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The prehistoric peopling of Southeast Asia

Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Takashi Gakuhari, J. Víctor Moreno-Mayar, George van Driem, Uffe Gram Wilken, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Morten E. Allentoft, Takehiro Sato, Anna-Sapfo Malaspinas, Farhang A. Aghakhanian, Thorfinn Korneliussen, Ana Prohaska, Ashot Margaryan, Peter de Barros Damgaard, Supannee Kaewsutthi, Patcharee Lertrit, Thi Mai Huong Nguyen, Hsiao-chun Hung, Thi Minh Tran, Huu Nghia Truong, Giang Hai Nguyen, Shaiful Shahidan, Ketut Wiradnyana, Hiromi Matsumae, Nobuo Shigehara, Minoru Yoneda, Hajime Ishida, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Tsunehiko Hanihara, Shigeki Nakagome, Thibaut Deviese, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Bérénice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham, Robert A. Foley, Marta Mirazón Lahr, Ludovic Orlando, Martin Sikora, Maude E. Phipps, Hiroki Oota, Charles Higham, David M. Lambert, and Eske Willerslev [email protected]Authors Info & Affiliations
6 Jul 2018
Vol 361, Issue 6397
pp. 88-92

Ancient migrations in Southeast Asia

The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations.
Science, this issue p. 92, p. 88; see also p. 31


The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

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Supplementary Material


Supplementary Text
Figs. S1 to S43
Tables S1 to S25
References (27111)


File (aat3628_mccoll_sm.pdf)
Correction (23 August 2018): The names of book editors A. Sanchez-Mazas and L. Sagart were misspelled in references 7 and 25, respectively. These errors have been corrected.

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Volume 361 | Issue 6397
6 July 2018

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We thank the National High-throughput DNA Sequencing Centre (Copenhagen Denmark) for advice and sequencing of samples, the Duckworth laboratory, University of Cambridge, for access to materials, K. Gregersen for making casts of teeth before sampling, and P. Tacon, ARCHE, Griffith University for assistance with sample transfer. E.W. thanks St. John’s College, University of Cambridge, for providing an inspiring environment for scientific thought. Funding: This work was supported by the Lundbeck Foundation, the Danish National Research Foundation, and the KU2016 program. H.Mc. is supported by the University of Adelaide’s George Murray Scholarship. R.S. thanks the Thailand Research Fund (TRF) for support (grants RTA6080001 and RDG55H0006). The excavation of the Jōmon individual was supported by a Grant-in-Aid for Scientific Research (B) (25284157) to Y.Y. The Jōmon genome project was organized by H.I.; as well as T.H. and H.O., who were supported by MEXT KAKENHI grants 16H06408 and 17H05132; and a Grants-in-Aid for Challenging Exploratory Research (23657167) and for Scientific Research (B) (17H03738). The Jōmon genome sequencing was supported by JSPS KAKENHI grant 16H06279 to A.T. and partly supported by the CHOZEN project in Kanazawa University and the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University. Computations for the Jōmon genome were partially performed on the NIG supercomputer at ROIS National Institute of Genetics. M.M.L. is supported by the ERC award 295907. D.M.L. was supported by ARC grants LP120200144, LP150100583, and DP170101313. A.P. is supported by Leverhulme Project Research grant RPG-2016-235. M.E.P. acknowledges the Cardio-Metabolic research cluster at Jeffrey Cheah School of Medicine & Health Sciences, TMB research platform, Monash University Malaysia, and MOSTI Malaysia for research grant 100-RM1/BIOTEK 16/6/2B. A.S.M. was financed by the European Research Council (starting grant) and the Swiss National Science Foundation. Author contributions: E.W. initiated and led the study. E.W., D.M.L., L.V., M.E.A., H.O., M.E.D., A.S.M., L.O., H.Mc., and F.D. designed the study. E.W. and D.M.L. supervised the overall project, and L.V., F.D., F.R., V.S., T.S., M.M.S., R.S., T.M.H.N., C.H., K.W., E.P.E., J.C.G., R.K., H.B., C.P., H.I., T.H., M.E.D., F.A.A., A.S.M., and H.O. supervised specific aspects of the project. H.Mc., L.V., F.D., U.G.W., C.D., M.E.A., V.S., T.S., M.M.S., R.S., S.K., P.L., T.M.H.N., H.C.H., T.M.T., T.H.N., S.S., G.H.N., K.W., N.S., T.M., Y.Y., A.M.B., P.D., J.L.P., L.S., E.P.E., N.A.T., B.B.P., J.C.G., R.K., H.B., M.E.D., F.A.A., and C.P. excavated, curated, sampled, and/or described samples. H.Mc., L.V., T.G., A.S.O., S.W., P.B.D., M.Y., A.Ta., H.S., A.To., S.R., T.D., M.E.D., F.A.A., A.S.M., and T.H. produced data for analysis. H.Mc., F.R., L.V., T.G., J.V.M.M., C.D., T.K, T.S., H.Ma., S.N., S.W., A.M., A.S.M., M.E.D., L.O., and M.S. analyzed or assisted in the analysis of data. H.Mc., F.R., L.V., F.D., T.G., A.M., L.O., M.S., C.H., D.M.L., and E.W. interpreted the results. H.Mc., F.R., L.V., F.D., T.G., H.O., M.M.L., R.A.F., C.H., D.M.L., and E.W. wrote the manuscript with considerable input from J.V.M.M., C.D., S.W., G.V.D., A.P., V.S., T.S., M.M.S., R.S., T.M.H.N., H.C.H., T.H.N., K.W., T.H., S.N., and M.S. All authors discussed the results and contributed to the final manuscript. Competing interests: The authors declare no competing interests. Data and materials availability: This study has been evaluated by the Danish Bioethical Committee (H-16018872) and the Department of Orang Asli Affairs, Malaysia [JHEOA.PP.30.052 Iss.5 (17)]. MoU’s exist with local institutions where the sampling took place. Genomic data are available for download at the ENA (European Nucleotide Archive) with accession number PRJEB26721.



Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Lasse Vinner*
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France.
Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan.
Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
J. Víctor Moreno-Mayar
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
George van Driem
Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland.
University of New England, Armidale, NSW, Australia.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France.
Constanza de la Fuente Castro
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia.
Rasmi Shoocongdej
Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand.
Viengkeo Souksavatdy
Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic.
Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic.
Mohd Mokhtar Saidin
Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia.
Morten E. Allentoft
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Takehiro Sato
Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan.
Anna-Sapfo Malaspinas
Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Farhang A. Aghakhanian
Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Department of Zoology, University of Cambridge, Cambridge, UK.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.
Peter de Barros Damgaard
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
Thi Mai Huong Nguyen
Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia.
Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
Giang Hai Nguyen
Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia.
Ketut Wiradnyana
Balai Archeology, Medan, Indonesia.
Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
Nobuo Shigehara
Nara National Research Institute for Cultural Properties, Nara, Japan.
Minoru Yoneda
University Museum, University of Tokyo, Tokyo, Japan.
Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan.
Tadayuki Masuyama
Educational Committee of Tahara City, Tahara, Japan.
Yasuhiro Yamada
National Museum of Japanese History, Sakura, Chiba, Japan.
Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan.
Hiroki Shibata
Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Center for Information Biology, National Institute of Genetics, Mishima, Japan.
Tsunehiko Hanihara
Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland.
Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK.
Anne-Marie Bacon
Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France.
École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France.
Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France.
Jean-Luc Ponche
Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France.
Laura Shackelford
Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
Natural History Museum of La Rochelle, La Rochelle, France.
Anh Tuan Nguyen
Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
Bérénice Bellina-Pryce
CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France.
Jean-Christophe Galipaud
Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France.
Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
Hallie Buckley
Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
Christophe Pottier
École Française d’Extrême-Orient, Paris, France.
Simon Rasmussen
Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK.
Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK.
Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Maude E. Phipps
Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia.
Hiroki Oota
Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
Charles Higham
Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand.
St. Catharine’s College, University of Cambridge, Cambridge, UK.
Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia.
Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
Department of Zoology, University of Cambridge, Cambridge, UK.
Wellcome Trust Sanger Institute, Hinxton, UK.

Funding Information

Sous-commission des fouilles, French Ministry of Foreign Affairs


These authors contributed equally to this work.
Corresponding author. Email: [email protected]

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