This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison.
What is phylogeny?
Phylogeny is the study of the evolutionary relationships between different organisms based on genetic or molecular sequencing. By understanding how similar two organisms are, one can usually learn more about unknown functions in proteins based on knowledge of another similar species. There are two main methods to determine how similar two species are:
Neighbor Joining % Identity - this method takes the scores found by percent identity (as shown in the Homology page) or BLOSSUM and uses them to determine which species are most similar. It forms a tree which is calculated based on the amount of change that occurred after the two species diverged. The difference between this and the average distance % identity, the branches are all different lengths.
Average distance % Identity - this method uses the scores to determine which species are most closely related and joins them with equal branch lengths with the assumption that both species have diverged equally from a common ancestor.
Neighbor Joining % Identity - this method takes the scores found by percent identity (as shown in the Homology page) or BLOSSUM and uses them to determine which species are most similar. It forms a tree which is calculated based on the amount of change that occurred after the two species diverged. The difference between this and the average distance % identity, the branches are all different lengths.
Average distance % Identity - this method uses the scores to determine which species are most closely related and joins them with equal branch lengths with the assumption that both species have diverged equally from a common ancestor.
What does the phylogeny tree of the gene product of COL5A1 look like?
Fig 1. Phylogenic tree based on Average Distance % Identity. This tree was created in Clustal Omega.
Analysis
From the trees, it is clear the Gorilla is contains a COL5A1 gene product most similar to humans. For experiments focusing on muscle ligaments, mice would be the best model organism to use due to their size and speed at which they grow. To test the relation between the rs12722 variant and speed, comparing speed among fast and slow organisms with both types of genes could be beneficial.
Website Author: Logan Silber
Contact email: [email protected]
Page last updated: 4/22/2015
Course Homepage: www.genetics564.weebly.com
Contact email: [email protected]
Page last updated: 4/22/2015
Course Homepage: www.genetics564.weebly.com