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The prehistoric peopling of Southeast Asia

Hugh McColl https://orcid.org/0000-0002-7568-4270, Fernando Racimo https://orcid.org/0000-0002-5025-2607, Lasse Vinner, Fabrice Demeter https://orcid.org/0000-0002-1288-5534, Takashi Gakuhari https://orcid.org/0000-0003-1855-8371, J. Víctor Moreno-Mayar, George van Driem, Uffe Gram Wilken https://orcid.org/0000-0003-3434-7312, Andaine Seguin-Orlando https://orcid.org/0000-0002-8265-3229, Constanza de la Fuente Castro https://orcid.org/0000-0002-2857-3615, Sally Wasef https://orcid.org/0000-0002-7207-7395, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy https://orcid.org/0000-0001-9467-0811, Mohd Mokhtar Saidin, Morten E. Allentoft, Takehiro Sato, Anna-Sapfo Malaspinas, Farhang A. Aghakhanian, Thorfinn Korneliussen https://orcid.org/0000-0001-7576-5380, Ana Prohaska https://orcid.org/0000-0001-5459-6186, Ashot Margaryan https://orcid.org/0000-0002-2576-2429, Peter de Barros Damgaard, Supannee Kaewsutthi https://orcid.org/0000-0002-3959-8420, Patcharee Lertrit https://orcid.org/0000-0002-4801-3834, Thi Mai Huong Nguyen, Hsiao-chun Hung https://orcid.org/0000-0001-5794-3040, Thi Minh Tran https://orcid.org/0000-0001-8833-693X, Huu Nghia Truong https://orcid.org/0000-0003-3291-5646, Giang Hai Nguyen, Shaiful Shahidan https://orcid.org/0000-0002-8367-3539, Ketut Wiradnyana, Hiromi Matsumae https://orcid.org/0000-0003-1858-3833, Nobuo Shigehara, Minoru Yoneda, Hajime Ishida https://orcid.org/0000-0002-5781-7914, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima https://orcid.org/0000-0001-6808-5491, Hiroki Shibata, Atsushi Toyoda https://orcid.org/0000-0002-0728-7548, Tsunehiko Hanihara, Shigeki Nakagome https://orcid.org/0000-0001-9613-975X, Thibaut Deviese https://orcid.org/0000-0003-0495-7398, Anne-Marie Bacon, Philippe Duringer https://orcid.org/0000-0001-6213-5726, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba https://orcid.org/0000-0002-9378-2202, Anh Tuan Nguyen, Bérénice Bellina-Pryce https://orcid.org/0000-0001-8790-1394, Jean-Christophe Galipaud https://orcid.org/0000-0003-3546-5265, Rebecca Kinaston https://orcid.org/0000-0001-7697-4950, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham https://orcid.org/0000-0002-5949-598X, Robert A. Foley https://orcid.org/0000-0003-0479-3039, Marta Mirazón Lahr https://orcid.org/0000-0001-5752-5770, Ludovic Orlando https://orcid.org/0000-0003-3936-1850, Martin Sikora https://orcid.org/0000-0003-2818-8319, Maude E. Phipps, Hiroki Oota, Charles Higham, David M. Lambert https://orcid.org/0000-0002-5821-3637, and Eske Willerslev https://orcid.org/0000-0002-7081-6748 [email protected]Authors Info & Affiliations
Science
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

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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Supplementary Material

Summary

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

Resources

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.

