A Mitogenomic Phylogeny of Living Primates

Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels.灵长目（Primates）是包含人类在内的哺乳纲类群，下辖78属、共计480个物种，为真兽类哺乳动物18个目中的第三大类群。尽管近年来灵长类的系统发育研究愈发依赖分子数据集，但其中绝大多数仅聚焦于该目内的特定分类亚群。完整线粒体（mitochondrial, mt）基因组已被证实对解析类群内的系统发育关系极为有效，即便对于深层演化节点亦是如此。本研究采用454测序技术，完成了32个全新完整线粒体基因组的测序工作，新增了20个此前未被纳入灵长类系统发育树重建的属级类群。通过新增的13条序列，阔鼻小目（Platyrrhini）下的完整线粒体基因组数量得到大幅扩充，使得新世界猴各科之间的分支模式得以基本解析。本研究向已有的15个线粒体基因组数据集中新增了10个原猴亚目（Strepsirrhini）的线粒体基因组，使得该演化支的线粒体基因组数量几乎翻倍。本研究的数据可对所有系统发育节点进行精确的年代估算，同时为灵长类演化研究提供全新视角。一项核心研究结果显示，现存所有灵长类的最近共同祖先的起源年代相对较晚，估算值为6600万至6900万年前，这表明现存灵长类的分化起始时间与白垩纪-古近纪（K/T）界线高度接近。尽管部分类群间的系统发育关系仍未明确，但本研究借助海量线粒体基因组数据，构建了可信度极高的灵长类系统发育树，其整体结果与此前已发表的研究基本一致。最后，本研究证实线粒体基因组是解决不同分类层级下灵长类系统发育关系的有效工具。