Prehistoric Peopling in Southeast Asia ‒ Genome Analysis of Jōmon and Other Ancient Skeletons
Current evidence suggests that Southeast Asia was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, but the human occupation history of Southeast Asia thereafter with farming economies developed and expanded remains heavily debated. By sequencing 26 ancient human genomes (25 from Southeast Asia, 1 Japanese Jōmon), we show that Southeast Asian history is more complex than previously thought; both Hòabìnhian hunter-gatherers and East Asian farmers with further migrations contributed to current Southeast Asian diversity. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
[Background]
Uncovering the expansion processes of human habitats in the past is of great importance for understanding the origins and establishment of present-day populations and the acquisition of genetic characteristics of individuals as well as for investigating mechanisms of resistance against diseases and pathogens.
Credit: Kanazawa University
In order to cope with these problems, the present international research team, led by researchers from the University of Copenhagen with the participation of three researchers from Kanazawa University has established technologies to efficiently extract human DNA from skeletons discovered at prehistoric remains even under very poor conditions for DNA preservation. At the same time, an international system of research collaboration has been established for objectively evaluating the effects of contamination by present-day human DNA. Thanks to these efforts, the team has uncovered the expansion processes of human habitats and genetic interactions in hot and wet Southeast Asia, which was not possible previously with conventional technologies and research systems (Figure 2).
Worthy of special mention, the present study has been successful in determining the “whole genome” sequence of an individual with typical Jōmon culture, while previous studies were only able to show a very limited “partial genome” sequence of two Jōmon individuals. Thus, the present study is the first successful example to show the possibility of whole genome sequencing of prehistoric individuals in regions like Japan where preservation conditions are quite poor, possibly leading to further major progress in prehistoric genome studies.
[Results]
In the present study, the international research team succeeded in extracting and sequencing DNA from 25 ancient individuals’ skeletons from Southeast Asian remains, where the condition of DNA preservation is very poor, and from one Japanese Jōmon female skeleton. Upon comparison of the genomic data of ancient human skeletons with those of present-day human skeletons, it has become clear that those prehistoric populations in Southeast Asia can be classified into six groups (Figure 3).
Group 1 contains Hòabìnhians from Pha Faen, Laos, hunter-gatherers (~8000 years ago), and prehistoric populations discovered from Gua Cha, Malaysia (~4000 years ago), being genetically close to present-day Önge and Jarawa from the Andaman Islands and Jehai from the Peninsular Malaysia. To our surprise, group 1 has higher genetic affinities with Ikawazu*3) Jōmon individual (Tahara, Aichi), a female adult*4), than other present-day Southeast Asians. In addition, the Ikawazu Jōmon genome*5) is best modelled contributing genetically present-day Japanese.
Model for migration routes into Southeast Asia uncovered by genomic data of prehistoric skeletons.
Credit: Kanazawa University
As above, Neolithic Southeast Asians are found to have been partially genetically influenced by ethnic groups in South China and to have had a genetic connection with populations in Taiwan; Neolithic Southeast Asians are found not to have been indigenous hunter-gatherers passively accepting farming but to have accepted farming gradually in the process of migrations of populations between the continent and islands. Conventional archaeology proposed the two-layer hypothesis that, in those periods, a large population with farming culture with rice and millet migrated into Southeast Asia and that they replaced the indigenous population. Additionally, the present study indicates that the genetic influence from South China with rice farming was only partial and that the migrating population did not replace the indigenous population completely. The present analysis shows that there were at least four big migration waves; migrations of Southeast Asians should be investigated with a new “complex model” framework.
The present study successfully elucidates for the first time the expansion/migration of prehistoric populations by genome analysis of skeletons discovered in Southeast Asia; conventionally, it was thought that such population expansion/migration could only be investigated using archaeological artifacts. An important outcome of the present study is that the same or analogous analyses could be applied to various regions to evaluate the history of population expansion/migration in much more detail and in a more scientific manner.
[Future prospects]
The genomic data obtained from ancient skeletons in Southeast Asia and from a Ikawazu Jōmon individual provides an important basis for investigations on the origins of populations in wider East Asia. The whole genome information of a Jōmon individual will be useful for direct comparison of genomic similarity with ancient East Asians of the corresponding period to Jōmon in present-day Korea, China, Russia and others in the vicinity of the Japanese archipelago. More comparative studies are in progress on populations in wider areas. Note that the whole genome sequence obtained in this study for a Jōmon individual corresponds to the Draft Genome Sequence in the Human Genome Project for the present-day humans. We aim at Complete Genome Sequence with higher accuracy.
This study is an interdisciplinary undertaking combining anthropology and archaeology in a close collaboration, allowing us to establish ourselves at the starting point for research on the origin of Jōmon and its diversity. By more genome analyses of more Jōmon skeletons from different Jōmon sites, genetic diversity of Jōmon populations will be explored over the Japanese archipelago. It is expected through such studies that various interactions among Jōmon groups should be revealed together with migrations of archaeological artifacts such as potteries and stone tools as well as migrations of populations. Based on the outcome of the present study, novel anthropological and archaeological approaches would be further developed.
Contacts and sources:
Kanazawa University
Citation: The prehistoric peopling of Southeast Asia.
Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Takashi Gakuhari, J. Víctor Moreno-Mayar, George van Driem, Uffe Gram Wilken, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Morten E. Allentoft, Takehiro Sato, Anna-Sapfo Malaspinas, Farhang A. Aghakhanian, Thorfinn Korneliussen, Ana Prohaska, Ashot Margaryan, Peter de Barros Damgaard, Supannee Kaewsutthi, Patcharee Lertrit, Thi Mai Huong Nguyen, Hsiao-chun Hung, Thi Minh Tran, Huu Nghia Truong, Giang Hai Nguyen, Shaiful Shahidan, Ketut Wiradnyana, Hiromi Matsumae, Nobuo Shigehara, Minoru Yoneda, Hajime Ishida, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Tsunehiko Hanihara, Shigeki Nakagome, Thibaut Deviese, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Bérénice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham, Robert A. Foley, Marta Mirazón Lahr, Ludovic Orlando, Martin Sikora, Maude E. Phipps, Hiroki Oota, Charles Higham, David M. Lambert, Eske Willerslev. Science, 2018; 361 (6397): 88 DOI: 10.1126/science.aat3628
Source: http://www.ineffableisland.com/2018/08/prehistoric-peopling-in-southeast-asia.html
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