References and Notes

1
F. Demeter, L. Shackelford, K. Westaway, L. Barnes, P. Duringer, J.-L. Ponche, J. Dumoncel, F. Sénégas, T. Sayavongkhamdy, J.-X. Zhao, P. Sichanthongtip, E. Patole-Edoumba, T. Dunn, A. Zachwieja, Y. Coppens, E. Willerslev, A.-M. Bacon, Early Modern Humans from Tam Pà Ling, Laos: Fossil Review and Perspectives. Curr. Anthropol. 58 (suppl. 17), S527–S538 (2017).
2
K. E. Westaway, J. Louys, R. D. Awe, M. J. Morwood, G. J. Price, J. X. Zhao, M. Aubert, R. Joannes-Boyau, T. M. Smith, M. M. Skinner, T. Compton, R. M. Bailey, G. D. van den Bergh, J. de Vos, A. W. G. Pike, C. Stringer, E. W. Saptomo, Y. Rizal, J. Zaim, W. D. Santoso, A. Trihascaryo, L. Kinsley, B. Sulistyanto, An early modern human presence in Sumatra 73,000-63,000 years ago. Nature 548, 322–325 (2017).
3
X. Ji, K. Kuman, R. J. Clarke, H. Forestier, Y. Li, J. Ma, K. Qiu, H. Li, Y. Wu, The oldest Hoabinhian technocomplex in Asia (43.5 ka) at Xiaodong rockshelter, Yunnan Province, southwest China. Quat. Int. 400, 166–174 (2016).
4
C. Higham, Early Mainland Southeast Asia: From First Humans to Angkor (River Books, 2014).
5
F. Aghakhanian, Y. Yunus, R. Naidu, T. Jinam, A. Manica, B. P. Hoh, M. E. Phipps, Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia. Genome Biol. Evol. 7, 1206–1215 (2015).
6
T. Hanihara, in Bioarchaeology of Southeast Asia, M. O. Oxenham, N. Tayles, Eds. (Cambridge Univ. Press, 2006), pp. 91–111.
7
M. Pietrusewsky, in The Peopling of East Asia: Putting Together Archaeology, Linguistics and Genetics, L. Sagart, R. Blench, A. Sanchez-Mazas, Eds. (Routledge, 2005), pp. 201–229.
8
H. Matsumura, M. Oxenham, in Bioarchaeology of East Asia, K. Pechenkina, M. Oxenham, Eds. (Univ. Press of Florida, 2013), pp. 179–209.
9
T. A. Jinam, M. E. Phipps, F. Aghakhanian, P. P. Majumder, F. Datar, M. Stoneking, H. Sawai, N. Nishida, K. Tokunaga, S. Kawamura, K. Omoto, N. Saitou, Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. Genome Biol. Evol. 9, 2013–2022 (2017).
10
R. D. Harter, “Acid soils of the tropics” (ECHO Technical Note, ECHO 2007).
11
See supplementary text.
12
G. Abraham, M. Inouye, Fast principal component analysis of large-scale genome-wide data. PLOS ONE 9, e93766 (2014).
13
M. A. Abdulla, I. Ahmed, A. Assawamakin, J. Bhak, S. K. Brahmachari, G. C. Calacal, A. Chaurasia, C.-H. Chen, J. Chen, Y.-T. Chen, J. Chu, E. M. C. Cutiongco-de la Paz, M. C. A. De Ungria, F. C. Delfin, J. Edo, S. Fuchareon, H. Ghang, T. Gojobori, J. Han, S.-F. Ho, B. P. Hoh, W. Huang, H. Inoko, P. Jha, T. A. Jinam, L. Jin, J. Jung, D. Kangwanpong, J. Kampuansai, G. C. Kennedy, P. Khurana, H.-L. Kim, K. Kim, S. Kim, W.-Y. Kim, K. Kimm, R. Kimura, T. Koike, S. Kulawonganunchai, V. Kumar, P. S. Lai, J.-Y. Lee, S. Lee, E. T. Liu, P. P. Majumder, K. K. Mandapati, S. Marzuki, W. Mitchell, M. Mukerji, K. Naritomi, C. Ngamphiw, N. Niikawa, N. Nishida, B. Oh, S. Oh, J. Ohashi, A. Oka, R. Ong, C. D. Padilla, P. Palittapongarnpim, H. B. Perdigon, M. E. Phipps, E. Png, Y. Sakaki, J. M. Salvador, Y. Sandraling, V. Scaria, M. Seielstad, M. R. Sidek, A. Sinha, M. Srikummool, H. Sudoyo, S. Sugano, H. Suryadi, Y. Suzuki, K. A. Tabbada, A. Tan, K. Tokunaga, S. Tongsima, L. P. Villamor, E. Wang, Y. Wang, H. Wang, J.-Y. Wu, H. Xiao, S. Xu, J. O. Yang, Y. Y. Shugart, H.-S. Yoo, W. Yuan, G. Zhao, B. A. Zilfalil; HUGO Pan-Asian SNP Consortium; Indian Genome Variation Consortium, Mapping human genetic diversity in Asia. Science 326, 1541–1545 (2009).
14
D. H. Alexander, J. Novembre, K. Lange, Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
15
E. Jørsboe, K. Hanghøj, A. Albrechtsen, fastNGSadmix: Admixture proportions and principal component analysis of a single NGS sample. Bioinformatics 33, 3148–3150 (2017).
16
N. Patterson, P. Moorjani, Y. Luo, S. Mallick, N. Rohland, Y. Zhan, T. Genschoreck, T. Webster, D. Reich, Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
17
M. A. Yang, X. Gao, C. Theunert, H. Tong, A. Aximu-Petri, B. Nickel, M. Slatkin, M. Meyer, S. Pääbo, J. Kelso, Q. Fu, 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. Curr. Biol. 27, 3202–3208.e9 (2017).
18
