Alu逆转座子及其在猕猴属动物系统进化和种群遗传学中的运用研究

Alu elements are a class of non-autonomous retroposons belonging to short interspersed elements (SINEs). They are primate-specific SINEs with a full-length of ~300bp long. Alu elements have enjoyed remarkable proliferation during the primate radiation and have expanded to more than one million copies in the macaque genome. With the essentially homoplasy-free set of characters, Alu elements have become widely recognized as powerful genetic markers for phylogenetic studies and population genetics researches, and multiple controversial relationships that can not be solved using traditional molecular data have been successfully elucidated. However, Alu elements based study has not been performed to resolve the phylogenetic relationships and population genetics issues existed in primate taxons of China. Animals from genus Macaca, a group of diverse primates closely related to humans, have been extensively used as model animals in biomedical and evolutionary studies. In the present study, a PCR-display methodology will be employed on the different marcaques to identify new lineage-specific Alu insertions from marcaque genoms to reconstruct the evolutionary relationships of of genus Macaca. In additon, a combination analysis on the presence/absence patterns of Alu elements as well as maternally, paternally and bi-parentally inherited markers will be conducted in our study to give new and comprehensive insights into the evolutionary history of genus Macaca, and reveal hybridization events and gene flow among ancestral lineages as the most likely cause for the previously observed phylogenetic incongruences. Furthermore, some Alu elements inserted so recently that they are polymorphic for presence or absence among macaque populations. Polymorphic Alu loci are going to be searched from Thibetan macaque which is endemic to China and will be used to investigate population structure and geography of the species. The present study is vaulable in constructing Alu based genetic marker system and providing powerful tool for further phylogenetic studies and population genetics within the primate order.

Alu是灵长目特有的一类非自主性逆转座子，其在猕猴动物基因组中拷贝数已超过一百万，是数量最丰富、最成功的可移动元件。由于Alu具有非平行演化的特征及丰富的拷贝数，是基因组中重要的中性遗传标记。Alu作为遗传标记已成功用于解决各种灵长目动物的系统进化和种群遗传学问题，而目前国内此方面的研究尚未开展。本项目拟采用PCR-Display技术系统地研究猕猴属动物的Alu逆转座子，筛选猕猴动物谱系特异的Alu作为遗传标记研究其系统进化。并结合Alu座位、Y、X、常染色体及线粒体基因组共同分析以阐明猕猴属动物间可能存在的杂交和基因交流。同时从我国特有的猕猴动物：藏酋猴基因组中筛选多态性的Alu座位，并基于Alu座位研究藏酋猴的遗传多样性、种群结构、地理起源等问题。本项目的开展对于猕猴属动物Alu的遗传标记系统的建立，阐明猕猴动物间复杂的杂交和基因交流等系统进化问题及种群遗传学问题等都具有深远意义。

本项目在猕猴属物种的Alu逆转座子和微卫星遗传标记筛选、线粒体基因组及全基因组测序方面开展了深入系统的研究，构建了丰富的猕猴属物种遗传标记系统；并结合多种遗传标记阐明了猕猴属的系统进化关系，此外还基于基因组学技术揭示了猕猴动物之间的遗传差异，首次证明了红面猴、藏酋猴、恒河猴等物种间可能存在古老的杂交和基因交流。. 作为灵长目动物基因组特有的、数量最丰富的可移动元件，我们从各猕猴属物种基因组中筛选了Alu逆转座子，并将其作为遗传标记，成功阐明了猕猴属系统进化及种群遗传学问题，从而为系统进化和种群遗传学研究积累了丰富的遗传标记。我们还从基因组水平比较了三种猕猴属动物、以及十种灵长目动物基因组中微卫星的特征、分布模式以及GC含量差异。发现存在各猕猴物种特异的微卫星基序，阐明了它们在重复序列上的遗传差异，而这些差异可能会对基因转录和转录调控存在一定影响。我们还首次报道了3个猕猴物种的线粒体基因组：红面猴、熊猴以及在2015年发现的猕猴属新种：白颊猕猴，从而为猕猴动物的分子生态学研究提供了重要的基础数据。. 联合Alu逆转座子，以及母源的、父源的、双亲的和线粒体基因组遗传标记共同阐明了猕猴属的系统进化关系，认为红面猴属于sinica种组，并追踪到其在进化历史中可能存在的古老的杂交事件，红面猴通过雄性介导的基因流进入到恒河猴种群中，并经历核基因淹没(nuclear swamping)，从而为猕猴属物种间杂交提供了最全面的分子证据。结合基因组学技术，我们首次报道了一个藏酋猴基因组，通过与恒河猴、食蟹猴比较，在基因组水平阐明了不同猕猴物种间的遗传差异，并发现藏酋猴基因组中最多达8.843%的区域可能来源于与恒河猴的基因渐渗。我们的研究认为杂交和基因渐渗可能广泛存在各猕猴物种间，并影响了整个猕猴属的物种分化和进化历史。