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The prehistoric peopling of Southeast Asia
Hugh McColl1,*, Fernando Racimo1,*, Lasse Vinner1,*, Fabrice Demeter1,2,*, Takashi Gakuhari3,4, J. Víctor Moreno-Mayar1, George van Driem5,6, Uffe Gram Wilken1, Andaine Seguin-Orlando1,7, 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 Margaryan1,16, 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 Duringer31,32, Jean-Luc Ponche33, Laura Shackelford34, Elise Patole-Edoumba35, Anh Tuan Nguyen18, Bérénice Bellina-Pryce36, Jean-Christophe Galipaud37, Rebecca Kinaston38,39, Hallie Buckley38, Christophe Pottier40, Simon Rasmussen41, Tom Higham29, Robert A. Foley42, Marta Mirazón Lahr42, Ludovic Orlando1,7, Martin Sikora1, Maude E. Phipps14, Hiroki Oota4, Charles Higham43,44, David M. Lambert8, Eske Willerslev1,15,45,†
Science 06 Jul 2018:
Vol. 361, Issue 6397, pp. 88-92
DOI: 10.1126/science.aat3628
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.
Anatomically modern humans expanded into Southeast Asia (SEA) at least 65 thousand years (ka) ago (1, 2), leading to the formation of the Hòabìnhian hunter-gatherer tradition first recognized by ~44 ka ago (3, 4). Though Hòabìnhian foragers are considered the ancestors of present-day hunter-gatherers from mainland Southeast Asia (MSEA) (5), the East Asian phenotypic affinities of the majority of present-day Southeast Asian populations suggest that diversity was influenced by later migrations involving rice and millet farmers from the north (4). These observations have generated two competing hypotheses: One states that the Hòabìnhian hunter-gatherers adopted agriculture without substantial external gene flow (6, 7), and the other (the “two-layer” hypothesis) states that farmers from East Asia (EA) replaced the indigenous Hòabìnhian inhabitants ~4 ka ago (8, 9). Studies of present-day populations have not resolved the extent to which migrations from EA affected the genetic makeup of SEA.
Obtaining ancient DNA evidence from SEA is challenging because of poor preservation conditions (10). We thus tested different whole-human-genome capture approaches and found that a modified version of MYbaits Enrichment performed best (11). We applied this method together with standard shotgun sequencing to DNA extracted from human skeletal material from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos, and Japan dating between 0.2 and 8 ka ago (11). We obtained 26 low-coverage ancient whole genomes, including those of a Japanese Ikawazu Jōmon individual and Hòabìnhian hunter-gatherers from Malaysia and Laos, as well as Late Neolithic, Bronze Age, and Iron Age farmers from across SEA (Fig. 1 and table S1) (11). We also sequenced mitochondrial DNA from 16 additional ancient individuals and high-coverage whole genomes from two present-day Jehai individuals from Northern Parak state, West Malaysia (table S3). All samples showed damage patterns typical of ancient DNA and minimal amounts of contamination (table S3) (11).
Fig. 1 Maps of ages and differential ancestry of ancient Southeast Asian genomes.
(A) Estimated mean sample ages for ancient individuals. (B to D) D statistics testing for differential affinity between (B) Papuans and Tiányuán (2240k dataset), (C) Önge and Tiányuán (2240k dataset), and (D) Mlabri and Hàn Chinese (Pan-Asia dataset).
We performed a principal component analysis (PCA) of worldwide present-day populations (12, 13) to find the strongest axes of genetic variation in our data and projected the ancient individuals onto the first two principal components. The two oldest samples—Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.
Fig. 2 Exploratory analyses of relationships of ancient Southeast Asian genomes to those of present-day populations.
Ancient samples are projected on the first two components of PCAs for (A) worldwide populations and (B) a subset of populations from EA and SEA. (C) fastNGSadmix plot at K = 13 (11). We refer to the following present-day language-speaking groups in relation to our ancient samples: Austroasiatic (bright green), Austronesian (pink), and Hmong-Mien (dark pink), along with a broad East Asian component (dark green). P.M., proto-Malay; M.N., Malaysian negrito; P.N., Philippines negrito; And. Is., Andaman Islands; NA, not applicable.
We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different present-day and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X = Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).
D-statistics of the form D(Papuan, Tiányuán; Y, Mbuti), where Y is a test population, are consistent with present-day East Asian populations and most populations of ancient and present-day SEA being more closely related to Tiányuán than to Papuans (Fig. 1) (11, 18). However, this D statistic is not significantly different from 0 for Y = Jehai, Önge, Jarawa or group 1 (the ancient Hòabìnhians) (table S12). D statistics of the form D(Önge, Tiányuán; X, Mbuti), where X is Jarawa, Jehai, or group 1, show that these populations share more ancestry with Önge than with Tiányuán (Fig. 1) (11). Using TreeMix and qpGraph (16, 19) to explore admixture graphs that could potentially fit our data, we find that group 1 individuals are best modeled as a sister group to present-day Önge (Fig. 3, and figs. S21 to S23 and S35 to S37). Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29).
