J Syst Evol ›› 2023, Vol. 61 ›› Issue (1): 179-197.DOI: 10.1111/jse.12826

• Research Articles • Previous Articles     Next Articles

Northern gene flow into southeastern East Asians inferred from genome-wide array genotyping

Guang‐Lin He1,2,3†*, Ying‐Xiang Li1,2†, Xing Zou4†, Hui‐Yuan Yeh3, Ren‐Kuan Tang5, Pei‐Xin Wang6, Jing‐Ya Bai7,8, Xiao‐Min Yang1,2, Zheng Wang4, Jian‐Xin Guo1,2, Jin‐Wen Chen1,2, Jing Chen9, Mei‐Qing Yang9, Jing Zhao1,2, Jin Sun1,2, Kong‐Yang Zhu1,2, Hao Ma1,2, Rui Wang1,2, Wen‐Jiao Yang1,2, Rong Hu1,2, Lan‐Hai Wei1,2, Yi‐Ping Hou4, Meng‐Ge Wang10,11*, Gang Chen12*, and Chuan‐Chao Wang1,2,13*   

  1. 1 State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen 361005, China
    2 Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
    3 School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore
    4 Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610065, China
    5 Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
    6 College of Medical Information, Chongqing Medical University, Chongqing 400331, China
    7 Department of Medicine, Northwest Minzu University, Lanzhou 730000, China
    8 Key Laboratory for Physique and Health of the Minorities, Northwest Minzu University, Lanzhou 730000, China
    9 Department of Forensic Medicine, Guizhou Medical University, Guiyang 550025, China
    10Guangzhou Forensic Science Institute, Guangzhou 510080, China
    11Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat‐sen University, Guangzhou 510080, China
    12Hunan Key Laboratory of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410075, China
    13State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China

    These authors contributed equally to this work and should be considered co‐first authors.
    * Authors for correspondence. Guang‐Lin He. E‐mail: guanglinhescu@163.com; Meng‐Ge Wang. E‐mail: menggewang2021@163.com; Gang Chen. E‐mail: chengangcs@gmail.com; Chuan‐Chao Wang. E‐mail: wang@xmu.edu.cn
  • Received:2020-12-31 Accepted:2021-12-03 Online:2022-01-07 Published:2023-01-01


The population history of Southeast (SE) China remains poorly understood due to the sparse sampling of present-day populations and limited modeling with ancient genomic data. We report genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien (HM)-speaking She people from Fujian and Taiwan Island, SE China. We coanalyzed 66 Early Neolithic to Iron Age ancient Fujian and Taiwan Island individuals obtained from previously published works to explore the genetic continuity and admixture based on patterns of genetic variations of the high-resolution time transect. We found the genetic differentiation between northern and southern East Asians was defined by a north–south East Asian genetic cline and our studied southern East Asians were clustered in the southern end of this cline. The southeastern coastal modern East Asians are genetically similar to other southern indigenous groups as well as geographically close to Neolithic-to-Iron Age populations, but they also shared excess alleles with post-Neolithic Yellow River ancients, which suggested a southward gene flow on the modern southern coastal gene pool. In addition, we identified one new HM genetic cline in East Asia with the coastal Fujian HM-speaking She localizing at the intersection between HM and Han clines. She people show stronger genetic affinity with southern East Asian indigenous populations, with the main ancestry deriving from groups related to southeastern ancient indigenous rice farmers. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Our estimated north–south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze Age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in SE Asia.

Key words: ancient DNA, genetic diversity, genome‐wide data, population genomics, population transformation