School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK.
Curr Biol. 2021 Apr 26;31(8):1771-1779.e7. doi: 10.1016/j.cub.2021.01.073. Epub 2021 Feb 15.
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales. As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
古基因组为实时研究进化过程提供了潜力，但这种潜力受到我们在长时间内恢复遗传数据的能力的限制。因此，迄今为止，大多数研究都集中在更新世晚期或全新世的样本上，这些样本只涵盖了许多进化枝和物种历史的一小部分。在这里，我们报告了从高加索山脉库达罗 1 洞穴的一只约 36 万年前的洞穴熊的岩骨中恢复的低覆盖率古基因组。对该基因组与几个更新世晚期洞穴熊的基因组进行分析，揭示了该群体中广泛存在的线粒体与核基因组不一致的现象。利用中更新世和晚更新世洞穴熊基因组之间的时间间隔，我们直接估计了熊科的核和线粒体取代率，以校准它们各自的系统发育。这表明，线粒体转移是解释其线粒体与核基因组不一致的主要因素。有趣的是，这些转移事件并没有伴随着大规模的核基因渗入。然而，我们确实在其他洞穴熊谱系之间以及洞穴熊和棕熊之间检测到了额外的核混合实例，这些混合事件与线粒体交换无关。从中更新世洞穴熊岩骨获得的基因组数据因此促进了这个已灭绝的巨型动物群的修订进化史。此外，它表明岩骨可能为在许多哺乳动物进化枝的大量进化历史中扩展古基因组检索的幅度和时间深度提供了一种手段。
