Assignment Task:
INSTRUCTIONS
The goal of this project is to plan and perform a bioinformatics investigation of the evolutionary relations among a set of species of your choice (see instructions below). You will make use of online databases, GenBank, Taxonomy Browser, BLAST, and PubMed (to access biological publications relevant to your question). They are all accessible via the same NCBI website. You will generate a report (max. 10 pages – recommended target length: 8 pages) while answering the questions. General Writing Advice: Also please add this: title / abstract / introduction stating the question you are addressing about the evolutionary history of a species. This should contain also a short summary of the data used, and of the main results / conclusions. You can use the same organism that you chose to study in earlier assignments of this course. (e.g.: Are dogs closer to foxes or wolves? What is the closest species to a bat? Did webbed feed evolve multiple times in birds? Are saber tooth tigers closest to cats or hyenas? What is the evolutionary relation between all sea mammals? etc.). The methods should be mentioned, but not explained at length, if they were part of the course already. Describe in detail any method that is not part of the course, if you use it. One of the key outcomes of the study will be various phylogenetic trees. These will be created by using 2 specific proteins in mtDNA (cytochrome B and C, see below for more). One of the questions requires also the use of a complete mtDNA sequence (see below for more). Remember to root your trees. You are expected to find at least one existing article in PubMed that relates to your data and/or question, (or that answers a similar question with different data) and compare at least some aspect of your project with the article. It is important that you use this to assess your results, and discuss your findings. References should always be complete and accurate. Also add a very short Conclusion at the end attempting to answer the opening question. It is OK if no stable answer is found, or if it is in conflict with some existing paper. What matters is that you ask a clear question to the data, in the right way, perform a scientific study, and draw sensible conclusions. It is OK if you replicate the investigations found in some existing paper, as long as you do your own computations on your own data, and refer to the paper. There are many papers in PubMed using similar methods to those we studied, to address fun evolutionary questions. Your project will have your chosen question as the framework and title, and will address all the tasks listed below, as part of the data analysis. Read online about CYTB and CYTC proteins in mitochondria (mitochondrially encoded cytochrome b and mitochondrially encoded cytochrome c). Pay attention to various aliases for their names, and note that the second one is formed by 3 different units. Choice of the Species to Investigate Task 1 involves using the complete mtDNA sequence of an organism. All remaining tasks only require the use of 2 mitochondrial proteins (CYTB and another, for example, CYTC). These 2 proteins have been sequenced for most organisms, and are available on Genbank, whereas it is less common for full mtDNA to be available. So, you can either make sure that you choose a species to investigate for which the full mtDNA is available, or you just focus on retrieving and analyzing the individual protein-coding sequences. In this case, you will need to answer Task 1 by using a related organism for which the full mtDNA is available. (Obviously: make sure that you work with a species that has a mitochondrion (so avoid bacteria, viruses, etc.) and avoid plants, unless you really want to work harder. Animals are a good type of organisms for this.) State a simple question relating to the evolutionary history of a group of species (see examples above or on accompanying slides). This should be a question that is answered by creating a phylogenetic tree, or a multiple alignment. A typical question would be: “Which species is closest to X?” or “What are the evolutionary relations among the species of group Y?”. Note that Genbank entries for sequences often point to PubMed entries for corresponding papers, and vice versa. Similarly Taxbrowser points from species to genomic sequences. This will help you. Please see the accompanying slides for help on obtaining sequences, papers etc. from the GenBank website. As you write, please keep in mind that you should always cite sources, DB numbers, formal species names, and state a clear biological question you are trying to address. Please make sure to include command lines from matlab, so I can see which settings you have used for the key commands.
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