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1. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Author

Thorfinn Sand Korneliussen, Minoru Yoneda, Tsunehiko Hanihara, Takehiro Sato, Nobuo Shigehara, Martin Sikora, Tadayuki Masuyama, Yasuhiro Yamada, Ryosuke Kimura, Tetsuaki Wakebe, Hiroki Shibata, Osamu Kondo, Shigeki Nakagome, Takashi Gakuhari, Hiroki Oota, Kae Koganebuchi, Blánaid Ní Chuinneagáin, Atsushi Toyoda, Simon Rasmussen, Hiromi Shitara, Ryan Schmidt, Eske Willerslev, Toshiyuki Tsurumoto, Morten E. Allentoft, Souichiro Mizushima, Atsushi Tajima, Hajime Ishida, Hiromi Matsumae, Gakuhari, Takashi [0000-0003-1855-8371], Nakagome, Shigeki [0000-0001-9613-975X], Sato, Takehiro [0000-0001-9866-0346], Matsumae, Hiromi [0000-0003-1858-3833], Kondo, Osamu [0000-0001-9729-1446], Kimura, Ryosuke [0000-0003-0100-273X], Ishida, Hajime [0000-0002-5781-7914], Yamada, Yasuhiro [0000-0003-4686-7243], Tajima, Atsushi [0000-0001-6808-5491], Toyoda, Atsushi [0000-0002-0728-7548], Willerslev, Eske [0000-0002-7081-6748], Sikora, Martin [0000-0003-2818-8319], Oota, Hiroki [0000-0003-0746-2729], and Apollo - University of Cambridge Repository

Subjects
OKHOTSK PEOPLE, JAPANESE, Population genetics, Statistics as Topic, Medicine (miscellaneous), Evolutionary biology, 631/208/457, Sequence (geology), 0302 clinical medicine, HISTORY, lcsh:QH301-705.5, 631/208/182, 0303 health sciences, Phylogenetic tree, Human migration, Asia, Eastern, article, Geography, Archaeology, 631/181/19, HUMAN GENETIC DIVERSITY, NONMETRIC CRANIAL VARIATION, General Agricultural and Biological Sciences, NEANDERTHAL, geographic locations, Human Migration, MITOCHONDRIAL-DNA ANALYSIS, AINU, Genomics, General Biochemistry, Genetics and Molecular Biology, Indigenous, Evolutionary genetics, 631/181/27, 03 medical and health sciences, Asian People, Humans, East Asia, DNA, Ancient, 030304 developmental biology, Base Sequence, business.industry, Genome, Human, Sequence Analysis, DNA, TIANYUAN CAVE, lcsh:Biology (General), 631/181/2474, Anthropology, ORIGINS, Biological dispersal, business, Far East, 030217 neurology & neurosurgery
Abstract

Funder: The excavation of the Ikawazu Jomon individual was supported by Grant-in-Aid for Scientific Research (B) (25284157) to YY. The Ikawazu Jomon genome project was organized by HI, and TH & HO who were supported by MEXT KAKENHI Grant Numbers 16H06408 and 17H05132, by Grant-in-Aid for Scientific Research on Innovative Areas (Cultural History of Paleoasia), and by Grant-in-Aid for Challenging Exploratory Research (23657167) and for Scientific Research (B) (17H03738). The Ikawazu Jomon genome sequencing was supported by JSPS KAKENHI Grant Number 16H06279 to ATo, and partly supported in the CHOZEN project in Kanazawa University, and in the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University. Computations for the Ikawazu Jomon genome were partially performed on the NIG supercomputer at ROIS National Institute of Genetics., Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

Published
2020
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2. The prehistoric peopling of Southeast Asia

