Evolutionary patterns in snake mitochondrial genomes

In this dissertation I describe a number of patterns and interesting aspects associated with the evolution of snake mitochondrial genomes (mtDNA). I also attempt to resolve the phylogeny of squamates, focusing on the relationship between the snakes and lizards. The results of this study indicate that snakes and worm lizards (amphisbaenians) appear to share an exclusive common ancestor, and snakes appear to have undergone strong selective pressure that shaped snake mtDNAs. Snake mtDNAs have several unique features, including a compact size, duplicated control regions, and an elevated evolutionary rate. Based on the correlation resulting from the asymmetric replication of mtDNA, the usage of control regions was inferred to be species specific. In snake mtDNAs, the magnitude of the rate acceleration varied considerably among genes and over time, and it appears that these changes at the nucleotide and protein level co-occurred with snake mtDNAs incurring a reduction in size and a duplication of the control region. In snake mtDNA, many unique amino acid substitutions were identified in all protein-coding genes. In the Cytochrome C Oxidase subunit I (COX1) protein, one of three proposed proton transfer channels was enhanced by several unique substitutions. Additionally, strong positive selection was detected on the COX1 gene of alethinophidian snakes. These may be causally related to the energetic demands imposed by the radical energy requirement in the early digestion period of alethinophidian snakes. Observations of change in COX1 gene suggest that, due to the relaxation of selective pressure or a population bottleneck, numerous deleterious substitutions accumulated on snake ancestral lineages. Then the impaired functions were recovered, or even enhanced by adaptation. During this period, the evolutionary rate of snakes was accelerated as well. In this research, the phylogenetic placement of snakes was inferred using the complete mtDNA of 65 vertebrates by maximum likelihood (ML) and partitioned-Bayesian inference. Snakes were placed as the sister taxon to worm lizards, and this branching pattern is strongly supported by Bayesian inference-derived posterior probability. The jackknife simulation also supports the sister relationship between snakes and worm lizards, cumulatively rejecting the hypothesis of marine origins of snakes