Evolutionary mechanism of vertbrate mitochondrial DNA

生物系统发育关系的建立是生物进化和生物多样性研究的前提。因此，分子遗传学在进化生物学中具有根本的重要性。本项目开发了具有良好统计基础的最大似然法推断分子系统发育的方法，并将其应用于线粒体基因组数据分析，采用最大似然法对哺乳动物线粒体基因组更新序列数据进行了广泛的系统发育分析，以解决真兽目进化中的深层分支问题。在哺乳动物树的分歧时间估计的线粒体蛋白质校准与多个参考宽松的分子钟。翼手目（Chiroptera）/真尾目（Eulipotyphla）（即，蝙蝠/鼹鼠）的进化枝，并再次证实了该进化枝与有蹄类（食肉目+奇蹄目+鲸偶蹄目）的密切关系，具有高度的统计学意义。然而，Fereuungulata相对于翼手目/Eulipotyphla分支的单系性的支持是脆弱的，我们认为食肉目，奇蹄目，鲸蹄目和翼手目/Eulipotyphla之间的3个分支相继发生在一个短的时间内，估计约为77 MyrBP。啮齿目的单系性，Lagomorpha/啮齿目分支（传统上称为Glires），和Afrotheria/Xenarthra分支是首选替代关系，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.