Hugh McCollFernando RacimoLasse VinnerFabrice DemeterTakashi GakuhariJ. Víctor Moreno-MayarGeorge Van DriemUffe Gram WilkenAndaine Seguin-OrlandoConstanza De la Fuente CastroSally WasefRasmi ShoocongdejViengkeo SouksavatdyThongsa SayavongkhamdyMohd Mokhtar SaidinMorten E. AllentoftTakehiro SatoAnna Sapfo MalaspinasFarhang A. AghakhanianThorfinn KorneliussenAna ProhaskaAshot MargaryanPeter De Barros DamgaardSupannee KaewsutthiPatcharee LertritThi Mai Huong NguyenHsiao chun HungThi Minh TranHuu Nghia TruongGiang Hai NguyenShaiful ShahidanKetut WiradnyanaHiromi MatsumaeNobuo ShigeharaMinoru YonedaHajime IshidaTadayuki MasuyamaYasuhiro YamadaAtsushi TajimaHiroki ShibataAtsushi ToyodaTsunehiko HaniharaShigeki NakagomeThibaut DevieseAnne Marie BaconPhilippe DuringerJean Luc PoncheLaura ShackelfordElise Patole-EdoumbaAnh Tuan NguyenBérénice Bellina-PryceJean Christophe GalipaudRebecca KinastonHallie BuckleyChristophe PottierSimon RasmussenTom HighamRobert A. FoleyMarta Mirazón LahrLudovic OrlandoMartin SikoraMaude E. PhippsHiroki OotaCharles HighamDavid M. LambertEske WillerslevÉcole française d’Extrême-OrientMax Planck Institute for the Science of Human HistoryInstitute of Molecular Biology of the National Academy of Sciences of ArmeniaUniversité de StrasbourgIPGS Institut de Physique du Globe de StrasbourgGriffith UniversityUniversity of CambridgeKøbenhavns UniversitetUniversity of Otago School of Biomedical SciencesUniversite Paris DescartesMuseum National d'Histoire NaturelleUniversity of the RyukyusUniversite Paul Sabatier Toulouse IIIUniversity of OxfordUniversity of TokyoKanazawa UniversityUniversity of BernNational Institute of Genetics MishimaMonash University MalaysiaSilpakorn UniversityUniversity of New England AustraliaUniversity of OtagoNational Institutes for the Humanities National Museum of Japanese HistoryDanmarks Tekniske UniversitetFaculty of Medicine, Siriraj Hospital, Mahidol UniversityTrinity College DublinKyushu UniversityAustralian National UniversityCNRS Centre National de la Recherche ScientifiqueWellcome Sanger InstituteKitasato University School of MedicineUniversiti Sains MalaysiaUniversity of Illinois at Urbana-ChampaignUniversité de Lausanne (UNIL)Balai ArcheologyNatural History Museum of La RochelleEducational Committee of Tahara CityMinistry of Information and CultureInstitute of ArchaeologyNara National Research Institute for Cultural Properties2019-08-282019-08-282018-07-06Science. Vol.361, No.6397 (2018), 88-9210959203003680752-s2.0-85049645767https://repository.li.mahidol.ac.th/handle/20.500.14594/47517© The Authors. 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.Mahidol UniversityMultidisciplinaryArticleSCOPUS10.1126/science.aat3628