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Jomon genome sheds light on East Asian population history

Takashi Gakuhari, Shigeki Nakagome, Simon Rasmussen, Morten Allentoft, Takehiro Sato, Thorfinn Korneliussen, Blánaid Ní Chuinneagáin, Hiromi Matsumae, Kae Koganebuchi, Ryan Schmidt, Souichiro Mizushima, Osamu Kondo, Nobuo Shigehara, Minoru Yoneda, Ryosuke Kimura, Hajime Ishida, Yoshiyuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Toshiyuki Tsurumoto, Tetsuaki Wakebe, Hiromi Shitara, Tsunehiko Hanihara, Eske Willerslev, Martin Sikora, Hiroki Oota
doi: https://doi.org/10.1101/579177
Takashi Gakuhari
Institute for Frontier Science Initiative, Kanazawa University, JapanKitasato University School of Medicine, Japan
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Shigeki Nakagome
School of Medicine, Trinity College Dublin, the University of Dublin, Ireland
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Simon Rasmussen
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Morten Allentoft
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Takehiro Sato
Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Japan
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Thorfinn Korneliussen
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DenmarkDepartment of Archaeology, The University of Tokyo, Japan
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Blánaid Ní Chuinneagáin
School of Medicine, Trinity College Dublin, the University of Dublin, Ireland
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Hiromi Matsumae
Kitasato University School of Medicine, Japan
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Kae Koganebuchi
Kitasato University School of Medicine, Japan
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Ryan Schmidt
Kitasato University School of Medicine, Japan
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Souichiro Mizushima
Department of Anatomy, St. Marianna University School of Medicine, Japan
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Osamu Kondo
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
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Nobuo Shigehara
Nara National Research Institute for Cultural Properties, Japan
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Minoru Yoneda
The University Museum, The University of Tokyo, Japan
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Ryosuke Kimura
Graduate School of Medicine, University of the Ryukyus, Japan
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Hajime Ishida
Graduate School of Medicine, University of the Ryukyus, Japan
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Yoshiyuki Masuyama
Educational Committee of Tahara City, Japan
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Yasuhiro Yamada
National Museum of Japanese History, Japan
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Atsushi Tajima
Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Japan
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Hiroki Shibata
Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Japan
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Atsushi Toyoda
National Institute of Genetics, Japan
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Toshiyuki Tsurumoto
Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Japan
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Tetsuaki Wakebe
Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Japan
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Hiromi Shitara
Department of Archaeology, The University of Tokyo, Japan
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Tsunehiko Hanihara
Kitasato University School of Medicine, Japan
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Eske Willerslev
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DenmarkGeoGenetics Groups, Department of Zoology, University of Cambridge, UKWellcome Trust Sanger Institute, UK
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Martin Sikora
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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  • For correspondence: martin.sikora@snm.ku.dk hiroki_oota@med.kitasato-u.ac.jp
Hiroki Oota
Kitasato University School of Medicine, Japan
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  • For correspondence: martin.sikora@snm.ku.dk hiroki_oota@med.kitasato-u.ac.jp
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Abstract

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

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Posted March 15, 2019.
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Jomon genome sheds light on East Asian population history
Takashi Gakuhari, Shigeki Nakagome, Simon Rasmussen, Morten Allentoft, Takehiro Sato, Thorfinn Korneliussen, Blánaid Ní Chuinneagáin, Hiromi Matsumae, Kae Koganebuchi, Ryan Schmidt, Souichiro Mizushima, Osamu Kondo, Nobuo Shigehara, Minoru Yoneda, Ryosuke Kimura, Hajime Ishida, Yoshiyuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Toshiyuki Tsurumoto, Tetsuaki Wakebe, Hiromi Shitara, Tsunehiko Hanihara, Eske Willerslev, Martin Sikora, Hiroki Oota
bioRxiv 579177; doi: https://doi.org/10.1101/579177
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Jomon genome sheds light on East Asian population history
Takashi Gakuhari, Shigeki Nakagome, Simon Rasmussen, Morten Allentoft, Takehiro Sato, Thorfinn Korneliussen, Blánaid Ní Chuinneagáin, Hiromi Matsumae, Kae Koganebuchi, Ryan Schmidt, Souichiro Mizushima, Osamu Kondo, Nobuo Shigehara, Minoru Yoneda, Ryosuke Kimura, Hajime Ishida, Yoshiyuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Toshiyuki Tsurumoto, Tetsuaki Wakebe, Hiromi Shitara, Tsunehiko Hanihara, Eske Willerslev, Martin Sikora, Hiroki Oota
bioRxiv 579177; doi: https://doi.org/10.1101/579177

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