S. Mallick, H. Li, M. Lipson, I. Mathieson, M. Gymrek, F. Racimo, M. Zhao, N. Chennagiri, S. Nordenfelt, A. Tandon, P. Skoglund, I. Lazaridis, S. Sankararaman, Q. Fu, N. Rohland, G. Renaud, Y. Erlich, T. Willems, C. Gallo, J. P. Spence, Y. S. Song, G. Poletti, F. Balloux, G. van Driem, P. de Knijff, I. G. Romero, A. R. Jha, D. M. Behar, C. M. Bravi, C. Capelli, T. Hervig, A. Moreno-Estrada, O. L. Posukh, E. Balanovska, O. Balanovsky, S. Karachanak-Yankova, H. Sahakyan, D. Toncheva, L. Yepiskoposyan, C. Tyler-Smith, Y. Xue, M. S. Abdullah, A. Ruiz-Linares, C. M. Beall, A. Di Rienzo, C. Jeong, E. B. Starikovskaya, E. Metspalu, J. Parik, R. Villems, B. M. Henn, U. Hodoglugil, R. Mahley, A. Sajantila, G. Stamatoyannopoulos, J. T. S. Wee, R. Khusainova, E. Khusnutdinova, S. Litvinov, G. Ayodo, D. Comas, M. F. Hammer, T. Kivisild, W. Klitz, C. A. Winkler, D. Labuda, M. Bamshad, L. B. Jorde, S. A. Tishkoff, W. S. Watkins, M. Metspalu, S. Dryomov, R. Sukernik, L. Singh, K. Thangaraj, S. Pääbo, J. Kelso, N. Patterson, D. Reich, The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).
19
J. K. Pickrell, J. K. Pritchard, Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genet. 8, e1002967 (2012).
20
G. L. van Driem, in Language Dispersal Beyond Farming, M. Robbeets, A. Savelyev, Eds. (John Benjamins Publishing Company, 2017), pp. 183–214.
21
G. Hudjashov, T. M. Karafet, D. J. Lawson, S. Downey, O. Savina, H. Sudoyo, J. S. Lansing, M. F. Hammer, M. P. Cox, Complex Patterns of Admixture across the Indonesian Archipelago. Mol. Biol. Evol. 34, 2439–2452 (2017).
22
M. Lipson, P.-R. Loh, N. Patterson, P. Moorjani, Y.-C. Ko, M. Stoneking, B. Berger, D. Reich, Reconstructing Austronesian population history in Island Southeast Asia. Nat. Commun. 5, 4689 (2014).
23
T. Simanjuntak, in New Perspectives in Southeast Asian and Pacific Prehistory, P. J. Piper, H. Matsumura, D. Bullock, Eds. (ANU Press, 2017), pp. 201–211.
24
R. A. Blust, The Austronesian Languages (Asia-Pacific Linguistics, Australian National University, 2009).
25
W. Ostapirat, in The Peopling of East Asia: Putting Together Archaeology, Linguistics and Genetics, L. Sagart, R. Blench, A. Sanchez-Mazas, Eds. (Routledge Curzon, 2005), pp. 107–131.
26
R. Shoocondej, Coffin Culture of Thailand in Southeast Asian Context (Charansanitwonge Press, 2017).
27
L. Vinner, T. Mourier, J. Friis-Nielsen, R. Gniadecki, K. Dybkaer, J. Rosenberg, J. L. Langhoff, D. F. S. Cruz, J. Fonager, J. M. G. Izarzugaza, R. Gupta, T. Sicheritz-Ponten, S. Brunak, E. Willerslev, L. P. Nielsen, A. J. Hansen, Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Sci. Rep. 5, 13201 (2015).
28
M. Schubert, S. Lindgreen, L. Orlando, AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).
29
H. Li, R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
30
M. Schubert, L. Ermini, C. Der Sarkissian, H. Jónsson, A. Ginolhac, R. Schaefer, M. D. Martin, R. Fernández, M. Kircher, M. McCue, E. Willerslev, L. Orlando, Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protoc. 9, 1056–1082 (2014).
31
M. Schubert, A. Ginolhac, S. Lindgreen, J. F. Thompson, K. A. S. Al-Rasheid, E. Willerslev, A. Krogh, L. Orlando, Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
32
C. Der Sarkissian, L. Ermini, M. Schubert, M. A. Yang, P. Librado, M. Fumagalli, H. Jónsson, G. K. Bar-Gal, A. Albrechtsen, F. G. Vieira, B. Petersen, A. Ginolhac, A. Seguin-Orlando, K. Magnussen, A. Fages, C. Gamba, B. Lorente-Galdos, S. Polani, C. Steiner, M. Neuditschko, V. Jagannathan, C. Feh, C. L. Greenblatt, A. Ludwig, N. I. Abramson, W. Zimmermann, R. Schafberg, A. Tikhonov, T. Sicheritz-Ponten, E. Willerslev, T. Marques-Bonet, O. A. Ryder, M. McCue, S. Rieder, T. Leeb, M. Slatkin, L. Orlando, Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse. Curr. Biol. 25, 2577–2583 (2015).
33
H. Jónsson, A. Ginolhac, M. Schubert, P. L. F. Johnson, L. Orlando, mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
34
A. W. Briggs, U. Stenzel, P. L. F. Johnson, R. E. Green, J. Kelso, K. Prüfer, M. Meyer, J. Krause, M. T. Ronan, M. Lachmann, S. Pääbo, Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. U.S.A. 104, 14616–14621 (2007).
35
T. Daley, A. D. Smith, Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325–327 (2013).
36
J. Z. Li, D. M. Absher, H. Tang, A. M. Southwick, A. M. Casto, S. Ramachandran, H. M. Cann, G. S. Barsh, M. Feldman, L. L. Cavalli-Sforza, R. M. Myers, Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100–1104 (2008).
37
