AERIAL ANCESTORS?
Page 3: Reliability of Molecular Phylogenies

CASE STUDY IN MOLECULAR EVOLUTION NO. 2
Written by Harold B. White, Sept 1995, revised February 2013
C-667 BIOCHEMICAL EVOLUTION, SPRING 2013

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?

Assignment Part 1: Constructing a Protein Phylogeny.

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, but one that has been sequenced from each of the taxa selected by the group and one that has a known three dimensional structure. Then 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 many organisms are now known.

Assignment Part 2: Protein Structure, Function, and Evolution

Phylogenetic trees for proteins are based on linear sequences that are compared and scored for their similarity. While this may show how orthologous proteins in different species are related, they tell little if anything about the evolutionary importance of the amino acid substitutions that have occurred in different lineages.  A protein’s function depends on its folded three-dimensional structure. Ideally, one would like to see how changes in the primary structure map onto the three-dimensional structure. By comparing many aligned sequences, the degree to which each residue in the sequence is conserved can be scored and represented by a color on a three-dimensional structure (20, 21, 22). Part 2 of your assignment is to take your protein and create an image (or images) displaying the degree to which amino acids are conserved in its structure. A web-server to do this is available.

Assignment due Friday, 8 March:

Take your results from Parts 1 & 2 and write a report on the phylogeny and evolution of your protein. Include phylogenetic diagrams and a three dimensional image of your selected protein. Discuss its rate of evolution, utility as a proxy for species relationships, and whether or not the pattern of amino acid replacements reveals anything about function or the process of molecular evolution.

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.

20. Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor-Shental, D., Martz, E., and Ben-Tal. N. (2003) Proteins by Surface-Mapping of Phylogenetic Information. Bioinformatics 19(1), 163–164

<>21. Berezin, C., Glaser, F., Rosenberg, J., Paz, I., Pupko, T., Fariselli, P., Casadio, R., and Ben-Tal, N. (2004) ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20(8), 1322–1324 DOI: 10.1093/bioinformatics/bth070<>
22. Doron-Faigenboim, A., Stern, A., Mayrose, I., Bacharach, E.,
and Pupko, T. (2005) Selecton: a server for detecting evolutionary forces at a single amino-acid site Bioinformatics 21 (9),2101–2103 doi:10.1093/bioinformatics/bti259

Return to:    Page 1: Blood Brothers
              Page 2: Using Hemoglobin to Track Blood Lines



Return to Department's Home Page, CHEM-667 Home Page, or Hal White's Home Page,
Created 17 July 2000. Last updated 27 february 2013 by Hal White
Copyright 2013, Harold B. White, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716