This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Protein Phylogeny
Homologs of the parkin protein exist in numerous types of organisms. The file below lists the amino acid sequences of parkin from different species:
| parkin_protein_sequences.doc |
Using the 3D Coffee alignment, TNT phylogeny, and TreeDyn tree rendering, the following phylogenetic tree was established (Figure 1) using the protein sequences of the different homologs of parkin. The advantage of this tree is that it has parsimony; that is, the phylogeny was constructed using the fewest evolutionary events possible, which lends credibilty to its likelihood. The disadvantage of this tree is that it does not contain any branch support values.
Figure 1: The phylogenetic relationship of homologs of the parkin protein, using 3D coffee alignment and TNT phylogeny (1).
Using 3D Coffee alignment, PhyML phylogeny,and TreeDyn tree rendering, the following phylogenetic tree was established (Figure 2) along with corresponding branch support values. As seen with the DNA sequence phylogenies, the monophyletic groups between the two trees are grouped into vertebrates and invertebrates. Because the monophyletic groups of the tree below more closely follow the DNA homolog alignments, my preference is to use this tree:
Figure 2: The phylogenetic relationship of homologs of the parkin protein, using 3D coffee alignment and PhyML phylogeny (1).
References
1. Phylogeny.fr. http://www.phylogeny.fr/
