Advance Publication

Anthropological Science

Preface

Preface to the special issue on the Yaponesia Genome Project
Naruya Saitou1,2*
1
Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa 903-0215, Japan2

We started the five-year ‘Yaponesia Genome Project’ in
2018. This project is one of those funded by a MEXT Grantin-Aid for Scientific Research on Innovative Areas. Theproject home page is at http://www.yaponesian.jp/index_e.
php. I am leader of this project. Please also see the introduction of this project reported by the Yaponesian Genome
Project Managing Group (2020) in the new journal iDarwin.
There are six research groups in this project as follows (*indicates the principal investigator of each group). GroupA01—study modern human genomes. Members: Naruya
Saitou*, Ituro Inoue, Koichiro Yoshiura, Timothy A. Jinam,and Masatoshi Matsunami. Group A02—study ancient human genomes. Members: Ken-ichi Shinoda*, Noboru
Adachi, Tsuneo Kakuda, Takehiro Sato, and Hideaki
Kanzawa-Kiriyama. Group A03—study animal and plantgenomes. Members: Hitoshi Suzuki*, Ryuichi Masuda,Takeshi Itoh, and Toshinori Endo. Group B01—study archeological data. Members: Shin’ichiro Fujio*, Naoko Kinoshita,Akira Seike, Yasuhiro Yamada, and Tatsuhiko Hamada.
Group B02—study linguistic data. Members: MitsuakiEndo, Nobuko Kibe, Shigehisa Karimata, Hiroshi Nakagawa,and Shinjiro Kazama. Group B03—study new genome data.
Members: Naoki Osada*, Yosuke Kawai, Akihiko Fujimoto,and Jun Gojobori.
There are also two-year limited research groups A04 andB04 as follows. Group A04 members: Kosuke Hanada,
Kazuyoshi Hosomichi, Tadashi Imanishi, Ryosuke Kimura,
Ken Naito, Kazuhiro Nakayama, Jun Ohashi, Hiroki Oota,
Yoichi Sato, Kazuhiro Satomura, and Yohey Terai. Group
B04 members: Reiko Aso, Kyoko Funahashi, Yuka Hayashi,
Masakado Kawata, Takumi Nishiuchi, and Masami Takenaka.
Professor Hiroki Oota of The University of Tokyo, who isa member of Group A04, is also editor-in-chief of Anthropological Science. He kindly offered to publish a special issueof Anthropological Science on the Yaponesia Genome Project. I thus asked the principal investigators of the six research groups to contribute either a review or an originalinvestigation of their research area to Anthropological Science. Group B01 declined to contribute an article; however,Professor Oota himself contributed one review article to thisissue. Thus, there are six articles, four original investigations

and two reviews, in this special issue as follows.
Two review articles were contributed by Group B03(Osada and Kawai) and by Group A04 (Koganebuchi andOota). Osada and Kawai (2021) reviewed usage of genomewide SNP data for estimating human migrations to Yaponesia. Koganebuchi and Oota (2021) reviewed human paleogenomic studies in East Asia including Yaponesia. Although it
is a review article, Osada and Kawai (2021) found a weak
but significant genetic tie of Jomon people to ancient North
Siberians through meta-analysis of publicly available datasets.
Four original articles were contributed by Groups A01
and B03 (Jinam, Kawai, and Saitou), Group A02 (Adachi,Kanzawa-Kiriyama, Nara, Kakuda, Nishida, and Shinoda),
Group A03 (Suzuki), and Group B02 (Endo).
Jinam et al. (2021b) analyzed three datasets of modern
Yaponesian genomes, and showed that the ‘inner dualstructure’ model of Yaponesia proposed and discussed by
Saitou (2015, 2017), Saitou and Jinam (2017), and Jinam etal. (2021a) is compatible with these datasets.
Adachi et al. (2021) reported the first Jomon genome datafrom the Higashimyo shell midden site, Kyushu, dated c.
8000 years ago. Their principal-components analysis showsthat the genome of Hokkaido Jomon people reported by
Kanzawa-Kiriyama et al. (2019) and that of Kyushu Jomon
reported by Adachi et al. (2021) are very similar, suggesting
striking homogeneity of the Jomon people over a long time.
Suzuki (2021) examined the substitution rates of rodent
mitochondrial DNA (mtDNA), and showed the existence ofa time dependence of those evolutionary rates. Based on thisfinding and using mtDNA data reported by Li et al. (2020),
he suggested there were two waves of mice migration toYaponesia: one by the subspecies M. m. castaneus 3500–
3000 years ago and the other by the subspecies M. m. musculus around 2700 years ago. These two migrations fit pretty
well with the second and third migrations of humans toYaponesia proposed by Saitou (2017).
Endo (2021) examined four kinds of toponyms from aliterature on the history of three kingdoms in the southernpart of the Korean peninsula by Busik et al. (1145). He concluded that Japonic-speaking people still dwelled in thecentral area of the peninsula and in the northern area of theYalu River during the three-kingdom period up to the 7th
century A.D.
I hope these six articles are useful for researchers studying
the origin and developments of Yaponesians.

*  Correspondence to: Naruya Saitou, National Institute of Genetics,Mishima, Shizuoka 411-8540, Japan.
E-mail: saitounr@nig.ac.jp
Published online 31 March 2021
in J-STAGE (www.jstage.jst.go.jp) DOI: 10.1537/ase.210114©  2021 The Anthropological Society of Nippon

12N. SAITOU

Anthropological Science

References
Adachi N., Kanzawa-Kiriyama H., Nara T., Kakuda T., Nishida I.,
and Shinoda K. (2021) Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago. Anthropological Science, DOI: 10.1537/ase.2012132 (in press).
Busik K. et al. (1145) History of the Three Kingdoms (in Chinese).
Endo M. (2021) Geographical distribution of certain toponyms inthe Samguk Sagi. Anthropological Science, DOI: 10.1537/ase.201229 (in press).
Jinam T.A., Kawai Y., Kamatani Y., Sonoda S., Makisumi K., et al.
(2021a) Genome-wide SNP data of Izumo and Makurazaki
populations support inner-dual-structure model for origin ofYamato people. Journal of Human Genetics, published online(https://doi.org/10.1038/s10038-020-00898-3).
Jinam T.A., Kawai Y., and Saitou N. (2021b) Modern human DNA
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