M. L. Carpenter, J. D. Buenrostro, C. Valdiosera, H. Schroeder, M. E. Allentoft, M. Sikora, M. Rasmussen, S. Gravel, S. Guillén, G. Nekhrizov, K. Leshtakov, D. Dimitrova, N. Theodossiev, D. Pettener, D. Luiselli, K. Sandoval, A. Moreno-Estrada, Y. Li, J. Wang, M. T. P. Gilbert, E. Willerslev, W. J. Greenleaf, C. D. Bustamante, Pulling out the 1%: Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93, 852–864 (2013).
38
D. I. Cruz-Dávalos, B. Llamas, C. Gaunitz, A. Fages, C. Gamba, J. Soubrier, P. Librado, A. Seguin-Orlando, M. Pruvost, A. H. Alfarhan, S. A. Alquraishi, K. A. S. Al-Rasheid, A. Scheu, N. Beneke, A. Ludwig, A. Cooper, E. Willerslev, L. Orlando, Experimental conditions improving in-solution target enrichment for ancient DNA. Mol. Ecol. Resour. 17, 508–522 (2017).
39
J. M. Enk, A. M. Devault, M. Kuch, Y. E. Murgha, J.-M. Rouillard, H. N. Poinar, Ancient whole genome enrichment using baits built from modern DNA. Mol. Biol. Evol. 31, 1292–1294 (2014).
40
J. Dabney, M. Meyer, Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87–94 (2012).
41
Y. Zheng, G. W. Crawford, L. Jiang, X. Chen, Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley. Sci. Rep. 6, 28136 (2016).
42
D. Q. Fuller, L. Qin, Y. Zheng, Z. Zhao, X. Chen, L. A. Hosoya, G.-P. Sun, The domestication process and domestication rate in rice: Spikelet bases from the Lower Yangtze. Science 323, 1607–1610 (2009).
43
Z. Yunfei, S. guoping, Q. ling, L. chunhai, W. xiaohong, C. xugao, Rice fields and modes of rice cultivation between 5000 and 2500 BC in east China. J. Archaeol. Sci. 36, 2609–2616 (2009).
44
K. A. Adelaar, in The Austronesians: Historical and Comparative Perspectives, P. Bellwood, J. J. Fox, D. Tyron, Eds. (Australian National University, 1995).
45
G. L. van Driem, Languages of the Himalayas: An Ethnolinguistic Handbook of the Greater Himalayan Region (BRILL, 2001).
46
R. von Heine-Geldern, Kopfjagd und Menschenopfer in Assam und Birma und ihre Ausstrahlungen nach Vorderindien (Im Selbstverlage der Anthropologischen Gesellschaft, 1917).
47
W. W. Skeat, C. O. Blagden, Pagan Races of the Malay Peninsula (2 vols) (Macmillan and Company, 1906).
48
M. Lipson, P. Skoglund, M. Spriggs, F. Valentin, S. Bedford, R. Shing, H. Buckley, I. Phillip, G. K. Ward, S. Mallick, N. Rohland, N. Broomandkhoshbacht, O. Cheronet, M. Ferry, T. K. Harper, M. Michel, J. Oppenheimer, K. Sirak, K. Stewardson, K. Auckland, A. V. S. Hill, K. Maitland, S. J. Oppenheimer, T. Parks, K. Robson, T. N. Williams, D. J. Kennett, A. J. Mentzer, R. Pinhasi, D. Reich, Population Turnover in Remote Oceania Shortly after Initial Settlement. Curr. Biol. 28, 1157–1165.e7 (2018).
49
P. Skoglund, C. Posth, K. Sirak, M. Spriggs, F. Valentin, S. Bedford, G. R. Clark, C. Reepmeyer, F. Petchey, D. Fernandes, Q. Fu, E. Harney, M. Lipson, S. Mallick, M. Novak, N. Rohland, K. Stewardson, S. Abdullah, M. P. Cox, F. R. Friedlaender, J. S. Friedlaender, T. Kivisild, G. Koki, P. Kusuma, D. A. Merriwether, F.-X. Ricaut, J. T. S. Wee, N. Patterson, J. Krause, R. Pinhasi, D. Reich, Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016).
50
R. Blench, Was there an Austroasiatic Presence in Island Southeast Asia prior to the Austronesian Expansion? Bull. Indo-Pacific Prehist. Assoc. 30, 133–144 (2011).
51
C. Posth, K. Nägele, H. Colleran, F. Valentin, S. Bedford, K. W. Kami, R. Shing, H. Buckley, R. Kinaston, M. Walworth, G. R. Clark, C. Reepmeyer, J. Flexner, T. Maric, J. Moser, J. Gresky, L. Kiko, K. J. Robson, K. Auckland, S. J. Oppenheimer, A. V. S. Hill, A. J. Mentzer, J. Zech, F. Petchey, P. Roberts, C. Jeong, R. D. Gray, J. Krause, A. Powell, Language continuity despite population replacement in Remote Oceania. Nat. Ecol. Evol. 2, 731–740 (2018).
52
N. Tayles, S. E. Halcrow, T. Sayavongkhamdy, V. Souksavatdy, A prehistoric flexed human burial from Pha Phen, Middle Mekong Valley, Laos: Its context in Southeast Asia. Anthropol. Sci. 123, 1–12 (2015).
53
D. Bulbeck, The Gua Cha Burials - Concordance, Chronology, Demography (Duckworth Laboratory, Cambridge Univ., 2001).
54
L. Shackelford, F. Demeter, K. Westaway, P. Duringer, J.-L. Ponche, T. Sayavongkhamdy, J.-X. Zhao, L. Barnes, M. Boyon, P. Sichanthongtip, F. Sénégas, E. Patole-Edoumba, Y. Coppens, J. Dumoncel, A.-M. Bacon, Additional evidence for early modern human morphological diversity in Southeast Asia at Tam Pa Ling, Laos. Quat. Int. 466, 93–106 (2018).
55
