Ancient genomes document multiple waves of migration in Southeast Asian prehistory Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, Michael Pietrusewsky, Thomas Oliver Pryce, Anna Willis, Hirofumi Matsumura, Hallie Buckley, et al. To cite this version: Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, et al.. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science, American Association for the Advancement of Science, 2018, 361 (6397), pp.92 - 95. 10.1126/science.aat3188. cea-01870144 HAL Id: cea-01870144 https://hal-cea.archives-ouvertes.fr/cea-01870144 Submitted on 19 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. RESEARCH HUMAN GENOMICS wide data using in-solution enrichment, yielding sequences from 18 individuals (Table 1 and table S1) (19). Because of poor preservation conditions in tropical environments, we observed both a low Ancient genomes document multiple rate of conversion of screened samples to work- ing data and also limited depth of coverage per waves of migration in Southeast sample, and thus we created multiple libraries per individual (102 in total in our final dataset). Asian prehistory We initially analyzed the data by performing principal component analysis (PCA) using two different sets of present-day populations (19). Mark Lipson1*, Olivia Cheronet2,3,4, Swapan Mallick1,5, Nadin Rohland1, First, compared to a set of diverse non-Africans Marc Oxenham6, Michael Pietrusewsky7, Thomas Oliver Pryce8,9,10, Anna Willis11, (East and Southeast Asians,Australasians,Central Hirofumi Matsumura12, Hallie Buckley13, Kate Domett14, Giang Hai Nguyen15, Americans, and Europeans), the ancient individuals Hoang Hiep Trinh15, Aung Aung Kyaw16, Tin Tin Win16, Baptiste Pradier9, fall close to present-day Chinese and Vietnamese Nasreen Broomandkhoshbacht1,17, Francesca Candilio18,19, Piya Changmai20, 2,3,21 1,17 3,4 1,17 when projected onto the first two axes, with Daniel Fernandes , Matthew Ferry , Beatriz Gamarra , Eadaoin Harney , Man Bac, Ban Chiang, and Vat Komnou shifted 22,23 24 1,17 3,25 Jatupol Kampuansai , Wibhu Kutanan , Megan Michel , Mario Novak , slightly in the direction of Onge (Andaman Islanders) 1,17 3,26 1,17 1 Jonas Oppenheimer , Kendra Sirak , Kristin Stewardson , Zhao Zhang , and Papuan (fig. S1). To focus on East and South- 20,27 2,3 1,5,17 Pavel Flegontov †, Ron Pinhasi *‡, David Reich *‡ east Asian diversity, we then used a panel of 16 present-day populations from the region, with Downloaded from Southeast Asia is home to rich human genetic and linguistic diversity, but the details of three primary directions in the first two dimen- past population movements in the region are not well known. Here, we report genome-wide sions represented by Han Chinese, Austroasiatic- ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic speaking groups (Mlabri and Htin from Thailand, period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac Nicobarese, and Cambodian, but not Kinh), and in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply aboriginal (Austronesian-speaking) Taiwanese diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic [right, left, and top, respectively; Fig. 1B; com- http://science.sciencemag.org/ speakers, with similar ancestry as far south as Indonesia providing evidence for pare (20)]. Man Bac, Ban Chiang (all periods), and an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel Vat Komnou cluster with Austroasiatic speakers, pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day whereas Nui Nap projects close to present-day majority groups, reflecting substantial additional influxes of migrants. Vietnamese and Dai near the center, and Oakaie projects close to present-day Myanmar and other he archaeological record of Southeast Asia people in Southeast Asia (e.g., Thai, Lao, Myanmar, Sino-Tibetan speakers. Present-day Lao are inter- documents a complex history of human oc- Malay) reflect later population movements. How- mediate between Austroasiatic speakers and Dai, cupation, with the first archaic hominins ever, no genetic study has resolved the extent to and western Indonesians (Semende from southern T arriving at least 1.6 million years before the which the spread of agriculture into the region and Sumatra and Barito from