Abstract：
Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species\' unique traits.
摘要：
低基因组多样性通常表明种群规模小，并且被认为通过降低长期适应性而有害。1,2,3,4,5,6此外，小种群可能会促进同源物和远交抑郁症的基因流7,8,9,10,11,12,13这里,我们研究了栖息地可用性之间的联系，有效种群规模(Ne)，通过从已灭绝的蓝色羚羊（Hippostragusleucophaeus）产生40倍核基因组来灭绝。历史上是非洲最南端相对较小的开普植物区特有的，人们认为14,15个种群在冰川-间冰期周期中扩张和收缩，跟踪合适的栖息地。16,17,18然而，我们发现Ne长期低,不受冰川周期的影响，这表明在公元1800年灭绝之前，基因组多样性低的持久性持续了几千年。缺乏近亲繁殖，伴随着高水平的基因净化，建议适应这种长期的低Ne，以及殖民时代的人类影响(例如，狩猎和景观改造)，而不是长期的生态过程，是它灭绝的中心。系统学分析揭示了roan(H.马）和蓝色羚羊，以及在罗马和黑貂羚羊之间(H.尼日尔)，大约在蓝色羚羊和黑貂羚羊的发散时间(~1.9Ma)。最后,我们确定了LYST和ASIP基因是蓝色羚羊同名蓝色毛皮颜色的候选基因。我们的结果修改了我们对基因组多样性和进化史之间相互作用的理解的许多方面，并为揭示这种灭绝物种的独特性状的遗传基础提供了资源。
