Genome diversity and signatures of natural selection in mainland Southeast Asia

Yaoxi He, Xiaoming Zhang, Min-Sheng Peng, Yu-Chun Li, Kai Liu, Yu Zhang, Leyan Mao, Yongbo Guo, Yujie Ma, Bin Zhou, Wangshan Zheng, Tian Yue, Yuwen Liao, Shen-Ao Liang, Lu Chen, Weijie Zhang, Xiaoning Chen, Bixia Tang, Xiaofei Yang, Kai Ye, Shenghan Gao, Yurun Lu, Yong Wang, Shijie Wan, Rushan Hao, Xuankai Wang, Yafei Mao, Shanshan Dai, Zongliang Gao, Li-Qin Yang, Jianxin Guo, Jiangguo Li, Chao Liu, Jianhua Wang, Tuot Sovannary, Long Bunnath, Jatupol Kampuansai, Angkhana Inta, Metawee Srikummool, Wibhu Kutanan, Huy Quang Ho, Khoa Dang Pham, Sommay Singthong, Somphad Sochampa, U. Win Kyaing, Wittaya Pongamornkul, Chutima Morlaeku, Kittisak Rattanakrajangsri, Qing-Peng Kong (), Ya-Ping Zhang () and Bing Su ()
Additional contact information
Yaoxi He: Chinese Academy of Sciences
Xiaoming Zhang: Chinese Academy of Sciences
Min-Sheng Peng: Chinese Academy of Sciences
Yu-Chun Li: Chinese Academy of Sciences
Kai Liu: Chinese Academy of Sciences
Yu Zhang: Chinese Academy of Sciences
Leyan Mao: Chinese Academy of Sciences
Yongbo Guo: Chinese Academy of Sciences
Yujie Ma: Chinese Academy of Sciences
Bin Zhou: Chinese Academy of Sciences
Wangshan Zheng: Chinese Academy of Sciences
Tian Yue: Chinese Academy of Sciences
Yuwen Liao: Chinese Academy of Sciences
Shen-Ao Liang: Fudan University
Lu Chen: Fudan University
Weijie Zhang: Chinese Academy of Sciences
Xiaoning Chen: China National Center for Bioinformation
Bixia Tang: China National Center for Bioinformation
Xiaofei Yang: Xi’an Jiaotong University
Kai Ye: Xi’an Jiaotong University
Shenghan Gao: Xi’an Jiaotong University
Yurun Lu: Chinese Academy of Sciences
Yong Wang: Chinese Academy of Sciences
Shijie Wan: Xi’an Jiaotong University
Rushan Hao: Yunnan University
Xuankai Wang: Shanghai Jiao Tong University
Yafei Mao: Shanghai Jiao Tong University
Shanshan Dai: Chinese Academy of Sciences
Zongliang Gao: Chinese Academy of Sciences
Li-Qin Yang: Chinese Academy of Sciences
Jianxin Guo: Chinese Academy of Sciences
Jiangguo Li: Chinese Academy of Sciences
Chao Liu: the Chinese Academy of Sciences
Jianhua Wang: Yunnan Minzu University
Tuot Sovannary: Royal University of Phnom Penh
Long Bunnath: Royal University of Phnom Penh
Jatupol Kampuansai: Chiang Mai University
Angkhana Inta: Chiang Mai University
Metawee Srikummool: Naresuan University
Wibhu Kutanan: Naresuan University
Huy Quang Ho: Ha Noi Medical University
Khoa Dang Pham: Ha Noi Medical University
Sommay Singthong: National University of Laos (NUOL)
Somphad Sochampa: Muang Sing District Hospital
U. Win Kyaing: Field School of Archaeology
Wittaya Pongamornkul: The Botanical Garden Organization
Chutima Morlaeku: Inter Mountain Peoples Education and Culture in Thailand Association (IMPECT)
Kittisak Rattanakrajangsri: Asia Indigenous Peoples Pact (AIPP)
Qing-Peng Kong: Chinese Academy of Sciences
Ya-Ping Zhang: Chinese Academy of Sciences
Bing Su: Chinese Academy of Sciences

Nature, 2025, vol. 643, issue 8071, 417-426

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41586-025-08998-w

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