Date of Award
Program or Major
Master of Science
David C Plachetzki
Phylogenetic analyses of gene trees commonly begin by searching large molecular datasets from the taxa of interest using some known query sequence. Resulting sequences that exceed some threshold are then concatenated, aligned, and analyzed phylogenetically. This approach has revealed much about the evolutionary history of gene families, but several problems are apparent. Here we apply a new approach that we call Phylogenetic Focusing that circumvents some issues related to global search strategies. Our approach first circumscribes the largest possible orthogroup containing the gene family of interest and then proceeds to focus in on the gene family of interest based on iterative rounds of phylogenetic analyses. We demonstrate this approach by using the phylogeny of eumetazoan rhodopsin class GPCRs to focus in on a clade containing melatonin receptors, opsins, and other genes. Our results clarify the evolutionary history of eumetazoan rhodopsin class GPCRs, the subclade containing opsins, and provide new hypotheses on the functional significance of these genes in cnidarians.
Provencher, Curtis, "Phylogenetic Focusing Reveals the Evolution of Eumetazoan Opsins" (2018). Master's Theses and Capstones. 1248.