H. Matsumura, M. Oxenham, T. Simanjuntak, M. Yamagata, in First Islanders: Prehistory and Human Migration in Island Southeast Asia, P. Bellwood, Ed. (xxxxxxxxxxx, 2017), pp. 98–106.
56
F. Demeter et al., Tam Hang Rockshelter: Preliminary Study of a Prehistoric Site in Northern Laos. Asian Perspect. 48, 291–308 (2009).
57
E. Patole-Edoumba, P. Duringer, P. Richardin, L. Shackelford, A.-M. Bacon, T. Sayavongkhamdy, J.-L. Ponche, F. Demeter, Evolution of the Hoabinhian techno-complex of Tam Hang rock shelter in Northeastern Laos. Archaeological Discovery 3, 140–157 (2015).
58
J. Fromaget, “Les récentes découvertes anthropologiques dans les formations préhistoriques de la chaîne annamitique” (Government Printer, Singapore, 51–59, 1940).
59
T. Devièse, D. Comeskey, J. McCullagh, C. Bronk Ramsey, T. Higham, New protocol for compound-specific radiocarbon analysis of archaeological bones. Rapid Commun. Mass Spectrom. 32, 373–379 (2018).
60
T. Devièse, I. Karavanić, D. Comeskey, C. Kubiak, P. Korlević, M. Hajdinjak, S. Radović, N. Procopio, M. Buckley, S. Pääbo, T. Higham, Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition. Proc. Natl. Acad. Sci. U.S.A. 114, 10606–10611 (2017).
61
K.D. Nguyễn, T.P. Bùi, V.H. Bùi, L.C. Nguyễn, T.H. Trần, T.T. Nguyễn, Khai quật di chỉ mộ táng ở Hòn Hai – Cô Tiên (Hạ Long) (Excavation Hon Hai Co Tien Cemetary site (Ha Long)). Những phát hiện mới khảo cổ học (New Archaeological Discoveries) 155–158 (2005).
62
L. C. Nguyễn, Hai bộ xương người cổ ở Nậm Tun (Lai Châu) (Two skeletons from Nam Tun (Lai Chau)). Khảo cổ học 16, 62–63 (1974).
63
L. C. Nguyễn, H. Võ, Người cổ Nậm Tun (Nam Tun ancient human). Kh?o c? h?c 17, 35–37 (1976).
64
A. Wipatayotin, “Finding common ground,” Bangkok Post (11 February 2018); www.bangkokpost.com/news/special-reports/1410471/finding-common-ground.
65
R. Shoocongdej, in Handbook of East and Southeast Asian Archaeology (Xxxxxxxxxxxx, 2017), pp. 97–109.
66
H.-C. Hung, thesis, Australian National University (2008).
67
H.-C. Hung, in First Islanders, P. Bellwod, Ed. (Routledge, 2017), pp. 232–240.
68
F. Valentin, F. Détroit, M. J. T. Spriggs, S. Bedford, Early Lapita skeletons from Vanuatu show Polynesian craniofacial shape: Implications for Remote Oceanic settlement and Lapita origins. Proc. Natl. Acad. Sci. U.S.A. 113, 292–297 (2016).
69
J.-C. Galipaud, R. Kinaston, S. Halcrow, A. Foster, N. Harris, T. Simanjuntak, J. Javelle, H. Buckley, The Pain Haka burial ground on Flores: Indonesian evidence for a shared Neolithic belief system in Southeast Asia. Antiquity 90, 1505–1521 (2016).
70
K. Wiradnyana, Hoabinhian and Austronesia: The Root of Diversity in the Western Part of Indonesia. Eur. Sci. J. 12, 131–145 (2016).
71
S. Chia, Wood Coffin Burial of Kinabatangan, Sabah (Penerbit USM, 2014).
72
H. B. Hansen, P. B. Damgaard, A. Margaryan, J. Stenderup, N. Lynnerup, E. Willerslev, M. E. Allentoft, Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PLOS ONE 12, e0170940 (2017).
73
M. T. P. Gilbert, H.-J. Bandelt, M. Hofreiter, I. Barnes, Assessing ancient DNA studies. Trends Ecol. Evol. 20, 541–544 (2005).
74
E. Willerslev, A. Cooper, Ancient DNA. Proc. Biol. Sci. 272, 3–16 (2005).
75
P. B. Damgaard, A. Margaryan, H. Schroeder, L. Orlando, E. Willerslev, M. E. Allentoft, Improving access to endogenous DNA in ancient bones and teeth. Sci. Rep. 5, 11184 (2015).
76
M. E. Allentoft, M. Sikora, K.-G. Sjögren, S. Rasmussen, M. Rasmussen, J. Stenderup, P. B. Damgaard, H. Schroeder, T. Ahlström, L. Vinner, A.-S. Malaspinas, A. Margaryan, T. Higham, D. Chivall, N. Lynnerup, L. Harvig, J. Baron, P. Della Casa, P. Dąbrowski, P. R. Duffy, A. V. Ebel, A. Epimakhov, K. Frei, M. Furmanek, T. Gralak, A. Gromov, S. Gronkiewicz, G. Grupe, T. Hajdu, R. Jarysz, V. Khartanovich, A. Khokhlov, V. Kiss, J. Kolář, A. Kriiska, I. Lasak, C. Longhi, G. McGlynn, A. Merkevicius, I. Merkyte, M. Metspalu, R. Mkrtchyan, V. Moiseyev, L. Paja, G. Pálfi, D. Pokutta, Ł. Pospieszny, T. D. Price, L. Saag, M. Sablin, N. Shishlina, V. Smrčka, V. I. Soenov, V. Szeverényi, G. Tóth, S. V. Trifanova, L. Varul, M. Vicze, L. Yepiskoposyan, V. Zhitenev, L. Orlando, T. Sicheritz-Pontén, S. Brunak, R. Nielsen, K. Kristiansen, E. Willerslev, Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).
77
M. Meyer, M. Kircher, Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 10.1101/pdb.prot5448 (2010).
