Rui Borges

Assignment 3

Detecting positive selection

In this assignment, you will determine whether your sequences evolve under positive selection by employing an LRT test between the M7 and M8 models. Please note that analyses will not run if stop codons are present in your multiple sequence alignment. Make sure to delete them before running codeml. For these assignment you should use the Bayesian phylogenetic tree obtained in the assignment 2. You can delete the branch lengths by opening this tree in Seaview and saving it as a cladogram.

1. Determine the average omega under the M7 and M8 models. Briefly explain how did you obtain such values. Also, indicate the proportion of positively selected sites and the corresponding omega value for such category of sites. Which model did you use to assess such parameters?

2. Are your sequences evolving under positive selection at a level of 0.05? Instead of comparing the critical value with the LRT, assess significance using a p-value. Please provide a table including the model likelihoods, number of parameters, degrees of freedom and the resulting LRT value.

3. Search your gene’s function (or functions) on public databases and the scientific literature. Please, indicate your sources in your answer. Based on the best fitting model obtained in the previous question and the function of your gene, suggest a possible biological explanation why your gene is evolving under negative or positive selection. Justify your answer adequately.

Some notes:

• Partial grading will be given to answers that, despite being incorrect, show a good understanding of phylogenetic concepts and technical procedures. Thus, do not forget to justify all your answers and show the steps leading you to the final solution.
• Do not submit any output files that you will obtain by running the required software. Instead, validate your answers by summarizing the information contained in these files in the form of tables or plots. Translating complex information into sentences, tables, or plots is an important skill that will be evaluated in your answers.
• Every assignment should be appropriately identified using the following name: RB_AssignmentNumber_YourStudentNumber. Upload each assignment as an independent PDF file into my vetcloud (link sent by email).