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Wang CC, Yeh HY, Popov AN, Zhang HQ, Matsumura H, Sirak K, Cheronet O, Kovalev A, Rohland N, Kim AM, Mallick S, Bernardos R, Tumen D, Zhao J, Liu YC, Liu JY, Mah M, Wang K, Zhang Z, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Carlson KSD, Culleton BJ, Eccles L, Freilich S, Keating D, Lawson AM, Mandl K, Michel M, Oppenheimer J, Özdoğan KT, Stewardson K, Wen S, Yan S, Zalzala F, Chuang R, Huang CJ, Looh H, Shiung CC, Nikitin YG, Tabarev AV, Tishkin AA, Lin S, Sun ZY, Wu XM, Yang TL, Hu X, Chen L, Du H, Bayarsaikhan J, Mijiddorj E, Erdenebaatar D, Iderkhangai TO, Myagmar E, Kanzawa-Kiriyama H, Nishino M, Shinoda KI, Shubina OA, Guo J, Cai W, Deng Q, Kang L, Li D, Li D, Lin R, Nini, Shrestha R, Wang LX, Wei L, Xie G, Yao H, Zhang M, He G, Yang X, Hu R, Robbeets M, Schiffels S, Kennett DJ, Jin L, Li H, Krause J, Pinhasi R, Reich D. Genomic insights into the formation of human populations in East Asia. Nature 2021; 591:413-419. [PMID: 33618348 PMCID: PMC7993749 DOI: 10.1038/s41586-021-03336-2] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.
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Affiliation(s)
- Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang, Singapore
| | - Alexander N Popov
- Scientific Museum, Far Eastern Federal University, Vladivostok, Russia
| | - Hu-Qin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | | | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Alexey Kovalev
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Dashtseveg Tumen
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Jing Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yi-Chang Liu
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Jiun-Yu Liu
- Department of Anthropology, University of Washington, Seattle, WA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Richard Chuang
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Jung Huang
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Hana Looh
- Institute of History and Philology, Institute of History and Philology, Academia Sinica, Taipei, Taiwan
| | - Chung-Ching Shiung
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Yuri G Nikitin
- Museum of Archaeology and Ethnology, Institute of History, Archaeology and Ethnology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Andrei V Tabarev
- Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey A Tishkin
- Department of Archeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Song Lin
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhou-Yong Sun
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiao-Ming Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xi Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Liang Chen
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Hua Du
- Xi'an AMS Center, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | | | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia
| | | | | | - Erdene Myagmar
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | | | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Olga A Shubina
- Department of Archeology, Sakhalin Regional Museum, Yuzhno-Sakhalinsk, Russia
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Qiongying Deng
- Department of Human Anatomy and Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China
| | - Dawei Li
- Institute for History and Culture of Science & Technology, Guangxi University for Nationalities, Nanning, China
| | - Dongna Li
- Department of Biology, Hainan Medical University, Haikou, China
| | - Rong Lin
- Department of Biology, Hainan Medical University, Haikou, China
| | - Nini
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China
| | - Rukesh Shrestha
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ling-Xiang Wang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lanhai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guangmao Xie
- College of History, Culture and Tourism, Guangxi Normal University, Guilin, China
- Guangxi Institute of Cultural Relics Protection and Archaeology, Nanning, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, China
| | - Manfei Zhang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Martine Robbeets
- Eurasia3angle Research group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Douglas J Kennett
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A, Suwa G, Ueda S, Yoneda M, Tajima A, Shinoda KI, Inoue I, Saitou N. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet 2016; 62:213-221. [PMID: 27581845 PMCID: PMC5285490 DOI: 10.1038/jhg.2016.110] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon' potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples' genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.
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Affiliation(s)
- Hideaki Kanzawa-Kiriyama
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Timothy A Jinam
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kazuyoshi Hosomichi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Aiko Saso
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Gen Suwa
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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