Author

Hsiao-chun Hung, Tadayuki Masuyama, Christophe Pottier, Farhang Aghakhanian, Thi Minh Tran, Anne-Marie Bacon, Lasse Vinner, Andaine Seguin-Orlando, Laura L. Shackelford, Thi Mai Huong Nguyen, Tsunehiko Hanihara, Anh Nguyen, Hajime Ishida, Ashot Margaryan, Yasuhiro Yamada, Thongsa Sayavongkhamdy, Hiroki Shibata, Constanza de la Fuente Castro, Rasmi Shoocongdej, Eske Willerslev, Silas Anselm Rasmussen, Peter de Barros Damgaard, Patcharee Lertrit, Nobuo Shigehara, Marta Mirazón Lahr, Jean Christophe Galipaud, Jean Luc Ponche, Thomas Higham, Shigeki Nakagome, Sally Wasef, Uffe Gram Wilken, David M. Lambert, Thibaut Devièse, Takashi Gakuhari, Robert Foley, George van Driem, Atsushi Tajima, Ludovic Orlando, Bérénice Bellina-Pryce, Morten E. Allentoft, Charles Higham, Hiroki Oota, J. Víctor Moreno-Mayar, Anna-Sapfo Malaspinas, Huu Nghia Truong, Giang Hai Nguyen, Maude E. Phipps, Fernando Racimo, Rebecca Kinaston, Elise Patole-Edoumba, Supannee Kaewsutthi, Ketut Wiradnyana, Ana Prohaska, Fabrice Demeter, Viengkeo Souksavatdy, Shaiful Shahidan, Hugh McColl, Mokhtar Saidin, Hallie R. Buckley, Thorfinn Sand Korneliussen, Minoru Yoneda, Atsushi Toyoda, Takehiro Sato, Hiromi Matsumae, Philippe Duringer, Martin Sikora, Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Préhistoire et Technologie (PréTech), Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Université Silpakorn, Department of Museums, Historic Buildings and Archaeology, Ministry of Information and Culture, Département des musées et de l'archéologie, Ministère de la Culture et de l?Information, Kyoto University [Kyoto], Dynamique de l'évolution humaine : individus, populations, espèces [Paris] (DEHIPE), Centre National de la Recherche Scientifique (CNRS), Centre de géochimie de la surface (CGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de chimie et procédés pour l'énergie, l'environnement et la santé (ICPEES), Université de Strasbourg (UNISTRA)-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Illinois at Urbana Champaign (UIUC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Museum d'Histoire Naturelle de La Rochelle, Service d'Anatomo-Cyto-Pathologie et de NeuroPathologie [Hôpital de la Timone - APHM] (ACPNP), Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE), Patrimoines Locaux et Gouvernance (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anatomy, University of Otago, Dunedin, University of Otago [Dunedin, Nouvelle-Zélande], École française d'Extrême-Orient (EFEO), Ctr Biol Sequence Anal, Technical University of Denmark [Lyngby] (DTU), Research Laboratory for Archaeology and the History of Art, University of Oxford [Oxford], Institut de Biologia Evolutiva (UPF-CSIC), Max-Planck-Institut für evolutionäre Anthropologie (MPI-EVA), Max-Planck-Gesellschaft, Silpakorn University [Bangkok, Thaïlande], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse et de Mathématiques Appliquées (LAMA), Université Paris-Est Marne-la-Vallée (UPEM)-Fédération de Recherche Bézout-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut national des sciences de l'Univers (INSU - CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Strasbourg (UNISTRA), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Illinois System, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Oxford, Kyoto University, Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), McColl, Hugh [0000-0002-7568-4270], Racimo, Fernando [0000-0002-5025-2607], Demeter, Fabrice [0000-0002-1288-5534], Gakuhari, Takashi [0000-0003-1855-8371], Gram Wilken, Uffe [0000-0003-3434-7312], Seguin-Orlando, Andaine [0000-0002-8265-3229], de la Fuente Castro, Constanza [0000-0002-2857-3615], Wasef, Sally [0000-0002-7207-7395], Sayavongkhamdy, Thongsa [0000-0001-9467-0811], Korneliussen, Thorfinn [0000-0001-7576-5380], Prohaska, Ana [0000-0001-5459-6186], Margaryan, Ashot [0000-0002-2576-2429], Kaewsutthi, Supannee [0000-0002-3959-8420], Lertrit, Patcharee [0000-0002-4801-3834], Hung, Hsiao-Chun [0000-0001-5794-3040], Minh Tran, Thi [0000-0001-8833-693X], Nghia Truong, Huu [0000-0003-3291-5646], Shahidan, Shaiful [0000-0002-8367-3539], Matsumae, Hiromi [0000-0003-1858-3833], Ishida, Hajime [0000-0002-5781-7914], Tajima, Atsushi [0000-0001-6808-5491], Toyoda, Atsushi [0000-0002-0728-7548], Nakagome, Shigeki [0000-0001-9613-975X], Deviese, Thibaut [0000-0003-0495-7398], Duringer, Philippe [0000-0001-6213-5726], Patole-Edoumba, Elise [0000-0002-9378-2202], Bellina-Pryce, Bérénice [0000-0001-8790-1394], Galipaud, Jean-Christophe [0000-0003-3546-5265], Kinaston, Rebecca [0000-0001-7697-4950], Higham, Tom [0000-0002-5949-598X], Foley, Robert A [0000-0003-0479-3039], Lahr, Marta Mirazón [0000-0001-5752-5770], Orlando, Ludovic [0000-0003-3936-1850], Sikora, Martin [0000-0003-2818-8319], Lambert, David M [0000-0002-5821-3637], Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Human Migration, Population, Southeast asian, Indigenous, Prehistory, 03 medical and health sciences, 0302 clinical medicine, Asian People, Humans, East Asia, 14. Life underwater, DNA, Ancient, education, Asia, Southeastern, History, Ancient, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Genome, Human, business.industry, Human migration, Genetic Variation, Sequence Analysis, DNA, Hoabinhian, 030104 developmental biology, Agriculture, Ethnology, [SHS.HIST]Humanities and Social Sciences/History, business, 030217 neurology & neurosurgery
Abstract

Ancient migrations in Southeast AsiaThe past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipsonet 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. McCollet 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

Published
2018
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