Rui Borges

Assignment 4

Testing the molecular clock hypothesis

In this assignment, you will be determining whether your sequences follow the molecular clock hypothesis. For that we will be using protein sequences, so the first thing you have to do is transalating your DNA sequences into aminoacids. For these assignmente 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. Use amino acid sequences for this task, and do not forget to use an appropriate empirical amino acid model. By an appropriate model, I am not asking you to perform a hierarchical LRT. All I need is a biological justification for the chosen amino acid model.

2. Test the molecular clock hypothesis for your sequences. Unrooted and rooted trees can also be obtained in Seaview: go to File and then Save unrooted tree or Save rooted tree. Please provide a table including the model likelihoods, number of parameters, degrees of freedom, the resulting LRT values, and critical value that you used to assess statistical significance. Perform the LRT using a significance level of 0.05.

3. Represent the estimated tree under the clock and no clock models in your answer. Use appropriate tree representations and identify them clearly.

4. Using the ultrametric tree obtained under the global clock hypothesis, determine the amino acid substitution rate per million years and the age of the great apes emergence. Use a calibration point at 6.4 mya for the human-chimp node; or 8.6 mya for the human-gorilla node if your alignment lacks chimp.

5. Considering the results of the LRT test, can this marker (i.e., your gene sequences) be used to date the primate tree? Justify your answer.

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).