This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison
What is phylogenetics?
Phylogenetics is the study of evolutionary relationships among biological entities. Phylogenetics helps us understand how species and genes evolve. Evolutionary relationships can be represented by a phylogenetic tree. On the tree, each branch represents an individual species or gene. The node connecting branches represents the most recent common ancestors the species shared before diverging. [1]
Figure 1: A phylogenetic tree diagram
Types of Phylogenetic Trees [2]
Neighbor Joining:Uses similarity scores from percent identity to determine which species are most closely related to each other. Branch length is calculated from these scores. Maximum Likelihood: This method builds a tree using another method and then adjust branch lengths based on maximum likelihood. Average Distance: Uses similarity scores between species to determine which species are most closely related and uses equal branch length from a common ancestor.
MSH6 Phylogenetic Tree Construction
1. Protein sequences of homologs to MSH6 from various organisms are found utilizing Ensemble. The sequences are annotated in a FASTA format.
The evolutionary relationships between the MSH6 protein homologs are shown through the construction of a phylogenetic tree. BLAST contained the percent similarity between these homologs, and the phylogenetic tree confirms the strength of these relationships. For example, humans and mice have a high similarity between their MSH6 proteins, and they are the most closely related, while yeast has a much lower similarity and is less closely related. The different methods of phylogenetic tree construction yielded the same resulting tree suggesting a high confidence in these evolutionary relationships between these MSH6 protein homologs.