78
G. A. Van der Auwera et al., From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Curr. Protoc. Bioinformatics 11, 11.10.1–11.10.33 (2013).
79
A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, M. A. DePristo, The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
80
M. Raghavan, M. Steinrücken, K. Harris, S. Schiffels, S. Rasmussen, M. DeGiorgio, A. Albrechtsen, C. Valdiosera, M. C. Ávila-Arcos, A.-S. Malaspinas, A. Eriksson, I. Moltke, M. Metspalu, J. R. Homburger, J. Wall, O. E. Cornejo, J. V. Moreno-Mayar, T. S. Korneliussen, T. Pierre, M. Rasmussen, P. F. Campos, P. de Barros Damgaard, M. E. Allentoft, J. Lindo, E. Metspalu, R. Rodríguez-Varela, J. Mansilla, C. Henrickson, A. Seguin-Orlando, H. Malmström, T. Stafford Jr.., S. S. Shringarpure, A. Moreno-Estrada, M. Karmin, K. Tambets, A. Bergström, Y. Xue, V. Warmuth, A. D. Friend, J. Singarayer, P. Valdes, F. Balloux, I. Leboreiro, J. L. Vera, H. Rangel-Villalobos, D. Pettener, D. Luiselli, L. G. Davis, E. Heyer, C. P. E. Zollikofer, M. S. Ponce de León, C. I. Smith, V. Grimes, K.-A. Pike, M. Deal, B. T. Fuller, B. Arriaza, V. Standen, M. F. Luz, F. Ricaut, N. Guidon, L. Osipova, M. I. Voevoda, O. L. Posukh, O. Balanovsky, M. Lavryashina, Y. Bogunov, E. Khusnutdinova, M. Gubina, E. Balanovska, S. Fedorova, S. Litvinov, B. Malyarchuk, M. Derenko, M. J. Mosher, D. Archer, J. Cybulski, B. Petzelt, J. Mitchell, R. Worl, P. J. Norman, P. Parham, B. M. Kemp, T. Kivisild, C. Tyler-Smith, M. S. Sandhu, M. Crawford, R. Villems, D. G. Smith, M. R. Waters, T. Goebel, J. R. Johnson, R. S. Malhi, M. Jakobsson, D. J. Meltzer, A. Manica, R. Durbin, C. D. Bustamante, Y. S. Song, R. Nielsen, E. Willerslev, POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015).
81
M. Sikora, A. Seguin-Orlando, V. C. Sousa, A. Albrechtsen, T. Korneliussen, A. Ko, S. Rasmussen, I. Dupanloup, P. R. Nigst, M. D. Bosch, G. Renaud, M. E. Allentoft, A. Margaryan, S. V. Vasilyev, E. V. Veselovskaya, S. B. Borutskaya, T. Deviese, D. Comeskey, T. Higham, A. Manica, R. Foley, D. J. Meltzer, R. Nielsen, L. Excoffier, M. Mirazon Lahr, L. Orlando, E. Willerslev, Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 659–662 (2017).
82
1000 Genomes Project Consortium, A global reference for human genetic variation. Nature 526, 68–74 (2015).
83
Q. Fu, A. Mittnik, P. L. F. Johnson, K. Bos, M. Lari, R. Bollongino, C. Sun, L. Giemsch, R. Schmitz, J. Burger, A. M. Ronchitelli, F. Martini, R. G. Cremonesi, J. Svoboda, P. Bauer, D. Caramelli, S. Castellano, D. Reich, S. Pääbo, J. Krause, A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).
84
T. S. Korneliussen, A. Albrechtsen, R. Nielsen, ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15, 356 (2014).
85
A. W. Briggs, U. Stenzel, M. Meyer, J. Krause, M. Kircher, S. Pääbo, Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).
86
N. Patterson, A. L. Price, D. Reich, Population structure and eigenanalysis. PLOS Genet. 2, e190 (2006).
87
P. Skoglund, H. Malmström, M. Raghavan, J. Storå, P. Hall, E. Willerslev, M. T. P. Gilbert, A. Götherström, M. Jakobsson, Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012).
88
S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. W. de Bakker, M. J. Daly, P. C. Sham, PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
89
L. Skotte, T. S. Korneliussen, A. Albrechtsen, Estimating individual admixture proportions from next generation sequencing data. Genetics 195, 693–702 (2013).
90
A. A. Behr, K. Z. Liu, G. Liu-Fang, P. Nakka, S. Ramachandran, pong: Fast analysis and visualization of latent clusters in population genetic data. Bioinformatics 32, 2817–2823 (2016).
91
M. Ratliff, Hmong-Mien Language History (Pacific Linguistics, Australian National University, 2010).
92
D. Lawson, L. van Dorp, D. Falush, A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots. bioRxiv 066431 [Preprint]. (28 July 2016).
93
R. E. Green, J. Krause, A. W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M. H. Y. Fritz, N. F. Hansen, E. Y. Durand, A. S. Malaspinas, J. D. Jensen, T. Marques-Bonet, C. Alkan, K. Prüfer, M. Meyer, H. A. Burbano, J. M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Höber, B. Höffner, M. Siegemund, A. Weihmann, C. Nusbaum, E. S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, C. Verna, P. Rudan, D. Brajkovic, Ž. Kucan, I. Gušic, V. B. Doronichev, L. V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R. W. Schmitz, P. L. F. Johnson, E. E. Eichler, D. Falush, E. Birney, J. C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich, S. Pääbo, A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
