中国科学院昆明动物研究所宿兵研究组近日取得一项新成果。经过不懈努力，他们研究出东南亚大陆的基因组多样性和自然选择特征。这一研究成果发表在2025年5月14日出版的国际学术期刊《自然》上。

在这里，该团队展示了SEA3K基因组数据集（第一阶段），该数据集由来自30个MSEA人群的3023个个体的深度短读全基因组测序和37个代表性个体的长读全基因组测序生成。研究人员发现了7959万个小变异和96384个结构变异，其中2283万个小变异和24622个结构变异是该数据集独有的。课题组人员观察到MSEA人群的遗传异质性很高，这反映在遗传成分的不同组合上。研究团队确定了44个具有达尔文正选择强特征的基因组区域，涵盖了89个涉及不同生理系统的基因，如身体特征和免疫反应。

此外，研究组观察到古代丹尼索瓦人在MSEA人群中渗入的不同模式，支持了至少两个丹尼索瓦人与亚洲现代人类融合的不同实例的提议。研究人员还检测到在MSEA人群中存在适应性古代基因渗入的基因组区域。MSEA人群中大量新的基因组变异突出了研究区域人群的必要性，这有助于回答与史前、遗传适应和复杂疾病相关的关键问题。

据介绍，东南亚大陆（MSEA）拥有近3亿人口，拥有丰富的民族和文化多样性。然而，来自MSEA的人在目前的人类基因组数据库中代表性不足。

附：英文原文

Title: Genome diversity and signatures of natural selection in mainland Southeast Asia

Author: He, Yaoxi, Zhang, Xiaoming, Peng, Min-Sheng, Li, Yu-Chun, Liu, Kai, Zhang, Yu, Mao, Leyan, Guo, Yongbo, Ma, Yujie, Zhou, Bin, Zheng, Wangshan, Yue, Tian, Liao, Yuwen, Liang, Shen-Ao, Chen, Lu, Zhang, Weijie, Chen, Xiaoning, Tang, Bixia, Yang, Xiaofei, Ye, Kai, Gao, Shenghan, Lu, Yurun, Wang, Yong, Wan, Shijie, Hao, Rushan, Wang, Xuankai, Mao, Yafei, Dai, Shanshan, Gao, Zongliang, Yang, Li-Qin, Guo, Jianxin, Li, Jiangguo, Liu, Chao, Wang, Jianhua, Sovannary, Tuot, Bunnath, Long, Kampuansai, Jatupol, Inta, Angkhana, Srikummool, Metawee, Kutanan, Wibhu, Ho, Huy Quang, Pham, Khoa Dang, Singthong, Sommay, Sochampa, Somphad, Kyaing, U. Win, Pongamornkul, Wittaya, Morlaeku, Chutima, Rattanakrajangsri, Kittisak, Kong, Qing-Peng, Zhang, Ya-Ping, Su, Bing

Issue&Volume: 2025-05-14

Abstract: Mainland Southeast Asia (MSEA) has rich ethnic and cultural diversity with a population of nearly 300 million1,2. However, people from MSEA are underrepresented in the current human genomic databases. Here we present the SEA3K genome dataset (phase I), generated by deep short-read whole-genome sequencing of 3,023 individuals from 30 MSEA populations, and long-read whole-genome sequencing of 37 representative individuals. We identified 79.59 million small variants and 96,384 structural variants, among which 22.83 million small variants and 24,622 structural variants are unique to this dataset. We observed a high genetic heterogeneity across MSEA populations, reflected by the varied combinations of genetic components. We identified 44 genomic regions with strong signatures of Darwinian positive selection, covering 89 genes involved in varied physiological systems such as physical traits and immune response. Furthermore, we observed varied patterns of archaic Denisovan introgression in MSEA populations, supporting the proposal of at least two distinct instances of Denisovan admixture into modern humans in Asia3. We also detected genomic regions that suggest adaptive archaic introgressions in MSEA populations. The large number of novel genomic variants in MSEA populations highlight the necessity of studying regional populations that can help answer key questions related to prehistory, genetic adaptation and complex diseases.

DOI: 10.1038/s41586-025-08998-w

Source: https://www.nature.com/articles/s41586-025-08998-w