白头叶猴及其近缘种的分化历史和毛色差异的基因组学研究

Primates exhibit striking examples of skin and pelage color variation. Closely related species often exhibit marked color differences, especially in Colobinae. We know little about how this color variation is generated and maintained by the processes of evolution. The genus Trachypithecus comprises up to 20 species. Trachypithecus francoisi, T. poliocephalus and T. leucocephalus occur in nearby distribution areas, but differ extremely in fur coloration, and are thus a good example to study evolutionary processes of species divergence and fur coloration variation in colobine monkeys. As the habitats of T. poliocephalus and T. leucocephalus are nested in the distribution range of T. francoisi, it is hypothesized that T. poliocephalus and T. leucocephalus might have evolved different fur coloration by mutations from the local population of T. francoisi. However, the opposite hypothesis could also been reasonable: there was a polymorphic ancestral condition and differences in descendant populations are the result of different characters becoming fixed over time, during which T. francoisi expanded its distribution range. Traditionally, T. poliocephalus and T. leucocephalus were classified as subspecies of T. francoisi suggesting that the three taxa are similarly related to each other and that the similar fur coloration in T. poliocephalus and T. leucocephalus evolved independently. Alternatively, T. leucocephalus was classified as a subspecies of T. poliocephalus and thus both of them separated from T. francoisi, mainly due to similarities in fur coloration. To assess the different hypotheses, we plan to launch the population genomics study of these three langurs. Base on the genome assembly of T. francoisi, we are willing to re-sequence the genome of individuals of these three langurs. We aim to estimated phylogenetic relationships, genomic polymorphisms and inferred demographic histories of langurs to determine the divergence of each taxon. We also would like to identify the selected regions in langur genomes to gain insights into genetic changes that supported the variation of fur coloration. Furthermore, the population genomics information would facilitate the conservation biology effort on langurs.

白头叶猴、黑叶猴和金头叶猴是乌叶猴属内的3个近缘种，其中白头叶猴是我国特有的灵长类动物。这三个近缘物种由于头部毛色变异而受到灵长类学者和进化生物学研究者的长期关注：黑叶猴头部毛色基本为黑色，白头叶猴头部毛色为白色，金头叶猴头部毛色为金黄色。由于这三个物种栖息地重叠，长期以来相互的进化关系一直不明确。一种假说认为白头叶猴是金头叶猴的一个亚种；另一种假说认为他们是分别由黑叶猴的种群变异形成。在基于黑叶猴基因组拼接的基础上，我们采集了三个物种代表种群的样品，计划进行基因组重测序，开展种群基因组学研究。以期判断三种灵长类动物最初的分化模式，物种分化的先后顺序，分化后是否有基因交流，基因流对物种分化过程是否有影响。重要的是，检测毛色相关基因所在区域的变异程度，判断是否受到正选择，与毛色变异的关系如何。本研究可以为生物多样性的演化与发展提供详细证据，为更好保护生物多样性提供依据。

白头叶猴、黑叶猴和金头叶猴是乌叶猴属内的3个近缘种，其中白头叶猴是我国特有的灵长类动物。这三个近缘物种由于头部毛色变异而受到灵长类学者和进化生物学研究者的长期关注：黑叶猴头部毛色基本为黑色，白头叶猴头部毛色为白色，金头叶猴头部毛色为金黄色。由于这三个物种栖息地重叠，长期以来相互的进化关系一直不明确。一种假说认为白头叶猴是金头叶猴的一个亚种；另一种假说认为它们是分别由黑叶猴的种群变异形成。在基于黑叶猴基因组拼接组装的基础上，我们采集了三个物种代表种群的样品，进行基因组重测序，开展种群基因组学研究。以期判断三种灵长类动物最初的分化模式。重要的是，检测毛色相关基因所在区域的变异程度，判断是否受到正选择，与毛色变异的关系如何。本研究可以为生物多样性的演化与发展提供详细证据，为更好保护生物多样性提供依据。我们首先组装了一个黑叶猴个体的基因组，contig N50 为16.3Mb。另外我们对23个不同叶猴的个体进行了基因组重测序。经过我们的研究表明，金头叶猴与黑叶猴和白头叶猴的分化时间是0.45个百万年前，而白头叶猴是随后从黑叶猴的地方种群分化而来，二者分化时间为0.35个百万年前。通过种群基因组学、选择消除分析和转录组分析验证，我们最终确定白头叶猴种群基因组中EDNRB基因所在的基因组区域受到的选择作用是白头叶猴特殊的白色头尾毛色的重要演化原因。本研究深入解析了灵长类动物物种分化过程，充分解释了形状学特征分化的基因组学基础，具有较高的科学研究意义。同时，将黑叶猴划分为2个管理保护单元，白头叶猴也划分出2个管理保护单元，在保护生物学上具有重要的实践意义。