African antelope diversity is a globally unique vestige of a much richer world-wide Pleistocene megafauna. Despite this, the evolutionary processes leading to the prolific radiation of African antelopes are not well understood. Here, we sequenced 145 whole genomes from both subspecies of the waterbuck (Kobus ellipsiprymnus), an African antelope believed to be in the process of speciation. We investigated genetic structure and population divergence and found evidence of a mid-Pleistocene separation on either side of the eastern Great Rift Valley, consistent with vicariance caused by a rain shadow along the so-called ‘Kingdon’s Line’. However, we also found pervasive evidence of both recent and widespread historical gene flow across the Rift Valley barrier. By inferring the genome-wide landscape of variation among subspecies, we found 14 genomic regions of elevated differentiation, including a locus that may be related to each subspecies’ distinctive coat pigmentation pattern. We investigated these regions as candidate speciation islands. However, we observed no significant reduction in gene flow in these regions, nor any indications of selection against hybrids. Altogether, these results suggest a pattern whereby climatically driven vicariance is the most important process driving the African antelope radiation, and suggest that reproductive isolation may not set in until very late in the divergence process. This has a significant impact on taxonomic inference, as many taxa will be in a gray area of ambiguous systematic status, possibly explaining why it has been hard to achieve consensus regarding the species status of many African antelopes. Our analyses demonstrate how population genetics based on low-depth whole genome sequencing can provide new insights that can help resolve how far lineages have gone along the path to speciation

中文翻译：

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持续的基因流动表明非洲羚羊物种形成模型中不存在生殖隔离


非洲羚羊多样性是全球更新世巨型动物群中全球独一无二的遗迹。尽管如此，导致非洲羚羊大量辐射的进化过程尚不清楚。在这里，我们对来自水羚 （Kobus ellipsiprymnus） 的两个亚种的 145 个全基因组进行了测序，这是一种被认为处于物种形成过程中的非洲羚羊。我们调查了遗传结构和种群分化，发现了东非大裂谷两侧更新世中期分离的证据，这与所谓的“金登线”沿线的雨影造成的替代作用一致。然而，我们还发现了最近和广泛的历史基因跨越裂谷屏障的普遍证据。通过推断亚种之间变异的全基因组景观，我们发现了 14 个分化升高的基因组区域，包括一个可能与每个亚种独特的皮毛色素沉着模式相关的基因座。我们将这些区域作为候选物种形成岛屿进行了调查。然而，我们没有观察到这些区域的基因流显着减少，也没有任何针对杂交种的选择迹象。总而言之，这些结果表明一种模式，即气候驱动的替代是驱动非洲羚羊辐射的最重要过程，并表明生殖隔离可能直到分化过程的后期才开始。这对分类学推断有重大影响，因为许多分类群将处于系统状态模棱两可的灰色地带，这可能解释了为什么很难就许多非洲羚羊的物种状况达成共识。我们的分析展示了基于低深度全基因组测序的群体遗传学如何提供新的见解，帮助解决谱系在物种形成过程中走了多远