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; Blanaid Ni Chuinneagain; 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, Blanaid Ni Chuinneagain, 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

Section for Geogenetics

Research output: Contribution to journal › Journal article › Research › peer-review

43 Citations (Scopus)

1029 Downloads (Pure)

Abstract

Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.

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
Number of pages	10
ISSN	2399-3642
DOIs	https://doi.org/10.1038/s42003-020-01162-2
Publication status	Published - 2020

Keywords

NONMETRIC CRANIAL VARIATION
MITOCHONDRIAL-DNA ANALYSIS
HUMAN GENETIC DIVERSITY
OKHOTSK PEOPLE
TIANYUAN CAVE
JAPANESE
ORIGINS
HISTORY
AINU
NEANDERTHAL

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Cite this

Gakuhari, T., Nakagome, S., Rasmussen, S., Allentoft, M. E., Sato, T., Korneliussen, T., Chuinneagain, 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; Chuinneagain, Blanaid Ni; 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, 2020.

Research output: Contribution to journal › Journal article › Research › peer-review

Gakuhari, T, Nakagome, S, Rasmussen, S, Allentoft, ME, Sato, T, Korneliussen, T, Chuinneagain, 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 ; Chuinneagain, Blanaid Ni ; 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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abstract = "Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.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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AU - Sato, Takehiro

AU - Korneliussen, Thorfinn

AU - Chuinneagain, Blanaid Ni

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AU - Schmidt, Ryan

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AU - Shigehara, Nobuo

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AU - Kimura, Ryosuke

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AU - Masuyama, Tadayuki

AU - Yamada, Yasuhiro

AU - Tajima, Atsushi

AU - Shibata, Hiroki

AU - Toyoda, Atsushi

AU - Tsurumoto, Toshiyuki

AU - Wakebe, Tetsuaki

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N2 - Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.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.

AB - Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.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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KW - HUMAN GENETIC DIVERSITY

KW - OKHOTSK PEOPLE

KW - TIANYUAN CAVE

KW - JAPANESE

KW - ORIGINS

KW - HISTORY

KW - AINU

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