southeastern Borneo) present (yr B.P.) and anatomically modern subsequent cultural and technological shifts were fall intermediate between Austroasiatic speakers humans becoming widely established by 50,000 yr achieved by movement of people or ideas. and aboriginal Taiwanese. on November 19, 2019 B.P. (1–3). Particularly profound changes in human Here we analyze samples from five ancient sites We measured levels of allele sharing between culture were propelled by the spread of agricul- (Table 1 and Fig. 1A): Man Bac (Vietnam, Neolithic; populations via outgroup f3-statistics and ob- ture. Rice farming began in the region ~4500 to 4100 to 3600 yr B.P.), Nui Nap (Vietnam, Bronze tained results consistent with those from PCA 4000 yr B.P. and was accompanied by a relatively Age; 2100 to 1900 yr B.P.), Oakaie 1 [Myanmar, (table S2). Nominally, the top sharing for each an- uniform and widespread suite of tools and pottery Late Neolithic/Bronze Age; 3200 to 2700 yr B.P. cient population is provided by another ancient styles displaying connections to southern China (15)], Ban Chiang [Thailand, Late Neolithic population, but this pattern may be an artifact (4–7). It has been hypothesized that this cultural through Iron Age; 3500 to 2400 yr B.P. (16)], due to correlated genotype biases between dif- transition was effected by a migration of people and Vat Komnou [Cambodia, Iron Age; 1900 to ferent ancient samples (table S3). Restricting to who were not closely related to the indigenous 1700 yr B.P. (17)]. We initially screened a total present-day comparisons, Man Bac, Ban Chiang, hunter-gatherers of Southeast Asia (5, 7–10)and of 350 next-generation sequencing libraries gen- and Vat Komnou share the most alleles with who may have spoken Austroasiatic languages, erated from petrous bone samples [specifically Austroasiatic-speaking groups (as Austroasiatic- which today have a wide, but fragmented, distribu- the high-yield cochlear region (18)] from 146 dis- speaking groups do with each other); Nui Nap tion in the region (4, 5, 11–14). In this scenario, the tinct individuals. For libraries with evidence of with Austronesian speakers, Dai, and Kinh; and languages spoken by the majority of present-day authentic ancient DNA, we generated genome- Oakaie with Sino-Tibetan-speaking groups. We 1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. 2Department of Anthropology, University of Vienna, 1090 Vienna, Austria. 3Earth Institute, University College Dublin, Dublin 4, Ireland. 4School of Archaeology, University College Dublin, Dublin 4, Ireland. 5Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. 6School of Archaeology and Anthropology, Australian National University, Canberra, ACT 0200, Australia. 7Department of Anthropology, University of Hawai‘iatMānoa, Honolulu, Hawai‘i 96822, USA. 8Centre National de la Recherche Scientifique, 75016 Paris, France. 9UMR 7055 Préhistoire et Technologie, Université Paris Nanterre, 92023 Nanterre, France. 10CEA/CNRS UMR 3685 NIMBE, 91191 Gif-sur-Yvette, France. 11College of Arts, Society and Education, James Cook University, Townsville, Queensland 4811, Australia. 12School of Health Science, Sapporo Medical University, Sapporo 060-8556, Japan. 13Department of Anatomy, University of Otago, Dunedin 9054, New Zealand. 14Division of Tropical Health and Medicine, College of Medicine and Dentistry, James Cook University, Townsville, Queensland 4811, Australia. 15Department of Prehistoric Archaeology, Vietnam Institute of Archaeology, Hanoi, Vietnam. 16Department of Archaeology, Ministry of Religious Affairs and Culture, Mandalay, Myanmar. 17Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. 18Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e per le Province di Oristano e Sud Sardegna, 09124 Cagliari, Italy. 19Physical Anthropology Section, University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA. 20Department of Biology and Ecology, Faculty of Science, University of Ostrava, 70103 Ostrava, Czech Republic. 21CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal. 22Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand. 23Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand. 24Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand. 25Institute for