基于系统发育基因组学的疣猴亚科进化格局与形成机制研究

Evolutionary pattern and its mechanism not only are basic science question in evolutionary biology, but also are critical and fundamental way to explore the evolution of biodiversity. The evolutionary process and history could be achieved by the reconstruction of phylogenetic relationships to clarify its evolutionary pattern and mechanism. The phylogenomics, which is one of the important trends in evolutionary biology, has been wildly used to try to resolve the reconstruction of phylogenetic relationships and evolutionary patterns in virtue of whole genomic sequences. The colobines (Primate Order, Cercopithecidae family, Colobinae subfamily) are a diverse clade of Old World primates and separated into Asian and African clades, which are also unique primates that use leaves rather than fruits and insects as their primary food source. At present, it has become the optimal object for studying of the origin of primates and its adaptive evolution because of almost exclusively herbivores and many other unique characters. In Colobinae subfamily, however, there are still many controversies and unknown causes about the phylogenetic relationships and formation mechanism of evolutionary pattern between Genus and species, because of different methodologies and molecular loci in previous studies. Especically, no any study was carried out to elucidate the phylogenetic relation, evolutionary patterns, and its formation mechanism within species and between the related species in this subfamily till now. This project, based on several known genome of primates and newly developed Sequence Targeted Capture technique and new high-throughput sequencing, aims to develop substantial orthologous genes and try to reconstruct the phylogenetic relationships so as to explore its evolutionary pattern and forming mechanism within Colobinae.

进化格局及其形成机制是进化生物学中最基本的科学问题和探讨生物多样性演变的根本问题。系统发育基因组学是从基因组层面上开展系统发育重建和进化格局研究。作为植食性最强的灵长类，疣猴亚科已成为探讨其起源、进化与适应机制的重要对象，目前由于分析手段和方法的不同，有关其各属种间以及种下和近缘种间的系统进化关系、进化格局及其形成机制仍存在诸多争议和不明之处。本项目以疣猴亚科为研究对象，通过定向序列捕获和高通量测序技术获得大量直系同源基因数据，利用系统发育基因组学方法，重建系统发育历史，从而揭示疣猴亚科的起源、进化格局及其形成机制。

作为植食性最强的灵长类，疣猴亚科已成为探讨其起源、进化与适应机制的重要对象。1）本项目利用川金丝猴de nove基因组测序和其它几种金丝猴的基因组重测，开展了金丝猴属的起源和演化历史分析。重建了疣猴亚科金丝猴属物种的系统演化关系，阐明了金丝猴北方类群的分化时间约为1.60百万年前，并紧邻金丝猴祖先种群的分化，青藏高原的抬升有可能引起了金丝猴属的分化以及随后的北方类群分化。2）对乌叶猴属的戴帽叶猴核内线粒体假基因（Numt）全长序列进行了研究。该基因全长15K以上，占线粒体全长的92%。进一步比对及构建亚洲疣猴Numt序列的系统发育树，发现戴帽叶猴Numt序列来源于长尾叶猴属的线粒体基因组，并在祖先杂交的过程中进入到戴帽叶猴核基因组中。本研究证实了长尾叶猴属和乌叶猴属物种祖先存在着祖先杂交现象。3）选取在灵长类尤其是猴科中呈单拷贝的直系同源基因，疣猴亚科中的7个属的11代表物种单个个体基因组进行分析，通过定向捕捉获取的序列，得到高质量测序数据约18G。选取猕猴Mmul051212版本作为参考基因组，得到约30万有效SNP位点构建的系统发育树，研究发现乌叶猴属的戴帽叶猴、黑叶猴和郁乌叶猴聚为一簇，而长尾叶猴属的长尾叶猴和紫脸叶猴；长鼻猴、黑腿白臀叶猴和川金丝猴同属于奇鼻猴类，也聚为一簇。而叶猴属的黑脊叶猴则位于整个亚洲疣猴的基部。我们又通过一致性网络方法对单基因树对戴帽叶猴、黑叶猴和长尾叶猴关系继续分析发现乌叶猴属和长尾叶猴属在分化过程中可能经历了快速分化，并且伴随有谱系重排。属和长尾叶猴属在分化过程中可能经历了快速分化，并且伴随有谱系重排。目前我们正在将所有系统发育树定位到染色体上，以判断单基因树的分支式样与其在染色体上的位置没有明显相关性。

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