基于从头组装的参考基因组和种群重测序研究红面猴进化历史及近缘物种的渐渗杂交机制

Interspecific hybridization or introgression has many and varied impacts on the process of differentiation and speciation. In recent years, speciation with hybridization or introgression has become a topic of major interest in the field of evolutionary biology. The speciation and evolutionary history of Macaca arctoides has been long debated because this species shares rapid radiation with its closely related species which are particularly prone to hybridization or introgression. Furthermore, secondary contacts after first divergence make their relationships more complicate. The present study will produce a de novo assembly genome of M. arctoides, which will be the first genome of sinica group in the genus Macaca. Analysis of the genome will highlight the genetic diversities of M. arctoides to other primates, as well as to other macaque species. Based on de novo genome and resequencing genomes from different M. arctoides populations, we focus on the hybridization and introgression between M. arctoides and its closely related species. Particularly, by combining analyses on the autosomal, X-chromosomal, Y-chromosomal and mitochondrial genome datasets, we aim to reveal the sex-biased introgressions mechanism and estimate the proportion of introgressive hybridization in M. arctoides genome. In addition, we will employ various population genetics analytical methods to investigate the contemporary and/or ancient hybridizations, with an emphasis on the patterns of temporal and spatial gene flow. Taken together, the present study will elucidate the evolutionary significance of hybridization and introgression during M. arctoides speciation, thus benefit our full understanding of the evolutionary history of the intriguing macaque species. In addition, our result will provide new insight into the role of hybridization and introgression in speciation.

近缘物种间的杂交或基因渐渗对于物种的分化与形成具有复杂而重要的影响，这已成为进化生物学领域研究的新的焦点。红面猴（Macaca arctoides）与其他猕猴属物种间具有较短的分化时间和快速的适应辐射，再加上分化后的二次接触，形成了复杂的种间杂交和基因交流机制，导致红面猴的物种形成与进化历史长期存在较大争议。本研究拟通过de novo测序，报道首个sinica种组物种：红面猴的从头组装参考基因组，阐明其与其他灵长目动物，尤其是猕猴属物种间的遗传差异。同时结合从头组装的基因组和不同种群个体的深度重测序，深入研究红面猴与近缘物种间的渐渗杂交，阐明性别偏岐的杂交机制；并基于分化种群遗传学方法阐明红面猴渐渗杂交的程度、基因流的时空模式。整合个体基因组和种群基因组数据，最终揭示杂交和基因渐渗对红面猴物种分化与形成的重要意义，重建这一长期存在争议物种的进化历史。

项目结合二代测序和10Xgenomics的技术，从头测序和组装了一个红面猴基因组，测序深度约为 230.69×，基因组大小为 2.84 Gb，scaffold N50 为 14.52 Mb，组装质量较高。此前公布的猕猴属物种基因组都来自fascicularis种组，这是首个sinica种组的从头测序的基因组。比较基因组揭示红面猴和南豚尾猴分化于约 391万年前，与恒河猴/食蟹猴分化于约 361万年前。利用组装的基因组分析了恒河猴、食蟹猴、南豚尾猴和红面猴四个猕猴属物种之间的渐渗杂交，发现南豚尾猴与红面猴、南豚尾猴与食蟹猴、红面猴与恒河猴之间之间均存在杂交信号。基于猕猴属物种重测序基因组，开展了红面猴及其近缘物种的基因流研究，共分析了20个猕猴动物基因组，包括10个物种，涵盖了迄今最全面的猕猴属动物，结合多种分析技术，全面揭示了猕猴物种之间复杂的基因流。其中以fascicularis种组和silenus种组之间的信号最强。特别是，我们检测到食蟹猴与豚尾猴之间存在双向的基因流，两个物种间通过基因流遗传的基因组比例估计为6.19%。然而在一些岛屿物种与其他猕猴之间也检测到基因流，我们认为这些杂交信号在很大程度上归因于近缘物种的祖先渗入或基因组相似性。本项目的研究揭示杂交和基因流在猕猴属的分化和进化具有重要意义。. 同时我们开展了红面猴血液转录组的从头组装注释，报道了一个高质量的血液转录组。我们还对一个红面猴血液甲基化组进行了测序并与普通猕猴的血液甲基化组进行了比较分析。此外我们还基于全基因组SNV和拷贝数变异（CNV）研究了猕猴属动物的遗传差异与适应性、研究了Alu逆转座子和TRIM基因在灵长类动物中的进化、藏酋猴的种群遗传学等。. 研究成果发表研究论文10篇，其中核心期刊论文3篇，SCI论文7篇，此外红面猴de novo基因组文章目前在Molecular Biology and Evolution杂志送审，有望发表高影响力论文。此外项目培养了博士研究生2名，硕士研究生3名。