Human and faunal low coverage genomes from 25,000 year old sediment from the Southern Caucasus

Archaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-wide data of mammalian species. We performed shotgun sequencing on sediment DNA from Satsurblia cave, Georgia, dated to 25,000 years ago, and retrieved three low-coverage mammalian genomes from a single soil sample. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. And last, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information.

已有研究证实，考古沉积物能够保存古DNA，但迄今为止尚未从中获取哺乳类物种的全基因组数据。我们对格鲁吉亚萨茨弗利亚洞穴距今25000年的沉积物DNA开展了鸟枪法测序，并从单个土壤样本中获取了3个低覆盖度的哺乳类全基因组。其一为一名女性人类的全基因组，其携带有显著的基底欧亚血统——该血统是近东、北非及欧洲部分地区绝大多数冰河时代后人群的血统组成部分。其二为狼的全基因组，该基因组是现存欧亚狼与家犬的基底类群，代表了一个此前未知、大概率已灭绝的高加索支系，该支系在现代狼与家犬的祖先类群发生分化之前便已与其分道扬镳。其三为野牛的全基因组，该基因组是现存野牛种群的基底类群，这表明自末次盛冰期以来，野牛的种群结构已发生了显著重塑。本研究结果证实，沉积物DNA不仅可用于物种鉴定，还可作为获取全基因组血统信息的来源。