Whole genome sequences reveal adaption of Snow sheep to subarctic climates and complex introgression across wild sheep species

To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use key model species with high sensitivity to such factors. Snow sheep could be a good candidate to this end; being the only large herbivores adapted to the cold and alpine habitats of Northeastern Siberia, it also plays a crucial role in the ecosystem. Despite having extensive geographical distribution among all Ovine species, it is also one of the least studied. Here, we sequenced and analyzed six genomes of Snow sheep in combination with 32 available from all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to sub-arctic environments. Despite their large census population size, Snow sheep genomes showed remarkably low heterozygosities, which could reflect the effect of isolation and historical bottlenecks that we inferred. We also found multiple instances of introgression involving Snow sheep with Argali and Dall sheep, suggesting that these species might have been more widespread during the Pleistocene than at present. Indeed, our results showed that during the last interglacials, these wild sheep apparently experienced severe population reductions. Further, introgressed segments covered genes which were associated with immunity, adipogenesis and morphology related traits, representing potential targets of adaptive introgression. We also identified several genes with traces of selection in Snow sheep. Their functions included mitochondrial functions and thermogenesis associated with adipose tissue, suggesting physiological mechanisms that contribute to the adaptation of Snow sheep to sub-arctic environments.

若要预测物种对人为干扰与气候变化的响应，选取对这类因素敏感度高的关键模式物种开展研究是合理的方案。雪羊（Snow sheep）可作为该研究方向的优质候选类群：作为唯一适应西伯利亚东北部寒冷高山生境的大型草食动物，其在生态系统中也发挥着至关重要的作用。尽管雪羊是所有羊属（Ovine）物种中地理分布范围最广的类群之一，但其相关研究却也是最为匮乏的。本研究对6份雪羊基因组进行测序与分析，并结合其他所有野生绵羊物种已公开的32份基因组数据，以此推断雪羊演化历程的关键特征，并揭示其适应亚北极环境的遗传基础。尽管雪羊的普查种群数量庞大，但其基因组展现出极低的杂合度（heterozygosity），这或可反映我们推断的隔离效应与历史瓶颈事件的影响。本研究还发现多例雪羊与盘羊（Argali）、白大角羊（Dall sheep）之间的基因渐渗（introgression）事件，表明这些物种在更新世（Pleistocene）时期的分布范围或比现今更广。事实上，本研究结果显示，在末次间冰期（last interglacials）期间，这些野生绵羊类群的种群数量曾经历剧烈缩减。进一步分析表明，携带基因渐渗片段的区域涵盖了与免疫、脂肪生成（adipogenesis）及形态相关性状相关的基因，这些基因或为适应性基因渐渗的潜在靶点。本研究还在雪羊基因组中鉴定出多个带有选择痕迹的基因，这些基因的功能涉及线粒体功能与脂肪组织相关的产热（thermogenesis）过程，这揭示了雪羊适应亚北极环境的潜在生理机制。