Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China.
Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Mol Phylogenet Evol. 2018 Oct;127:376-386. doi: 10.1016/j.ympev.2018.03.038. Epub 2018 Mar 31.
The evolutionary history of the stump-tailed macaque (Macaca arctoides) and its genetic relationship to other macaques is a subject of continuing controversy. Here, we have reported the first genome sequences of two stump-tailed macaques and one Assamese macaque (M. assamensis). Additionally, we have investigated the genetic diversity between macaque species and analyzed ancient hybridization events. Genome-wide analyses demonstrated that the stump-tailed macaque is more closely related to sinica species than to fascicularis/mulatta species. This topology contradicts the mitochondrial sequence-based phylogeny that places the stump-tailed macaque into the fascicularis/mulatta group. However, our results further show that stump-tailed macaques have genetic backgrounds distinct from sinica species, and present evidence of gene flows with rhesus macaques. We suggest that an ancient introgression occurred after stump-tailed macaques diverged from sinica species. The distinct gene flow between proto-arctoides and proto-mulatta resulted in the transfer of rhesus macaque-type mitochondria into proto-arctoides. The rhesus macaque-type mitochondria remained in populations because of genetic drift during the bottleneck. The PSMC results and morphological and geographic evidence are consistent with the mitochondria capture pattern in the stump-tailed macaque. The molecular clock estimates suggest that the mitochondrial transference into stump-tailed macaques occurred 0.4-1.4 million years ago. Furthermore, we detected extensive admixtures between different macaque species, indicating that gene flow has played an important role in the evolutionary history of the genus Macaca.
短尾猴（Macaca arctoides）的进化历史及其与其他猕猴的遗传关系是一个持续存在争议的问题。在这里，我们报告了两个短尾猴和一个阿萨姆猕猴（M. assamensis）的第一个基因组序列。此外，我们还研究了不同猕猴物种之间的遗传多样性，并分析了古代杂交事件。全基因组分析表明，短尾猴与 sinica 种的关系比与 fascicularis/mulatta 种的关系更为密切。这种拓扑结构与基于线粒体序列的系统发育树相矛盾，后者将短尾猴置于 fascicularis/mulatta 组中。然而，我们的结果进一步表明，短尾猴与 sinica 种具有不同的遗传背景，并存在与恒河猴杂交的证据。我们认为，在短尾猴与 sinica 种分化后发生了一次古老的基因渗入事件。proto-arctoides 和 proto-mulatta 之间明显的基因流导致了恒河猴型线粒体转移到 proto-arctoides 中。由于瓶颈期的遗传漂变，恒河猴型线粒体在种群中得以保留。PSMC 结果和形态学及地理证据与短尾猴中的线粒体捕获模式一致。分子钟估计表明，线粒体转移到短尾猴中发生在 0.4-1.4 百万年前。此外，我们还检测到不同猕猴物种之间存在广泛的混合，表明基因流在猕猴属的进化历史中发挥了重要作用。
