Virtual library - PhD theses
- Doctoral thesis title: Genomic signatures of evolutionary processes on cetacean evolution: footprints of the return of mammals to the sea
- Institution: Universidad Austral de Chile
- Supervisor: Dr. Juan C. Opazo
- Year of defense: 2012
Cetaceans are among the most specialized of all mammals and are unique in being the only mammals completely dependent and adapted to an aquatic environment. The adaptation to this lifestyle has required complex changes and sometimes a complete restructuration of physiological systems, behavior and morphology. Identifying genes that have been subjected to selection pressure during cetacean evolution would greatly enhance our knowledge of the ways in which genetic variation in this mammalian order has been shaped by natural selection. This work aimed to provide the first step towards the searching for genome-wide evidence of positive selection (chapter 2) and case-by-case analysis of candidate loci associated with adaptation to a fully aquatic life from a terrestrial life (chapters 3, 4 and 5). Since a stable phylogenetic classification is a prerequisite to provide a reliable framework for comparative genomic studies, chapter 1 was born. In this chapter we performed a phylogenomic analysis of Laurasiatheria group and found a high support for the sister relationship between Chiroptera (bat) and Cetartiodactyla (cetaceans and artiodactyls). Also we demonstrated the utility of very large and conserved genomic dataset to clarify our understanding of the evolutionary relationships among mammals. Once we had a stable and reliable phylogenetic tree, we could perform a genome-wide scan for positive selection in cetacean lineage. We employed models of codon substitutions that account for variation of selective pressure over branches on the tree and across number of sites. In total we analyzed 7859 nuclear-coding orthologs and using likelihood ratio tests, we identified 378 genes (4.8%) that possess patterns of genetic variation consistent with the hypothesis of positive selection in dolphin lineage. Of particular interest for the cetacean adaptation to an aquatic life are some GOs (gene ontology) under positive selection: genes related to kidney, heart, lung, eye, ear and nervous system development. Regarding the case-by-case analysis, the globins were chosen given their important role in hypoxic adaptation. We characterized the genomic structure of alpha and beta globin genes, and assigned orthology and paralogy relationships among the copies. We analyzed each of these genes and additionaly the myoglobin and the neuroglobin in cetacean lineage in comparison with other terrestrial mammals through codon-based maximum likelihood models to look for evidence of adaptive molecular evolution. Our results show that, indeed, in cetacean lineage, these genes show an increased rate of evolution when compared to their terrestrial counterparts. Taken all together, our analyses provide a first insight into the type of biological processes that have been targets of selection in cetacean evolution.
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