Proteins and DNA sequences provide rich sources of phylogenetic information. Although the rate at which orthologous proteins evolve in divergent lineages is more or less constant, the process is not metronomic and selection can alter the rates of evolution significantly. Such rate changes create dilemmas such as you have discovered in deciding whether an ancestor of humans could fly.  How big a problem is this?

Within your group, select four species (each representing different taxa at the Order level or above) for which there are many protein or gene sequences known. Each group should pick a different set of four organisms. Then each person should pick a different protein or gene, but one that has been sequenced from each of the taxa selected by the group, and construct a phylogeny based on the four sequences. Thus one person might be investigating lactate dehydrogenase sequences from human, chicken, alligator, and a fish while another group member in that group might be analyzing cytochrome c from the same set of species. Please help each other locate sequences, run the BLAST program (available through the National Center for Biotechnology Information, NCBI, at <http://www.ncbi.nlm.nih.gov/BLAST/>), construct phylogenies, and discuss what you find in your group. If you have trouble selecting a protein or gene, Doolittle (19) provides a list of 57 enzymes that have been sequenced from a variety of organisms. Also remember that the genomes for more than 120 organisms are now known.

Assignment due on Friday 4 October:

Take each of the phylogenies generated by your group and compare them.  Discuss your protein or gene and its phylogeny with respect to the others from your group.  Did your protein generate the same phylogeny as the others?  Were the branch lengths similar or different? Is its rate of evolution faster or slower than that for the other proteins?  How might various factors influence the differences and similarities you observe?  Make some assessment of the reliability of protein or gene sequences in deducing the phylogeny of organisms based on your group's analysis.  Aside from the topology of your phylogenetic tree, can you identify any interesting structural changes in the evolution of the molecule you selected?  If you were to construct a phylogeny for another set of organisms, what factors would you consider in selecting proteins or genes to use?  Reports should be about three pages of text with attached diagrams and references.

19. Doolittle, R. F., Feng, D-F., Tsang, S., Cho, G. and Little, E. (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470 - 477.

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