Phylogeny
Introduction
Phylogeny is the study of how organisms have diverged - and what key characteristics have been conserved - throughout evolutionary time. Phylogenetic trees are a way of visualizing these relationships, and can identify speciation events and shared most recent common ancestors [2]. These trees are generated using algorithms like maximum-likelihood and neighbor joining, and assessed using statistical methods like bootstrapping [1].
Phylogenetic software first aligns the protein (or nucleotide) sequences of interest - in this lab, ClustalW was used. Then, using the aligned sequences, the software (in this lab, MEGA-X) runs multiple trials to generate hundreds of possible trees. Then, a consensus (or "best" tree) is selected based on the algorithm selected. Bootstrapping confidence intervals are then calculated based on what percentage of the randomly generated trees contained that grouping [3].
Phylogenetic software first aligns the protein (or nucleotide) sequences of interest - in this lab, ClustalW was used. Then, using the aligned sequences, the software (in this lab, MEGA-X) runs multiple trials to generate hundreds of possible trees. Then, a consensus (or "best" tree) is selected based on the algorithm selected. Bootstrapping confidence intervals are then calculated based on what percentage of the randomly generated trees contained that grouping [3].
Results
Discussion
Based on these results, it appears the mouse and rat sequences have diverged most recently from the human ROBO3 sequence. This is visually represented by the similarity in sequence and function between the protein domains of these two homologs as well. It is interesting that C. elegans and Drosophila appear to be an outgroup set apart from the rest of the sequences. I also find it interesting that the model frog shares a more recent common ancestor with the coelacanth than does the zebrafish. I would like to run more algorithms to see how the trees compare.
References
- Baldauf, Sandra L. "Phylogeny For The Faint Of Heart: A Tutorial". Trends In Genetics, vol 19, no. 6, 2003, pp. 345-351. Elsevier BV, doi:10.1016/s0168-9525(03)00112-4. Accessed 20 Mar 2020.
- Baum, D. (2008) Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups. Nature Education 1(1):190
- "MEGAX-Help". Megasoftware.Net, 2020, https://www.megasoftware.net/web_help_10/index.htm#t=First_Time_User.htm.