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Practice set 2, question #1

1. 2. 4. 3. Practice set 2, question #1. 1 2 3. 2 4. 1. 3. 2. 2 3 4. 10 11 14 11 4 13. 2. 5.25. 3.25. 6.3. 1.05. UPGMA tree. Gap scored as difference. Favoured maximum parsimony tree:. Question #2.

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Practice set 2, question #1

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  1. 1 2 4 3 Practice set 2, question #1 1 2 3 2 4 1 3 2 2 3 4 • 10 • 11 14 • 11 4 13 2 5.25 3.25 6.3 1.05 UPGMA tree Gap scored as difference Favoured maximum parsimony tree:

  2. 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 H C/PC G O Gi C/PC G O Gi 2 • 4 • 5 5 • 9 5 8 • 11 9 10 12 2 2.5 3.65 0.5 5.25 1.15 1.35

  3. Question #3 www.icefish.neu.edu/ photo/ “Are red blood cells really necessary? ... a fish species that lives without them” Gene tree Species tree b globin unscaled vs. scaled tree Long branches = rapid evolution Due to reduced functional constraint? or maybe evolving new function (adaptive evolution)? Do the 2 trees show the same topology? KA vs. KS values? Implications of differences in branch lengths on gene tree? low confidence in topology? (eg. if no bootstrap values given) short internode distances? Bargelloni PNAS 95:8670, 1998

  4. Question #4 Some points for consideration: Does the gene tree show the same topology as the species tree? - possible reasons for any discrepancies? When did IL-1 gene duplication events occur? 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) 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

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