The prehistoric peopling of Southeast Asia

Hugh McColl¹, Fernando Racimo¹, Lasse Vinner¹, Fabrice Demeter^{1

2}, Takashi Gakuhari^{3

4}, J Víctor Moreno-Mayar¹, George van Driem^{5

6}, Uffe Gram Wilken¹, Andaine Seguin-Orlando^{1

7}, Constanza de la Fuente Castro¹, Sally Wasef⁸, Rasmi Shoocongdej⁹, Viengkeo Souksavatdy¹⁰, Thongsa Sayavongkhamdy¹⁰, Mohd Mokhtar Saidin¹¹, Morten E Allentoft¹, Takehiro Sato¹², Anna-Sapfo Malaspinas¹³, Farhang A Aghakhanian¹⁴, Thorfinn Korneliussen¹, Ana Prohaska¹⁵, Ashot Margaryan^{1

16}, Peter de Barros Damgaard¹, Supannee Kaewsutthi¹⁷, Patcharee Lertrit¹⁷, Thi Mai Huong Nguyen¹⁸, Hsiao-Chun Hung¹⁹, Thi Minh Tran¹⁸, Huu Nghia Truong¹⁸, Giang Hai Nguyen¹⁸, Shaiful Shahidan¹¹, Ketut Wiradnyana²⁰, Hiromi Matsumae⁴, Nobuo Shigehara²¹, Minoru Yoneda²², Hajime Ishida²³, Tadayuki Masuyama²⁴, Yasuhiro Yamada²⁵, Atsushi Tajima¹², Hiroki Shibata²⁶, Atsushi Toyoda²⁷, Tsunehiko Hanihara⁴, Shigeki Nakagome²⁸, Thibaut Deviese²⁹, Anne-Marie Bacon³⁰, Philippe Duringer^{31

32}, Jean-Luc Ponche³³, Laura Shackelford³⁴, Elise Patole-Edoumba³⁵, Anh Tuan Nguyen¹⁸, Bérénice Bellina-Pryce³⁶, Jean-Christophe Galipaud³⁷, Rebecca Kinaston^{38

39}, Hallie Buckley³⁸, Christophe Pottier⁴⁰, Simon Rasmussen⁴¹, Tom Higham²⁹, Robert A Foley⁴², Marta Mirazón Lahr⁴², Ludovic Orlando^{1

7}, Martin Sikora¹, Maude E Phipps¹⁴, Hiroki Oota⁴, Charles Higham^{43

44}, David M Lambert⁸, Eske Willerslev^{45

15

46}

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
² National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l'Homme, Paris, France.
³ Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan.
⁴ Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
⁵ Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland.
⁶ University of New England, Armidale, NSW, Australia.
⁷ Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France.
⁸ Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia.
⁹ Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand.
¹⁰ Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People's Democratic Republic.
¹¹ Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia.
¹² Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan.
¹³ Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
¹⁴ Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia.
¹⁵ Department of Zoology, University of Cambridge, Cambridge, UK.
¹⁶ Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.
¹⁷ Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
¹⁸ Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
¹⁹ Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia.
²⁰ Balai Archeology, Medan, Indonesia.
²¹ Nara National Research Institute for Cultural Properties, Nara, Japan.
²² University Museum, University of Tokyo, Tokyo, Japan.
²³ Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan.
²⁴ Educational Committee of Tahara City, Tahara, Japan.
²⁵ National Museum of Japanese History, Sakura, Chiba, Japan.
²⁶ Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
²⁷ Center for Information Biology, National Institute of Genetics, Mishima, Japan.
²⁸ School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland.
²⁹ Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK.
³⁰ Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France.
³¹ École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France.
³² Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France.
³³ Laboratory "Image Ville et Environnement LIVE," UMR7362, CNRS and Université de Strasbourg, Strasbourg, France.
³⁴ Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
³⁵ Natural History Museum of La Rochelle, La Rochelle, France.
³⁶ CNRS, UMR7055 "Préhistoire et Technologie," Maison Archéologie et Ethnologie, Nanterre, France.
³⁷ Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France.
³⁸ Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
³⁹ Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
⁴⁰ École Française d'Extrême-Orient, Paris, France.
⁴¹ Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
⁴² Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK.
⁴³ Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand.
⁴⁴ St. Catharine's College, University of Cambridge, Cambridge, UK.
⁴⁵ Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. ewillerslev@snm.ku.dk.
⁴⁶ Wellcome Trust Sanger Institute, Hinxton, UK.

PMID: 29976827
DOI: 10.1126/science.aat3628

The prehistoric peopling of Southeast Asia

Hugh McColl et al. Science. 2018.

. 2018 Jul 6;361(6397):88-92.

doi: 10.1126/science.aat3628.

Authors

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.
² National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l'Homme, Paris, France.
³ Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan.
⁴ Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
⁵ Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland.
⁶ University of New England, Armidale, NSW, Australia.
⁷ Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France.
⁸ Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia.
⁹ Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand.
¹⁰ Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People's Democratic Republic.
¹¹ Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia.
¹² Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan.
¹³ Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
¹⁴ Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia.
¹⁵ Department of Zoology, University of Cambridge, Cambridge, UK.
¹⁶ Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.
¹⁷ Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
¹⁸ Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam.
¹⁹ Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia.
²⁰ Balai Archeology, Medan, Indonesia.
²¹ Nara National Research Institute for Cultural Properties, Nara, Japan.
²² University Museum, University of Tokyo, Tokyo, Japan.
²³ Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan.
²⁴ Educational Committee of Tahara City, Tahara, Japan.
²⁵ National Museum of Japanese History, Sakura, Chiba, Japan.
²⁶ Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
²⁷ Center for Information Biology, National Institute of Genetics, Mishima, Japan.
²⁸ School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland.
²⁹ Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK.
³⁰ Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France.
³¹ École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France.
³² Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France.
³³ Laboratory "Image Ville et Environnement LIVE," UMR7362, CNRS and Université de Strasbourg, Strasbourg, France.
³⁴ Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
³⁵ Natural History Museum of La Rochelle, La Rochelle, France.
³⁶ CNRS, UMR7055 "Préhistoire et Technologie," Maison Archéologie et Ethnologie, Nanterre, France.
³⁷ Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France.
³⁸ Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
³⁹ Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
⁴⁰ École Française d'Extrême-Orient, Paris, France.
⁴¹ Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
⁴² Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK.
⁴³ Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand.
⁴⁴ St. Catharine's College, University of Cambridge, Cambridge, UK.
⁴⁵ Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark. ewillerslev@snm.ku.dk.
⁴⁶ Wellcome Trust Sanger Institute, Hinxton, UK.

PMID: 29976827
DOI: 10.1126/science.aat3628

Abstract

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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Comment in

The search for ancient DNA heads east.
Bellwood P. Bellwood P. Science. 2018 Jul 6;361(6397):31-32. doi: 10.1126/science.aat8662. Science. 2018. PMID: 29976814 No abstract available.

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The prehistoric peopling of Southeast Asia

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The prehistoric peopling of Southeast Asia

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