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Week 4 - Phylogenies and presentations

After having identified an abundance of coxL in the Warren cave metagenome last week, I spent the first half of this week building a phylogenetic tree in order to learn more about the evolutionary radiation of the coxL gene and the relatedness of the cave samples to cultured and uncultured microbial species. In order to begin the tree-building process, I first had to align the contiguous sequences from the metagenome with the coxL IMG database and translate the nucleotide sequences to amino acids. Once the sequences were aligned and translated, I used RAxML ( to build the phylogenetic tree and MEGA ( to edit to topology of the tree. The tree had a very peculiar topology, where a speciose clade was very divergent from the rest of the sequences. These sequences belonged to genes encoding the enzyme aldehyde oxidase xanthine dehydrogenase, a distant relative of carbon monoxide dehydrogenase. These sequences severely skewed the tree topology, so I removed them from the IMG database and reconstructed an unrooted tree with RAxML using a WAG model of amino acid substitution (Whelan and Goldman 2001). (An unrooted tree does not contain information about ancestry, only relatedness of species and the evolution of the sequences.) The resulting tree was more refined and reflective of coxL evolution. I then used RAxML to create a consensus tree with bootstrapping. Bootstrapping is a statistical technique to test the reliability of data and is often used during phylogenetic tree construction to evaluate how robust a tree is. I had high bootstrap values, suggesting that the topology of my tree was reliable.

The second half of the week I spent analyzing my data and preparing for midterm presentations on Friday. Our presentations were restrained to 5 minutes and supposed to inform the other interns and CMOP staff about the specifics of our project and provide preliminary results. However, I had finished a significant portion of my project and had more than enough data to fit on a few slides. I spent a good deal of time identifying which results were most essential to the understanding of my project. I was also a bit nervous about presenting, yet eager to talk about my work. Presentations went very well on Friday. I enjoyed learning about everyones projects, since we had only briefly discussed our projects on orientation. All of the interns are performing such interesting and diverse research.