Hugh McColl1,*, Fernando Racimo1,*, Lasse Vinner1,*, Fabrice Demeter1,2,*, Takashi Gakuhari3,4, J. Víctor Moreno-Mayar1, George van Driem5,6, Uffe Gram Wilken1, Andaine Seguin-Orlando1,7, 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 Margaryan1,16, 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 Duringer31,32, Jean-Luc Ponche33, Laura Shackelford34, Elise Patole-Edoumba35, Anh Tuan Nguyen18, Bérénice Bellina-Pryce36, Jean-Christophe Galipaud37, Rebecca Kinaston38,39, Hallie Buckley38, Christophe Pottier40, Simon Rasmussen41, Tom Higham29, Robert A. Foley42, Marta Mirazón Lahr42, Ludovic Orlando1,7, Martin Sikora1, Maude E. Phipps14, Hiroki Oota4, Charles Higham43,44, David M. Lambert8, Eske Willerslev1,15,45,†
Science 06 Jul 2018:
Vol. 361, Issue 6397, pp. 88-92
DOI: 10.1126/science.aat3628
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.
Anatomically modern humans expanded into Southeast Asia (SEA) at least 65 thousand years (ka) ago (1, 2), leading to the formation of the Hòabìnhian hunter-gatherer tradition first recognized by ~44 ka ago (3, 4). Though Hòabìnhian foragers are considered the ancestors of present-day hunter-gatherers from mainland Southeast Asia (MSEA) (5), the East Asian phenotypic affinities of the majority of present-day Southeast Asian populations suggest that diversity was influenced by later migrations involving rice and millet farmers from the north (4). These observations have generated two competing hypotheses: One states that the Hòabìnhian hunter-gatherers adopted agriculture without substantial external gene flow (6, 7), and the other (the “two-layer” hypothesis) states that farmers from East Asia (EA) replaced the indigenous Hòabìnhian inhabitants ~4 ka ago (8, 9). Studies of present-day populations have not resolved the extent to which migrations from EA affected the genetic makeup of SEA.
Obtaining ancient DNA evidence from SEA is challenging because of poor preservation conditions (10). We thus tested different whole-human-genome capture approaches and found that a modified version of MYbaits Enrichment performed best (11). We applied this method together with standard shotgun sequencing to DNA extracted from human skeletal material from Malaysia, Thailand, the Philippines, Vietnam, Indonesia, Laos, and Japan dating between 0.2 and 8 ka ago (11). We obtained 26 low-coverage ancient whole genomes, including those of a Japanese Ikawazu Jōmon individual and Hòabìnhian hunter-gatherers from Malaysia and Laos, as well as Late Neolithic, Bronze Age, and Iron Age farmers from across SEA (Fig. 1 and table S1) (11). We also sequenced mitochondrial DNA from 16 additional ancient individuals and high-coverage whole genomes from two present-day Jehai individuals from Northern Parak state, West Malaysia (table S3). All samples showed damage patterns typical of ancient DNA and minimal amounts of contamination (table S3) (11).
Fig. 1 Maps of ages and differential ancestry of ancient Southeast Asian genomes.
(A) Estimated mean sample ages for ancient individuals. (B to D) D statistics testing for differential affinity between (B) Papuans and Tiányuán (2240k dataset), (C) Önge and Tiányuán (2240k dataset), and (D) Mlabri and Hàn Chinese (Pan-Asia dataset).
We performed a principal component analysis (PCA) of worldwide present-day populations (12, 13) to find the strongest axes of genetic variation in our data and projected the ancient individuals onto the first two principal components. The two oldest samples—Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.
Fig. 2 Exploratory analyses of relationships of ancient Southeast Asian genomes to those of present-day populations.
Ancient samples are projected on the first two components of PCAs for (A) worldwide populations and (B) a subset of populations from EA and SEA. (C) fastNGSadmix plot at K = 13 (11). We refer to the following present-day language-speaking groups in relation to our ancient samples: Austroasiatic (bright green), Austronesian (pink), and Hmong-Mien (dark pink), along with a broad East Asian component (dark green). P.M., proto-Malay; M.N., Malaysian negrito; P.N., Philippines negrito; And. Is., Andaman Islands; NA, not applicable.
We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different present-day and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X = Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).
D-statistics of the form D(Papuan, Tiányuán; Y, Mbuti), where Y is a test population, are consistent with present-day East Asian populations and most populations of ancient and present-day SEA being more closely related to Tiányuán than to Papuans (Fig. 1) (11, 18). However, this D statistic is not significantly different from 0 for Y = Jehai, Önge, Jarawa or group 1 (the ancient Hòabìnhians) (table S12). D statistics of the form D(Önge, Tiányuán; X, Mbuti), where X is Jarawa, Jehai, or group 1, show that these populations share more ancestry with Önge than with Tiányuán (Fig. 1) (11). Using TreeMix and qpGraph (16, 19) to explore admixture graphs that could potentially fit our data, we find that group 1 individuals are best modeled as a sister group to present-day Önge (Fig. 3, and figs. S21 to S23 and S35 to S37). Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29).
