Evolutionary mechanism of vertbrate mitochondrial DNA

建立生物之间的系统发育关系是研究生物进化和生物多样性的前提。因此，分子系统发育学在进化生物学中具有重要的基础意义。在本项目中，我们开发了具有良好统计基础的最大似然推断分子系统发育的方法，并将该方法应用于线粒体基因组数据分析。利用最大似然方法对最新的哺乳动物线粒体基因组序列数据进行了广泛的系统发育分析，以解决真动物进化中的深层分支问题。哺乳动物树的分化时间是通过线粒体蛋白的宽松分子钟与多个参考校准来估计的。再次确认了翼翅目/狐蝠目（即蝙蝠/鼹鼠）分支与fereuungula（食肉目+鬼趾目+鲸趾目）的亲缘关系，具有较高的统计学意义。然而，相对于翼翅目/真翅目分支的单系性支持是脆弱的，我们认为食肉目、鸟趾目、鲸趾目和翼翅目/真翅目的3个分支是在很短的时间内先后发生的，估计约为77mybp。Chiroptera/Eulipotyphla的分化大致与白垩纪-第三纪界线重合（65 MyrBP）。啮齿类的单系、狐形目/啮齿目分支（传统上称为Glires）和非洲目/异种目分支比其他关系更受青睐，但这些分支的支持不足以排除其他可能性。

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.