This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Summary of Phylogenies
Using www.phylogeny.fr was mostly painless to align the sequences. Also, using it to make the trees took a little bit of learning on my part, but the not much. It was mostly intuitive. I would prefer a little more explanation of the statistical analysis on the website. However, with not much effort one can find such information. The following phylogenies were generated using the above website.
The first phylogeny, figure 1, seems to fit most with other evolutionary studies excepting Pan troglodytes (chimpanzee). Most likely, the major gaps seen in the sequence for the androgen receptor (AR) are causing the chimpanzee receptor to be an outlier.
It is unlikely that much divergence occurred between humans and chimpanzees within ar. This protein regulates sexual dimorphism and should have highly conserved domains such as the DNA binding site. Mus musculus (mouse) and Rattus norveicus (rat) are more related based on this phylogeny, which is exactly what would be expected as they are very closely related organisms.
The other phylogenies, figures 2 and 3, have many of the same features as the first. However, both place the chimpanzee in odd locations. Figure 2 places the chimpanzee more recently with Danio rerio (zebra fish), which seems unlikely considering the other mammals included. Figure 3 places the chimpanzee with Gallus gallus (chicken). This assessment also seems to be incorrect. However, the other arrnagements are mostly expected. Figure 3 places humans in odd place though. The mammals should be closer together with the us.
Figure 1: Generated with PhyML from alignments with t-coffee.
Figure 2: Generated with BioNJ from alignments with t-coffee
Figure 3: Generated with TNT from alignments with t-coffee
Figure 4: Alignment information using T-Coffee.
| alignment_with_t-coffee.pdf | |
| File Size: | 117 kb |
| File Type: | |
Phylogenies for nhr-69 with AR
I was curious how closely related nhr-69, the homolog of AR in C. elegans, is to AR in the above species. I aligned the sequences using t-coffee. I then used the same method as above to make the phylogenic trees. These trees mostly confirm what I would think based on the identity with AR in the species. Around 25% of the seqeunce is identical between nhr-69 and AR in all species. With humans, the identifiy is 26%. This finding suggests that though functionally nhr-69 is similar to AR, it should not be used to study AIS.
The C. elegan gene should not be more closely related to cattle AR in the second phylogeny nor in its relationship to the other species in the third. This erroneous placement is the result of gaps between the sequences. nhr-69 is a much smaller protein than AR in the other species. Therefore, the programs are having trouble placing in the same way as with AR in chimpanzees
Figure 5: Generated with PhyML from alignments with t-coffee
Figure 6: Generated with BioNJ from alignments with t-coffee
Figure 7: Generated with TNT from alignments with t-coffee
| alignment_for_nhr-69.doc | |
| File Size: | 72 kb |
| File Type: | doc |
References
1. All figures taken from: http://www.phylogeny.fr/
Website authored by Sam Trammell. Email: [email protected]. Last updated: May 9, 2009.
