This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009.
Profile Homology Phylogeny Motifs
Phylogenetic Analysis
By using Treefam the entire known phylogenetic tree for SRD5A2, can be viewed alongside a corresponding alignment (7). There are some interesting things about the Treefam results though. First, it shows the chimpanzee as being the closest related to the human, which makes sense of what we now know from evolution. It also shows the split in evolutionary history that lead to the homologous isoforms of this gene. Also the splitting off at the top of the tree shows the homologous structures in Arabidopsis. The wide conservation between organism of this family of genes indicates its importance in evolutionary functions.
Also on the tree is the other isozyme, SRD5A1. Genetic sequencing has shown that both forms are composed of 5 exons and 4 introns. Although the sequences are not very identical, the fact that they have similar structures but are on different chromosomes suggests an ancestral gene duplication (1).
A much simpler tree using only the model organisms I chose, was made using Phlogeny.fr(2-6). The Treefam analysis is much more complete and is very useful with the sequence alignments alongside the tree. There are also some differences in the branch points. Without many other sequences to compare, the lower tree is probably the most parsimonious. As more and more sequences are added however, the best relationships may be slightly different.
References
1. Russell, D. W., and Wilson, J.D. 1994. Steroid 5alpha-Reductase:Two genes/Two Enzymes. Annu. Rev. Biochem. 63:25-61, doi:10.1146/annurev.bi.63.070194.000325
2. Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
3. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, Mar 19;32(5):1792-7. (PubMed)
4. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, Apr;17(4):540-52. (PubMed)
5. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, Oct;52(5):696-704. (PubMed)
6. Anisimova M., Gascuel O. Approximate likelihood ratio test for branchs: A fast, accurate and powerful alternative. Syst Biol. 2006, Aug;55(4):539-52. (PubMed)
7. Li, et al. 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. Jan 1; 34(database issue):D572-80.
