Evolutionary mechanism of vertbrate mitochondrial DNA

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It is prerequisite to establish the phylogenetic relationships among organisms in the study of evolution and biodiversity. Therefore, molecular phylogenetics is of fundamental importance in evolutionary biology. In this project, we developed methods for inferring molecular phylogeny with the maximum likelihood, which has a sound statistical basis, and applied the methods in analyzing mitochondrial genome data.Extensive phylogenetic analyses of updated sequence data of mammalian mitochondrial genomes were carried out using the maximum likelihood method in order to resolve deep branchings in eutherian evolution. The divergence times in the mammalian tree were estimated by a relaxed molecular clock of the mitochondrial proteins calibrated with multiple references. A Chiroptera/Eulipotyphla (i.e., bat/mole) clade and a close relationship of this clade to Fereuungulata (Carnivora + Perissodactyla + Cetartiodactyla) were reconfirmed with high statistical significance. However, support for the monophyly of Fereuungulata relative to the Chiroptera/Eulipotyphla clade was fragile, and we suggest that the 3 branchings among Carnivora, Perissodactyla, Cetartiodactyla and Chiroptera/Eulipotyphla occurred successively in a short time period, estimated to be approximately 77 MyrBP.The Chiroptera/Eulipotyphla divergence was estimated to roughly coincide with the Cretaceous-Tertiary boundary (65 MyrBP). The monophyly of Rodentia, the Lagomorpha/Rodentia clade (traditionally called Glires), and the Afrotheria/Xenarthra clade were preferred over alternative relationships, but the supports of these clades were not strong enough to exclude other possibilities.