Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow

Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis – a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller’s sea cows’ reportedly bark-like skin. Finally, we found that Steller’s sea cows’ abundance was continuously declining for tens of thousands of years prior to their description, implying that environmental changes also contributed to their extinction.

Methods
We extracted ancient DNA from fragmentary remains of 12 Steller’s sea cow individuals recovered from beaches of Bering Island, which we radiocarbon dated to 2205–1155 BP. We sequenced the genomes of two of the best preserved of these (SNMB N51667 from the Braunschweig Natural History Museum and SC16.JK045 from the collection of the Kamchatka Branch of the Pacific Geographical Institute, RAS Museum) to 15.86 and 15.63× coverage, respectively, and the remaining ten to an average coverage of 2.78× (range 1.97–3.95×).

斯特拉海牛（Steller’s sea cow）是一种已灭绝的海牛目（Sirenia）动物，亦是第四纪（Quaternary）体型最大的哺乳动物之一，由格奥尔格·斯特拉（Georg Steller）于1741年首次科学描述，并在后续27年内被人类彻底捕杀灭绝。本研究利用12个个体的古基因组数据，对斯特拉的原始描述进行了补充。研究发现，斯特拉海牛与鲸类存在趋同演化（convergent evolution）现象，但与现生海牛目动物并未出现此类演化特征，提示多个基因在其适应寒冷环境的过程中发挥了关键作用。其中包括脂氧合酶（lipoxygenase）基因的失活，这类基因在人类和小鼠模型中会引发鱼鳞病（ichthyosis）——一种以表皮增厚、过度角质化为特征的皮肤病，其表型与此前报道的斯特拉海牛"树皮状皮肤"特征高度吻合。此外，研究团队发现，斯特拉海牛的种群丰度在其被首次描述前的数万年里便持续下降，这表明环境变化同样参与促成了该物种的灭绝。

研究方法
我们从白令岛海滩出土的12件斯特拉海牛残缺遗骸中提取了古DNA，经放射性碳定年法测定，其年代为2205–1155 BP（距今年代，Before Present）。对其中保存最为完好的2个个体（不伦瑞克自然历史博物馆馆藏的SNMB N51667，以及俄罗斯科学院（Russian Academy of Sciences, RAS）太平洋地理研究所堪察加分馆馆藏的SC16.JK045）进行了全基因组测序，测序深度分别达15.86×和15.63×；剩余10个个体的平均测序深度为2.78×（区间为1.97–3.95×）。