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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持续的基因流表明非洲羚羊物种形成模型中不存在生殖隔离


非洲羚羊的多样性是全球更新世巨型动物群更加丰富的全球独特遗迹。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，我们对水羚 (Kobus ellipsiprymnus) 两个亚种的 145 个完整基因组进行了测序，水羚是一种非洲羚羊，据信正处于物种形成过程中。我们调查了遗传结构和种群分化，发现了东大裂谷两侧存在中更新世分离的证据，这与沿所谓的“金登线”的雨影造成的差异一致。然而，我们还发现了近期和广泛的历史基因跨越裂谷屏障的普遍证据。通过推断亚种之间的全基因组变异格局，我们发现了 14 个基因组区域的分化程度较高，其中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。我们研究了这些区域作为候选物种岛。然而，我们观察到这些区域的基因流没有显着减少，也没有任何针对杂交种的选择迹象。总而言之，这些结果表明了一种模式，即气候驱动的差异是驱动非洲羚羊辐射的最重要过程，并表明生殖隔离可能要到分化过程的很晚才开始出现。这对分类学推断产生了重大影响，因为许多分类单元将处于系统地位不明确的灰色地带，这可能解释了为什么很难就许多非洲羚羊的物种地位达成共识。我们的分析表明，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的道路上走了多远