Data from: Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter

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 to the tropical freshwater-living giant otter
(Pteronura brasiliensis) to assess common and divergent genomic trends
between otter species, and to 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 pre-date 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.

尽管海獭（sea otter, Enhydra lutris）近年来才拓展至海洋生境，但其已演化出一系列适配寒冷沿海水域生活的适应性特征，包括肢体形态特化与浓密的保温被毛。这种独特浓密的被毛曾导致海獭在18至20世纪的毛皮贸易中濒临灭绝，并引发了极端的种群瓶颈事件。我们借助南部海獭（E. l. nereis）的从头组装基因组（de novo genome），重构了其演化历史，鉴定了影响水生适应的关键基因，并检测了种群瓶颈的基因组信号。我们将南部海獭的基因组与热带淡水栖居的巨獭（Pteronura brasiliensis）进行比对，以解析水獭物种间共有的与分化的基因组演化趋势；同时与亲缘关系密切的北部海獭（E. l. kenyoni）的基因组对比，以揭示种群水平的演化特征。研究发现，与水生适应相关的基因中存在正选择信号，尤其在肢体发育相关基因中，同时还检测到毛囊发育相关基因的多基因选择特征。我们在海獭与巨獭两个演化支系中均观察到嗅觉受体基因的广泛假基因化现象，这与其他水生哺乳动物的感官基因丢失模式一致。在种群层面，南部海獭与北部海獭均表现出极低的基因组多样性、近期近交的基因组信号，以及以种群衰退为核心的种群历史。此类种群衰退早于毛皮贸易时期，且似乎导致了潜在有害变异的积累，或对海獭未来的种群恢复造成不利影响。