Article open access publication

The prehistoric peopling of Southeast Asia

Science, American Association for the Advancement of Science (AAAS), ISSN 0036-8075

Volume 361, 6397, 2018

DOI:10.1126/science.aat3628, Dimensions: pub.1105322464, PMID: 29976827,


Margaryan, Ashot (1) (15)
Duringer, Philippe (30) (31)
Willerslev, Eske (1) (14) (39)



  1. (1) Natural History Museum of Denmark, grid.507616.3
  2. (2) National Museum of Natural History, grid.410350.3
  3. (3) Kanazawa University, grid.9707.9
  4. (4) Kitasato University, grid.410786.c
  5. (5) University of Bern, grid.5734.5
  6. (6) University of New England, grid.1020.3
  7. (7) Paul Sabatier University, grid.15781.3a
  8. (8) Griffith University, grid.1022.1
  9. (9) Silpakorn University, grid.412620.3
  10. (10) Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
  11. (11) Universiti Sains Malaysia, grid.11875.3a
  12. (12) Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
  13. (13) Monash University Malaysia, grid.440425.3
  14. (14) University of Cambridge, grid.5335.0
  15. (15) Institute of Molecular Biology, grid.429238.6
  16. (16) Mahidol University, grid.10223.32
  17. (17) Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
  18. (18) Australian National University, grid.1001.0
  19. (19) Balai Archeology, Medan, Indonesia
  20. (20) Nara National Research Institute for Cultural Properties, grid.471847.9
  21. (21) University of Tokyo, grid.26999.3d
  22. (22) University of the Ryukyus, grid.267625.2
  23. (23) Educational Committee of Tahara City, Tahara, Japan
  24. (24) National Museum of Japanese History, grid.471895.6
  25. (25) Kyushu University, grid.177174.3
  26. (26) National Institute of Genetics, grid.288127.6
  27. (27) Trinity College Dublin, grid.8217.c
  28. (28) University of Oxford, grid.4991.5
  29. (29) University of Paris, grid.508487.6
  30. (30) Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
  31. (31) University of Strasbourg, grid.11843.3f
  32. (32) University of Illinois at Urbana Champaign, grid.35403.31
  33. (33) Natural History Museum of La Rochelle, La Rochelle, France
  34. (34) French National Centre for Scientific Research, grid.4444.0
  35. (35) Max Planck Institute for the Science of Human History, grid.469873.7
  36. (36) University of Otago, grid.29980.3a
  37. (37) École Française d'Extrême-Orient, grid.434187.d
  38. (38) Technical University of Denmark, grid.5170.3, DTU
  39. (39) Wellcome Sanger Institute, grid.10306.34


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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