Molecular Evolution - Mini Project #1

An important aim of the mini projects is to place the competences you learn on this course in the context of a full bioinformatics/systems biology work flow, and at the same time to get you to think about how to solve practical bioinformatics type problems. The idea is that you should use everything you've learned so far (also on other courses!) so you will only get minimal instructions. If you get stuck, then check previous exercises and reading material (also from other courses!).

Report:The results of your mini project should be put in a brief report that you hand in at CampusNet. Make sure that your report includes everyting requested below.

Part 1: Tree Thinking Quizz

Take this tree quizz to check you understanding of evolutionary trees. Put the answers in the start of your report: Tree Quiz

Part 2: Building a tree from scratch: What are the closest relatives of whales?

How did whales evolve? What taxonomic groups are closely related to whales? What is the closest (non-whale) relative of whales that you can find? Follow the guidelines below and use everything you know about phylogenetic reconstruction (and bioinformatics, and molecular biology) to answer these questions. Have fun!

1. Using database searching, construct a data set consisting of about 25-30 homologous DNA sequences. The set should include 1-3 whale sequences. Make sure to cover a wide range of taxonomic groups (fish, amphibia, insects, birds, mammals), but put a special emphasis on having many different subgroups of mammals. Important: Make sure to include an outgroup in the data set. The outgroup can be a single sequence (or more if you prefer). Save as Fasta file. Include the data set at the end of your report and describe how you constructed it. Also include arguments for your choice of outgroup.

2. Align using three different alignment methods (make sure to mention what methods you have used in the report). Prepare each of the three alignments for use in PAUP. Also include the alignments at the end of your report (e.g., in fasta or clustal format).

3. Construct a rooted phylogenetic tree from each of the three alignments using tree-rearrangements of the following two types:

   • NNI
   • SPR

   Include the commands you used, as well as plots of all 6 trees, in your report. Also briefly explain:

   • The purpose of tree-rearrangement
   • The difference between NNI and SPR

4. Check whether the 6 reconstructed trees differ. Quantify HOW different the trees are using the treedist command (find each pairwise distance). Again make sure to include the commands used in your report. Briefly discuss alignment uncertainty and the impact of the type of tree-rearrangement move.

5. Answer the questions you set out to analyze: How did whales evolve? What taxonomic groups are closely related to whales? What is the closest (non-whale) relative of whales that you can find?

6. Hand in at CampusNet ("Assignments" -> "Mini project #1").