Final Project Bioinformatics for Biologists

Alternative A Alternative B

Undergraduates (Alternative A) Assigned project Undergraduates (Alternative B) Self designed project agreed upon in advance. Must obtain permission from Dr. Dan Graur Graduate Students (Alternative A) Assigned project Graduate Students (Alternative B) Self designed project agreed upon in advance. MUST NOT HAVE ANYTHING TO DO WITH THE THESIS Must obtain permission from Dr. Dan Graur

Phylogenetic reconstructions by using mitochondrial protein sequences (I) The objective is to use the tools of bioinformatics to study evolutionary relationships among taxa. Each student will have an individual assignment. The first part will consist of a very short summary of the current taxonomic knowledge pertaining to the ingroup taxa in the assignment. This summary will be presented in class and the PowerPoint file will be submitted for grading.

Phylogenetic reconstructions by using mitochondrial protein sequences (II) In the second part, each student will perform a comprehensive study and submit a written report in the form of a scientific paper.

In the short oral presentation, the student will: 1. Describe the taxa in the assignment. 2. Outline the current phylogenetic views pertaining to the taxa in the assignment. 3. Describe the methods that have been used in these studies. 4. Present open questions (if any).

Materials and Methods: Collect all protein sequences encoded by the mitochondria in the ingroup. By using one ingroup sequence, identify one or more outgroup species. Align sequences. Construct NJ and MP trees. Bootstrap the trees. Estimate branch lengths. Identify groups of congruent trees.

Based on your work: 1. Does your analysis solve the phylogenetic assignment? 2. Are there contradicting trees? If so, what is the reason for the incongruence? 3. Does your study agree with previous studies? Why (or Why not)? 4. Are there large differences in the rate of evolution among lineages? Why?

Submit your study as a scientific paper: Abstract: Summarize briefly objectives, hypotheses, data, methods, results, and conclusions. Introduction: State purpose, review literature, list phylogenetic hypothesis to be tested. Materials and Methods: Provide details of sequences and methods, present succinct description of data collection, provide sufficient detail to allow precise replication of the study. Results: Summarize data in tabular or graphic form, present data without interpretation, describe important aspects of data. Discussion: Provide interpretation of results with regard to hypotheses, compare results with previous studies, address limitations and sources of errors, summarize major conclusions. Bibliography: List at least 3 literature sources.

Bonus points: Two questions related to genomics, 2D, 3D, codon usage, etc.

Example Crustacea MaxillopodaPentastomida Brachipoda Malacostraca CephalocardiaRemipedia Ostracoda Identify the phylogenetic relationships within Crustacea. Your study should include: 1 species belonging to the Maxillopoda, 1 species belonging to the Pentastomida, 1 species belonging to the Brachipoda, 1 species belonging to the Malacostraca, 1 species belonging to the Cephalocardia, 1 species belonging to the Remipedia, 1 species belonging to the Ostracoda + the closest outgroup to all these taxa that you can find.