A High-coverage Ancient Genome for Analyzing Arctic Adaptation Mechanisms – the Steller’s Sea Cow Case

生物如何对气候和环境变化做出反应是一个非常有趣的话题，人们花费了大量的精力来探索不同的适应情景。虽然现存的海牛（儒艮、海牛）是热带和亚热带动物，它们不能在寒冷或凉爽的水中长期生存，但它们灭绝的亲戚，斯特勒海牛（H. gigas）居住在北半球的寒冷水域。有趣的是，所有sirenia动物（包括H. gigas）体内都缺少一种允许非寒颤产热的蛋白质UCP1。巨鳉调节体温的机制尚不清楚。我们建议利用H. gigas的古基因组来研究更新世北极适应的特定特征。分子生物学和测序技术的最新进展使得建立一个古老的DNA文库成为可能，并且已经对H. gigas基因组进行了7.8次测序。为了获得接近的参考基因组，我们将对儒艮基因组进行测序和重新组装。通过对海牛、儒艮和海牛的古基因组进行更深入的测序（30次），我们将能够进行海牛、儒艮和海牛之间的比较分析，揭示海牛物种特异性特征的遗传基础（如体温调节、缺少趾、体型增大、下颌形态）。利用二倍体基因组，我们有足够的信息来模拟人口历史，并测量灭绝的H. gigas对最近的Sirenians的遗传影响，反之亦然。通过对一个物种（其灭绝直接或间接是由浪费的狩猎造成的）的基因组进行测序，并对现存的濒危近亲进行基因组组装，该项目将提高人们对保护资源的认识，这些资源被错误地认为是“无限的”。

How organisms respond to climatic and environmental changes is a topic of considerable interest, and considerable effort is spent to explore different scenarios about adaptation. While extant Sirenians (dugongs, manatees) are tropical and subtropical animals, who cannot survive for long in cold or cool water, their extinct relative, the Steller’s sea cow (H. gigas) inhabited cold waters from the northern hemisphere. Intriguingly, the protein that allows non-shivering heat production, UCP1, is missing in all Sirenians, including H. gigas. The mechanism, how H. gigas regulated its body temperature, is unknown. We propose to use the ancient genome of H. gigas for investigating specific traits of Pleistocene arctic adaptation. Recent advances in molecular biology and sequencing technologies made it possible to build an ancient DNA library and already sequence the H. gigas genome to 7.8 times. To have a close reference genome, we will sequence and de novo assemble the dugong genome. By deeper sequencing the H. gigas ancient genome (30 times), we will be able to perform comparative analyses between sea cow, dugong, and manatee and reveal the genetic basis of species-specific traits in H. gigas (e.g. body temperature regulation, lack of digits, increased body size, jaw morphology). Using the diploid genome, we have enough information to model the demographic history and measure the genetic influence of extinct H. gigas on recent Sirenians or vice versa. By sequencing the genome of a species, whose extinction was directly or indirectly driven by wasteful hunting, and assembling the genome of extant endangered relatives, this project will raise awareness on preserving resources, which are mistakenly perceived as "infinite".