Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.

中文翻译：

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水生适应和多样性枯竭：深入研究海獭和巨水獭的基因组。


尽管海獭（EnHydra lutris）最近入侵了海洋领域，但它已经进化出了一系列适应寒冷沿海水域生活的能力，包括肢体变形和浓密的绝缘皮毛。这种独特的致密皮毛导致海獭在 18 至 20 世纪的毛皮贸易期间几近灭绝，并出现了极端的种群瓶颈。我们利用南部海獭（E. l. nereis）的从头基因组来重建其进化历史，识别影响水生适应的基因，并检测种群瓶颈的信号。我们将南方海獭与热带淡水巨水獭（Pteronura brasiliensis）的基因组进行了比较，以评估水獭物种之间共同和不同的基因组趋势，并与密切相关的北方海獭（E. l. kenyoni）进行比较，以揭示种群数量级趋势。我们发现了与水生适应相关的基因的正选择信号，特别是与毛囊发育相关的四肢发育和多基因选择的基因。我们在海獭和巨型水獭谱系中发现了嗅觉受体基因的广泛假基因化，这与其他水生哺乳动物的感觉基因丧失模式一致。在种群水平上，南方海獭和北方海獭表现出极低的基因组多样性、近期近亲繁殖的信号以及以种群下降为标志的人口历史。这些下降可能早于毛皮贸易，并且似乎导致了假定的有害变种的增加，可能影响海獭未来的恢复。