The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonisation. Here, we analysed 73 re-sequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, MSMC2 recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analysed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune-genes that we surmise reflect the changing land-use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity, and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.

中文翻译：

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基因组分析捕获了广泛鹿科动物中人为引起的人口崩溃和恢复

第四纪的冰川循环通过种群数量的连续收缩和扩张对物种产生了严重影响。同样，人口也受到人类压力的强烈影响，例如不受管制的狩猎和土地利用的变化。白尾鹿和长耳鹿在末次盛冰期期间在不同的避难所生存，在欧洲殖民统治后，它们的数量严重减少。在这里，我们分析了来自北美地区的 73 只鹿的基因组重新测序，以了解气候和人为压力对鹿的种群和适应历史的影响。我们发现了气候引起的差异和人口下降的强烈信号；值得注意的是，MSMC2 恢复了末次盛冰期末大陆白尾鹿有效种群规模 (Ne) 的严重下降。我们发现了殖民地过度捕捞的有力证据，其形式是所有分析种群中 Ne 值最近急剧下降。历史普查规模和放养数据显示与历史 Ne 估计值明显相似，时间 Ne/Nc 比率显示了长尾鹿的保护关注模式。选择的特征突出了与温度相关的基因，包括先前在猛犸象中突出显示的冷受体。我们还检测到了免疫基因，我们推测这些基因反映了北美不断变化的土地利用模式。我们的研究提供了人为和气候引起的鹿多样性下降的详细情况，并为了解黑尾鹿的保护问题和白尾鹿种群数量的成功恢复提供了线索。