Veeramah Krishna R, Woerner August E, Johnstone Laurel, Gut Ivo, Gut Marta, Marques-Bonet Tomas, Carbone Lucia, Wall Jeff D, Hammer Michael F
Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721 Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794.
Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721.
Genetics. 2015 May;200(1):295-308. doi: 10.1534/genetics.115.174425. Epub 2015 Mar 12.
Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10(-9)/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.
长臂猿被认为在约1680万年前与体型更大的类人猿分化，如今栖息在东南亚的雨林中。根据其二倍体染色体数目，长臂猿科分为四个属，即黑冠长臂猿属、合趾猿属、白眉长臂猿属和长臂猿属。利用核型、线粒体DNA（mtDNA）、Y染色体和短常染色体序列来阐明长臂猿系统发育关系的遗传学研究尚无定论。为了更深入地研究长臂猿属之间的关系，我们对每个属的两个个体进行了平均覆盖度约为15倍的二代全基因组测序（WGS）。我们开发了一种基于溯祖的近似贝叶斯计算（ABC）方法，该方法纳入了由高覆盖度外显子验证产生的测序错误模型，以推断长臂猿类群的分支顺序、分化时间和有效种群大小。尽管白眉长臂猿属和合趾猿属可能是姐妹类群，但尽管分析了大量数据，我们仍无法确定一个单一的二叉树。相反，我们的结果支持了所有四个长臂猿属大约在同一时间分化的假设。假设常染色体突变率为1×10^(-9)/位点/年，这种物种形成过程发生在约500万年前上新世早期的一个时期，其特征是气候转变和巽他陆架森林的碎片化。对更多个体进行全基因组测序对于推断长臂猿属分离后物种间基因流动的程度至关重要。
