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Molecular evolution of the mitochondrial genome in marine mammals.

Dijk, S. van (2015) Molecular evolution of the mitochondrial genome in marine mammals. Master's Thesis / Essay, Biology.

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Abstract

The Cetaceans, Pinnipeds and Sirenians are three lineages of mammals that returned secondarily to an aquatic life. Along with this major transition, these groups convergently evolved multiple physiological, morphological and anatomical adaptations. To this date, we still poorly understand what the molecular bases underlying these phenotypic changes are, how natural selection shaped the molecular evolution of their genomes and whether convergent evolution at the phenotypic level implies convergent evolution at the molecular level. Environmental changes during such a major transition likely caused changes in energetic requirements (thermoregulation and metabolic) in these lineages. This could have left detectable footprints of natural selection acting on the proteins involved in those functions, such as the mitochondrial proteins which are involved in the majority of energy production in most eukaryote cells. Here we investigated the molecular evolution of the thirteen proteins encoded by the mitochondrial genome. Specifically, we investigated evidence of natural selection acting on the mitochondrial genome of 47 Cetaceans, 24 Pinnipeds and 2 Sirenians species and their closest terrestrial relatives. By analyzing the codon evolution in each gene along the phylogenetic tree, we found that most amino acids (AAs) on the mitochondrial genome were under strong conservative evolution (or negative selection) in the three lineages of marine mammals. However, a minority of amino acid changes (23 in total) displayed evidence of positive or directional selection. Sirenian species displayed the largest number of sites (11), followed by Cetacean (8) and Pinniped (4) species, consistent with their respective divergence time from their closest terrestrial relatives. None of the candidate sites under positive selection were shared among the three groups of marine mammals, but interestingly some were concentrated in some regions of the mitochondrial genome for the three groups (for ex. region 40-45 of the ATP8 gene). We also investigated how amino acid changes correlated with changes in biochemical properties and if some could have evolved under natural selection. Overall, 855 amino acids changes correlated with changes in biochemical properties under potential positive selection. Three were shared between all groups and 61 between Cetaceans and Pinnipeds, while the other pairs shared much less sites (5 between Pinnipeds and Sirenians, and 15 between Cetacean and Sirenians). The large proportion of shared changes between cetaceans and pinnipeds likely reflecting their closer phylogenetic relationships. Future work will be required to better understand how the amino acid changes we have identified as potentially under positive selection could actually change the structure of the proteins and impact the coupling of the mitochondrial Oxidative phosphorylation (OXPHOS) cascade at the origin of the energy and heat production of the cell. Furthermore, this work should be extended to the mitochondrial proteins encoded by the nuclear genome.

Item Type: Thesis (Master's Thesis / Essay)
Degree programme: Biology
Thesis type: Master's Thesis / Essay
Language: English
Date Deposited: 15 Feb 2018 08:10
Last Modified: 15 Feb 2018 08:10
URI: http://fse.studenttheses.ub.rug.nl/id/eprint/13541

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