 78 61 62 76 -

6 77 70 68 73 66 -

Revised matrix

1 2 3 4 5 6

1 -

2

352.5 -

4 84 74.5 -

5 78 61.5 76 -

6 77 70 68 73 66 -

Revised matrix

1 2 3 4 5 6

1 -

2

352.5 -

4 84 74.5 -

5 78 61.5 76 -

6 77 69 73 66 -

Revised matrix

1 2 3 4 5 6

1 -

2

352.5 -

4 84 74.5 -

5 78 61.5 76 -

6 77 69 73 66 -

1 is sister to 2 & 3

2

3

1 Flying fox

Roundleafbat

Little brownbat

Revise the matrix again

1 2, 3 4 5 6

1 -

2, 3 52.5 -

4 84 74.5 -

5 78 61.5 76 -

6 77 69 73 66 -

Revise the matrix again

1, 2, 3 4 5 6

1, 2, 3-

52.5 -

4 84 74.5 -

5 78 61.5 76 -

6 77 69 73 66 -

Revise the matrix again

1, 2, 3 4 5 6

1, 2, 3 -

4 84 74.5 -

5 78 61.5 76 -

6 77 69 73 66 -

Revise the matrix again

1, 2, 3 4 5 6

1, 2, 3 -

4 79.25 -

5 78 61.5 76 -

6 77 69 73 66 -

Revise the matrix again

1, 2, 3 4 5 6

1, 2, 3 -

4 79.25 -

5 69.75 76 -

6 77 69 73 66 -

Revise the matrix again

1, 2, 3 4 5 6

1, 2, 3 -

4 79.25 -

5 69.75 76 -

6 73 73 66 -

Revise the matrix again

1, 2, 3 4 5 6

1, 2, 3 -

4 79.25 -

5 69.75 76 -

6 73 73 66 -

5 is sister to 6

2

3

1

6

Flying fox

Roundleafbat

Little brownbat

Mouselemur

5 Treeshrew

Revise the matrix again

1, 2, 3 4 5, 6

1, 2, 3 -

4 79.25 -

5

6

69.75 76 -

73 73 66 -

Revise the matrix again

1, 2, 3 4 5, 6

1, 2, 3 -

4 79.25 -

5, 6 71.325 76 -

73 66 -

Revise the matrix again

1, 2, 3 4 5, 6

1, 2, 3 -

4 79.25 -

5, 6 71.325 74.5 -

66 -

Revise the matrix again

1, 2, 3 4 5, 6

1, 2, 3 -

4 79.25 -

5, 6 71.325 74.5 -

Revise the matrix again

1, 2, 3 4 5, 6

1, 2, 3 -

4 79.25 -

5, 6 71.325 74.5 -

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

2

3

1

6

Flying fox

Roundleafbat

Little brownbat

Mouselemur

5 Treeshrew

All that’s left is 4

4 Flyinglemur

2

3

1

6

Flying fox

Roundleafbat

Little brownbat

Mouselemur

5 Treeshrew

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