Cahill James A, Soares André E R, Green Richard E, Shapiro Beth
Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.
Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.
Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). doi: 10.1098/rstb.2015.0138.
Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
了解物种何时分化有助于确定物种形成的驱动因素，但从遗传数据中很难确定种群间基因流动的终止时间。我们探讨了使用成对顺序马尔可夫合并（PSMC）模型来推断物种和种群之间的分化时间。使用人工杂交基因组生成的PSMC图显示，在两个亲本谱系分化时，有效种群大小迅速增加，并且这种方法此前已被用于推断人类谱系之间的分化。我们表明，即使没有高覆盖率或分阶段的输入数据，通过将人工杂交种的PSMC输出与具有已知种群历史的模拟输出进行比较，PSMC也能检测到种群间显著基因流动的终止。然后，我们应用PSMC来检测两个真实数据集内谱系之间的分化时间：大猩猩和熊属中的熊。我们的结果证实了这些谱系之前提出的大多数分化时间，并表明最近分化的谱系之间的基因流动在熊和大猩猩中可能很常见，包括在刚果河形成后，黑猩猩和倭黑猩猩之间持续了长达一百万年的基因流动。本文是主题为“利用岩石和时钟确定物种分化时间”的特刊的一部分。
