Wang Xi, Pedersen Casper-Emil Tingskov, Athanasiadis Georgios, Garcia-Erill Genís, Hanghøj Kristian, Bertola Laura D, Rasmussen Malthe Sebro, Schubert Mikkel, Liu Xiaodong, Li Zilong, Lin Long, Balboa Renzo F, Jørsboe Emil, Nursyifa Casia, Liu Shanlin, Muwanika Vincent, Masembe Charles, Chen Lei, Wang Wen, Moltke Ida, Siegismund Hans R, Albrechtsen Anders, Heller Rasmus
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820, Gentofte, Denmark.
Syst Biol. 2024 Nov 29;73(6):979-994. doi: 10.1093/sysbio/syae037.
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.
非洲羚羊的多样性是全球独特的遗迹，见证了更为丰富的更新世全球巨型动物群。尽管如此，导致非洲羚羊大量辐射的进化过程仍未得到充分理解。在此，我们对水羚（Kobus ellipsiprymnus）两个亚种的145个全基因组进行了测序，水羚是一种非洲羚羊，被认为正处于物种形成过程中。我们研究了遗传结构和种群分化，发现了东非大裂谷两侧在更新世中期分离的证据，这与沿所谓“金登线”的雨影导致的隔离相一致。然而，我们也发现了近期和广泛的历史基因流跨越裂谷屏障的普遍证据。通过推断亚种间全基因组的变异格局，我们发现了14个分化增强的基因组区域，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位点。我们将这些区域作为候选物种形成岛进行了研究。然而，我们并未观察到这些区域的基因流有显著减少，也没有发现对杂交种进行选择的迹象。总的来说，这些结果表明，气候驱动的隔离是推动非洲羚羊辐射的最重要过程，并且表明生殖隔离可能直到分化过程的很晚阶段才会出现。这对分类学推断有重大影响，因为许多分类单元将处于系统地位模糊的灰色地带，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能够提供新的见解，有助于解决谱系在物种形成道路上已经走了多远的问题。
