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

Takashi Gakuhari; Shigeki Nakagome; Simon Rasmussen; Morten E. 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; Tadayuki Masuyama; Yasuhiro Yamada; Atsushi Tajima; Hiroki Shibata; Atsushi Toyoda; Toshiyuki Tsurumoto; Tetsuaki Wakebe; Hiromi Shitara; Tsunehiko Hanihara; Eske Willerslev; Martin Sikora; Hiroki Oota

doi:10.1038/s42003-020-01162-2

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

Takashi Gakuhari, Shigeki Nakagome, Simon Rasmussen, Morten E. 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, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki ShibataAtsushi Toyoda, Toshiyuki Tsurumoto, Tetsuaki Wakebe, Hiromi Shitara, Tsunehiko Hanihara, Eske Willerslev, Martin Sikora, Hiroki Oota

Research Center for Transomics Medicine

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

Abstract

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.

Original language	English
Article number	437
Journal	Communications Biology
Volume	3
Issue number	1
DOIs	https://doi.org/10.1038/s42003-020-01162-2
Publication status	Published - Dec 1 2020

All Science Journal Classification (ASJC) codes

Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)

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10.1038/s42003-020-01162-2

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Gakuhari, T., Nakagome, S., Rasmussen, S., Allentoft, M. E., Sato, T., Korneliussen, T., Chuinneagáin, B. N., Matsumae, H., Koganebuchi, K., Schmidt, R., Mizushima, S., Kondo, O., Shigehara, N., Yoneda, M., Kimura, R., Ishida, H., Masuyama, T., Yamada, Y., Tajima, A., ... Oota, H. (2020). Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Communications Biology, 3(1), [437]. https://doi.org/10.1038/s42003-020-01162-2

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. / Gakuhari, Takashi; Nakagome, Shigeki; Rasmussen, Simon; Allentoft, Morten E.; Sato, Takehiro; Korneliussen, Thorfinn; Chuinneagáin, Blánaid Ní; Matsumae, Hiromi; Koganebuchi, Kae; Schmidt, Ryan; Mizushima, Souichiro; Kondo, Osamu; Shigehara, Nobuo; Yoneda, Minoru; Kimura, Ryosuke; Ishida, Hajime; Masuyama, Tadayuki; Yamada, Yasuhiro; Tajima, Atsushi; Shibata, Hiroki; Toyoda, Atsushi; Tsurumoto, Toshiyuki; Wakebe, Tetsuaki; Shitara, Hiromi; Hanihara, Tsunehiko; Willerslev, Eske; Sikora, Martin; Oota, Hiroki.

In: Communications Biology, Vol. 3, No. 1, 437, 01.12.2020.

Research output: Contribution to journal › Article › peer-review

Gakuhari, T, Nakagome, S, Rasmussen, S, Allentoft, ME, Sato, T, Korneliussen, T, Chuinneagáin, BN, Matsumae, H, Koganebuchi, K, Schmidt, R, Mizushima, S, Kondo, O, Shigehara, N, Yoneda, M, Kimura, R, Ishida, H, Masuyama, T, Yamada, Y, Tajima, A, Shibata, H, Toyoda, A, Tsurumoto, T, Wakebe, T, Shitara, H, Hanihara, T, Willerslev, E, Sikora, M & Oota, H 2020, 'Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations', Communications Biology, vol. 3, no. 1, 437. https://doi.org/10.1038/s42003-020-01162-2

Gakuhari, Takashi ; Nakagome, Shigeki ; Rasmussen, Simon ; Allentoft, Morten E. ; Sato, Takehiro ; Korneliussen, Thorfinn ; Chuinneagáin, Blánaid Ní ; Matsumae, Hiromi ; Koganebuchi, Kae ; Schmidt, Ryan ; Mizushima, Souichiro ; Kondo, Osamu ; Shigehara, Nobuo ; Yoneda, Minoru ; Kimura, Ryosuke ; Ishida, Hajime ; Masuyama, Tadayuki ; Yamada, Yasuhiro ; Tajima, Atsushi ; Shibata, Hiroki ; Toyoda, Atsushi ; Tsurumoto, Toshiyuki ; Wakebe, Tetsuaki ; Shitara, Hiromi ; Hanihara, Tsunehiko ; Willerslev, Eske ; Sikora, Martin ; Oota, Hiroki. / Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. In: Communications Biology. 2020 ; Vol. 3, No. 1.

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title = "Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations",

abstract = "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.",

author = "Takashi Gakuhari and Shigeki Nakagome and Simon Rasmussen and Allentoft, {Morten E.} and Takehiro Sato and Thorfinn Korneliussen and Chuinneag{\'a}in, {Bl{\'a}naid N{\'i}} and Hiromi Matsumae and Kae Koganebuchi and Ryan Schmidt and Souichiro Mizushima and Osamu Kondo and Nobuo Shigehara and Minoru Yoneda and Ryosuke Kimura and Hajime Ishida and Tadayuki Masuyama and Yasuhiro Yamada and Atsushi Tajima and Hiroki Shibata and Atsushi Toyoda and Toshiyuki Tsurumoto and Tetsuaki Wakebe and Hiromi Shitara and Tsunehiko Hanihara and Eske Willerslev and Martin Sikora and Hiroki Oota",

note = "Funding Information: The excavation of the Ikawazu Jomon individual was supported by Grant-in-Aid for Scientific Research (B) (25284157) to Y.Y. The Ikawazu Jomon genome project was organized by H.I., and T.H. & H.O. 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 Ika-wazu Jomon genome sequencing was supported by JSPS KAKENHI Grant Number 16H06279 to A.To., 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. Publisher Copyright: {\textcopyright} 2020, The Author(s).",

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AU - Gakuhari, Takashi

AU - Nakagome, Shigeki

AU - Rasmussen, Simon

AU - Allentoft, Morten E.

AU - Sato, Takehiro

AU - Korneliussen, Thorfinn

AU - Chuinneagáin, Blánaid Ní

AU - Matsumae, Hiromi

AU - Koganebuchi, Kae

AU - Schmidt, Ryan

AU - Mizushima, Souichiro

AU - Kondo, Osamu

AU - Shigehara, Nobuo

AU - Yoneda, Minoru

AU - Kimura, Ryosuke

AU - Ishida, Hajime

AU - Masuyama, Tadayuki

AU - Yamada, Yasuhiro

AU - Tajima, Atsushi

AU - Shibata, Hiroki

AU - Toyoda, Atsushi

AU - Tsurumoto, Toshiyuki

AU - Wakebe, Tetsuaki

AU - Shitara, Hiromi

AU - Hanihara, Tsunehiko

AU - Willerslev, Eske

AU - Sikora, Martin

AU - Oota, Hiroki

N1 - Funding Information: The excavation of the Ikawazu Jomon individual was supported by Grant-in-Aid for Scientific Research (B) (25284157) to Y.Y. The Ikawazu Jomon genome project was organized by H.I., and T.H. & H.O. 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 Ika-wazu Jomon genome sequencing was supported by JSPS KAKENHI Grant Number 16H06279 to A.To., 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. Publisher Copyright: © 2020, The Author(s).

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Y1 - 2020/12/1

N2 - 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.

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

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