Practice set 2, question #1 1 G T C T T T C G T C A G G - T G G A C G T C C C C A G C C C A G 2 G T C T C G A G C C A G T C T G G G T G T T C T C A G C C C A G 3 G T C T T T G A - C A A G A T G A T G A T C C T T A G C C C A G 4 G T C T C G T A A C A G T C T G G G - G T T C T C A G C C C A G

1 2 3

2

3

4

10

11 14

11 4 13

2 4

22

5.25

6.33.25

1.05

Gap scored as difference

1 3

1

3

2

4

Favoured maximum parsimony tree:

UPGMA tree

H C/PC G O Gi

22

2.53.65

5.25

0.5

1.15

1.35

Question #2

Score as difference if restriction site is not at exactly same position or if different symbol at same position

H C/PC G O

C/PC

G

O

Gi

4

5 5

9 5 8

11 9 10 12

Bargelloni PNAS 95:8670, 1998

“Are red blood cells really necessary? ... a fish species that lives without them”

www.icefish.neu.edu/ photo/

Do the 2 trees show the same topology?

Species tree Gene tree

globin

Implications of differences in branch lengths on gene tree?

Long branches = rapid evolution

low confidence in topology?(eg. if no bootstrap values given)

unscaled vs. scaledtree

short internode distances?

Due to reduced functional constraint? or maybe evolving new function (adaptive evolution)? KA vs. KS values?

Question #3

Note: paralogous copies may have been lost from certain lineages during evolution or data sets may be incomplete for some organisms (This study was done before complete genome sequences were available)

When did IL-1 gene duplication events occur?

Does the gene tree show the same topology as the species tree?

Some points for consideration:

Question #4

- possible reasons for any discrepancies?

Question #5

Is the presence of only one EF gene an ancestral trait or derived trait?

Would you use a highly-conserved gene.. or rapidly-evolving one... or both in your analysis? Why?

Note: EF gene is not a good choice because it may have been subject to atypical constraints because only one copy in your microbe