94
E. Y. Durand, N. Patterson, D. Reich, M. Slatkin, Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).
95
P. Endicott, M. T. P. Gilbert, C. Stringer, C. Lalueza-Fox, E. Willerslev, A. J. Hansen, A. Cooper, The genetic origins of the Andaman Islanders. Am. J. Hum. Genet. 72, 178–184 (2003).
96
C. Jeong, S. Nakagome, A. Di Rienzo, Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu. Genetics 202, 261–272 (2016).
97
N. Rustagi, A. Zhou, W. S. Watkins, E. Gedvilaite, S. Wang, N. Ramesh, D. Muzny, R. A. Gibbs, L. B. Jorde, F. Yu, J. Xing, Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics 18, 396 (2017).
98
A. Basu, N. Sarkar-Roy, P. P. Majumder, Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proc. Natl. Acad. Sci. U.S.A. 113, 1594–1599 (2016).
99
P. Skoglund, S. Mallick, M. C. Bortolini, N. Chennagiri, T. Hünemeier, M. L. Petzl-Erler, F. M. Salzano, N. Patterson, D. Reich, Genetic evidence for two founding populations of the Americas. Nature 525, 104–108 (2015).
100
M. Meyer, M. Kircher, M.-T. Gansauge, H. Li, F. Racimo, S. Mallick, J. G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, P. H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, A. Tandon, M. Siebauer, R. E. Green, K. Bryc, A. W. Briggs, U. Stenzel, J. Dabney, J. Shendure, J. Kitzman, M. F. Hammer, M. V. Shunkov, A. P. Derevianko, N. Patterson, A. M. Andrés, E. E. Eichler, M. Slatkin, D. Reich, J. Kelso, S. Pääbo, A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).
101
A. Seguin-Orlando, T. S. Korneliussen, M. Sikora, A.-S. Malaspinas, A. Manica, I. Moltke, A. Albrechtsen, A. Ko, A. Margaryan, V. Moiseyev, T. Goebel, M. Westaway, D. Lambert, V. Khartanovich, J. D. Wall, P. R. Nigst, R. A. Foley, M. M. Lahr, R. Nielsen, L. Orlando, E. Willerslev, Genomic structure in Europeans dating back at least 36,200 years. Science 346, 1113–1118 (2014).
102
M. Lipson, D. Reich, A working model of the deep relationships of diverse modern human genetic lineages outside of Africa. Mol. Biol. Evol. 34, 889–902 (2017).
103
Chimpanzee Sequencing and Analysis Consortium, Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69–87 (2005).
104
B. Paten, J. Herrero, K. Beal, S. Fitzgerald, E. Birney, Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 18, 1814–1828 (2008).
105
K. Prüfer, F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P. H. Sudmant, C. de Filippo, H. Li, S. Mallick, M. Dannemann, Q. Fu, M. Kircher, M. Kuhlwilm, M. Lachmann, M. Meyer, M. Ongyerth, M. Siebauer, C. Theunert, A. Tandon, P. Moorjani, J. Pickrell, J. C. Mullikin, S. H. Vohr, R. E. Green, I. Hellmann, P. L. F. Johnson, H. Blanche, H. Cann, J. O. Kitzman, J. Shendure, E. E. Eichler, E. S. Lein, T. E. Bakken, L. V. Golovanova, V. B. Doronichev, M. V. Shunkov, A. P. Derevianko, B. Viola, M. Slatkin, D. Reich, J. Kelso, S. Pääbo, The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).
106
D. Reich, N. Patterson, M. Kircher, F. Delfin, M. R. Nandineni, I. Pugach, A. M.-S. Ko, Y.-C. Ko, T. A. Jinam, M. E. Phipps, N. Saitou, A. Wollstein, M. Kayser, S. Pääbo, M. Stoneking, Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011).
107
I. Lazaridis, N. Patterson, A. Mittnik, G. Renaud, S. Mallick, K. Kirsanow, P. H. Sudmant, J. G. Schraiber, S. Castellano, M. Lipson, B. Berger, C. Economou, R. Bollongino, Q. Fu, K. I. Bos, S. Nordenfelt, H. Li, C. de Filippo, K. Prüfer, S. Sawyer, C. Posth, W. Haak, F. Hallgren, E. Fornander, N. Rohland, D. Delsate, M. Francken, J.-M. Guinet, J. Wahl, G. Ayodo, H. A. Babiker, G. Bailliet, E. Balanovska, O. Balanovsky, R. Barrantes, G. Bedoya, H. Ben-Ami, J. Bene, F. Berrada, C. M. Bravi, F. Brisighelli, G. B. J. Busby, F. Cali, M. Churnosov, D. E. C. Cole, D. Corach, L. Damba, G. van Driem, S. Dryomov, J.