Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
Mol Biol Evol. 2023 Oct 4;40(10). doi: 10.1093/molbev/msad205.
The Tibetan Plateau is populated by diverse ethnic groups, but most of them are underrepresented in genomics studies compared with the Tibetans (TIB). Here, to gain further insight into the genetic diversity and evolutionary history of the people living in the Tibetan Plateau, we sequenced 54 whole genomes of the Deng people with high coverage (30-60×) and analyzed the data together with that of TIB and Sherpas, as well as 968 ancient Asian genomes and available archaic and modern human data. We identified 17.74 million novel single-nucleotide variants from the newly sequenced genomes, although the Deng people showed reduced genomic diversity and a relatively small effective population size. Compared with the other Tibetan highlander groups which are highly admixed, the Deng people are dominated by a sole ancestry that could be traced to some ancient northern East Asian populations. The divergence between Deng and Tibetan people (∼4,700-7,200 years) was more recent than that between highlanders and the Han Chinese (Deng-HAN, ∼9,000-14,000 years; TIB-HAN, 7,200-10,000 years). Adaptive genetic variants (AGVs) identified in the Deng are only partially shared with those previously reported in the TIB like HLA-DQB1, whereas others like KLHL12 were not reported in TIB. In contrast, the top candidate genes harboring AGVs as previously identified in TIB, like EPAS1 and EGLN1, do not show strong positive selection signals in Deng. Interestingly, Deng also showed a different archaic introgression scenario from that observed in the TIB. Our results suggest that convergent adaptation might be prevalent on the Tibetan Plateau.
青藏高原上居住着众多民族，但与藏族人（TIB）相比，他们在基因组学研究中的代表性不足。为了深入了解生活在青藏高原上的人群的遗传多样性和进化历史，我们对 54 名邓人进行了高覆盖度（30-60×）的全基因组测序，并将数据与 TIB 和夏尔巴人以及 968 个亚洲古基因组和现有的古人类和现代人类数据进行了分析。我们从新测序的基因组中鉴定出了 1774 万个新的单核苷酸变异，尽管邓人表现出基因组多样性降低和相对较小的有效种群规模。与其他高度混合的藏高原人群相比，邓人主要由一种可以追溯到一些古代东亚人群的单一祖先血统所主导。邓人和藏族人（约 4700-7200 年前）的分化比高海拔人群和汉族人（Deng-HAN，约 9000-14000 年前；TIB-HAN，7200-10000 年前）的分化更为近期。在邓人中发现的适应性遗传变异（AGVs）仅部分与之前在 TIB 中报道的 HLA-DQB1 等基因共享，而其他基因如 KLHL12 则未在 TIB 中报道。相比之下，之前在 TIB 中鉴定出的携带 AGVs 的顶级候选基因，如 EPAS1 和 EGLN1，在邓人中并没有表现出强烈的正选择信号。有趣的是，邓人也表现出与 TIB 中观察到的不同的古人类基因渗入情景。我们的研究结果表明，趋同适应可能在青藏高原上很普遍。