-M. Dugoujon, S. A. Fedorova, I. Gallego Romero, M. Gubina, M. Hammer, B. M. Henn, T. Hervig, U. Hodoglugil, A. R. Jha, S. Karachanak-Yankova, R. Khusainova, E. Khusnutdinova, R. Kittles, T. Kivisild, W. Klitz, V. Kučinskas, A. Kushniarevich, L. Laredj, S. Litvinov, T. Loukidis, R. W. Mahley, B. Melegh, E. Metspalu, J. Molina, J. Mountain, K. Näkkäläjärvi, D. Nesheva, T. Nyambo, L. Osipova, J. Parik, F. Platonov, O. Posukh, V. Romano, F. Rothhammer, I. Rudan, R. Ruizbakiev, H. Sahakyan, A. Sajantila, A. Salas, E. B. Starikovskaya, A. Tarekegn, D. Toncheva, S. Turdikulova, I. Uktveryte, O. Utevska, R. Vasquez, M. Villena, M. Voevoda, C. A. Winkler, L. Yepiskoposyan, P. Zalloua, T. Zemunik, A. Cooper, C. Capelli, M. G. Thomas, A. Ruiz-Linares, S. A. Tishkoff, L. Singh, K. Thangaraj, R. Villems, D. Comas, R. Sukernik, M. Metspalu, M. Meyer, E. E. Eichler, J. Burger, M. Slatkin, S. Pääbo, J. Kelso, D. Reich, J. Krause, Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).
108
D. Reich, N. Patterson, D. Campbell, A. Tandon, S. Mazieres, N. Ray, M. V. Parra, W. Rojas, C. Duque, N. Mesa, L. F. García, O. Triana, S. Blair, A. Maestre, J. C. Dib, C. M. Bravi, G. Bailliet, D. Corach, T. Hünemeier, M. C. Bortolini, F. M. Salzano, M. L. Petzl-Erler, V. Acuña-Alonzo, C. Aguilar-Salinas, S. Canizales-Quinteros, T. Tusié-Luna, L. Riba, M. Rodríguez-Cruz, M. Lopez-Alarcón, R. Coral-Vazquez, T. Canto-Cetina, I. Silva-Zolezzi, J. C. Fernandez-Lopez, A. V. Contreras, G. Jimenez-Sanchez, M. J. Gómez-Vázquez, J. Molina, A. Carracedo, A. Salas, C. Gallo, G. Poletti, D. B. Witonsky, G. Alkorta-Aranburu, R. I. Sukernik, L. Osipova, S. A. Fedorova, R. Vasquez, M. Villena, C. Moreau, R. Barrantes, D. Pauls, L. Excoffier, G. Bedoya, F. Rothhammer, J.-M. Dugoujon, G. Larrouy, W. Klitz, D. Labuda, J. Kidd, K. Kidd, A. Di Rienzo, N. B. Freimer, A. L. Price, A. Ruiz-Linares, Reconstructing Native American population history. Nature 488, 370–374 (2012).
109
Q. Fu, H. Li, P. Moorjani, F. Jay, S. M. Slepchenko, A. A. Bondarev, P. L. F. Johnson, A. Aximu-Petri, K. Prüfer, C. de Filippo, M. Meyer, N. Zwyns, D. C. Salazar-García, Y. V. Kuzmin, S. G. Keates, P. A. Kosintsev, D. I. Razhev, M. P. Richards, N. V. Peristov, M. Lachmann, K. Douka, T. F. G. Higham, M. Slatkin, J.-J. Hublin, D. Reich, J. Kelso, T. B. Viola, S. Pääbo, Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).
110
M. Raghavan, P. Skoglund, K. E. Graf, M. Metspalu, A. Albrechtsen, I. Moltke, S. Rasmussen, T. W. Stafford Jr.., L. Orlando, E. Metspalu, M. Karmin, K. Tambets, S. Rootsi, R. Mägi, P. F. Campos, E. Balanovska, O. Balanovsky, E. Khusnutdinova, S. Litvinov, L. P. Osipova, S. A. Fedorova, M. I. Voevoda, M. DeGiorgio, T. Sicheritz-Ponten, S. Brunak, S. Demeshchenko, T. Kivisild, R. Villems, R. Nielsen, M. Jakobsson, E. Willerslev, Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).
111
Q. Fu, C. Posth, M. Hajdinjak, M. Petr, S. Mallick, D. Fernandes, A. Furtwängler, W. Haak, M. Meyer, A. Mittnik, B. Nickel, A. Peltzer, N. Rohland, V. Slon, S. Talamo, I. Lazaridis, M. Lipson, I. Mathieson, S. Schiffels, P. Skoglund, A. P. Derevianko, N. Drozdov, V. Slavinsky, A. Tsybankov, R. G. Cremonesi, F. Mallegni, B. Gély, E. Vacca, M. R. G. Morales, L. G. Straus, C. Neugebauer-Maresch, M. Teschler-Nicola, S. Constantin, O. T. Moldovan, S. Benazzi, M. Peresani, D. Coppola, M. Lari, S. Ricci, A. Ronchitelli, F. Valentin, C. Thevenet, K. Wehrberger, D. Grigorescu, H. Rougier, I. Crevecoeur, D. Flas, P. Semal, M. A. Mannino, C. Cupillard, H. Bocherens, N. J. Conard, K. Harvati, V. Moiseyev, D. G. Drucker, J. Svoboda, M. P. Richards, D. Caramelli, R. Pinhasi, J. Kelso, N. Patterson, J. Krause, S. Pääbo, D. Reich, The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).

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Published In

Science
Volume 361 | Issue 6397
6 July 2018

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Received: 21 February 2018
Accepted: 29 May 2018
Published in print: 6 July 2018

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Acknowledgments

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.

Authors

Affiliations

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 https://orcid.org/0000-0002-2857-3615
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 https://orcid.org/0000-0001-8790-1394
CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France.
Jean-Christophe Galipaud https://orcid.org/0000-0003-3546-5265
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

Notes

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

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