2
|
Kim J, Mizuno F, Matsushita T, Matsushita M, Aoto S, Ishiya K, Kamio M, Naka I, Hayashi M, Kurosaki K, Ueda S, Ohashi J. Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago. J Hum Genet 2025; 70:47-57. [PMID: 39402381 DOI: 10.1038/s10038-024-01295-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 09/09/2024] [Accepted: 09/09/2024] [Indexed: 01/07/2025]
Abstract
Mainland Japanese have been recognized as having dual ancestry, originating from indigenous Jomon people and immigrants from continental East Eurasia. Although migration from the continent to the Japanese Archipelago continued from the Yayoi to the Kofun period, our understanding of these immigrants, particularly their origins, remains insufficient due to the lack of high-quality genome samples from the Yayoi period, complicating predictions about the admixture process. To address this, we sequenced the whole nuclear genome of a Yayoi individual from the Doigahama site in Yamaguchi prefecture, Japan. A comprehensive population genetic analysis of the Doigahama Yayoi individual, along with ancient and modern populations in East Asia and Northeastern Eurasia, revealed that the Doigahama Yayoi individual, similar to Kofun individuals and modern Mainland Japanese, had three distinct genetic ancestries: Jomon-related, East Asian-related, and Northeastern Siberian-related. Among non-Japanese populations, the Korean population, possessing both East Asian-related and Northeastern Siberian-related ancestries, exhibited the highest degree of genetic similarity to the Doigahama Yayoi individual. The analysis of admixture modeling for Yayoi individuals, Kofun individuals, and modern Japanese respectively supported a two-way admixture model assuming Jomon-related and Korean-related ancestries. These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.
Collapse
Affiliation(s)
- Jonghyun Kim
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, 143-8540, Japan.
| | | | - Masami Matsushita
- The Doigahama Site Anthropological Museum, Yamaguchi, 759-6121, Japan
| | - Saki Aoto
- Medical Genome Center, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Koji Ishiya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Mami Kamio
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, 143-8540, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, 143-8540, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, 143-8540, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| |
Collapse
|
3
|
Sato M, Muto K, Momozawa Y, Joly Y. (Not So) Lost in Translation: Considering the GA4GH Diversity in Datasets Policy in the Japanese Context. Asian Bioeth Rev 2025; 17:59-72. [PMID: 39896083 PMCID: PMC11785831 DOI: 10.1007/s41649-024-00305-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 02/04/2025] Open
Abstract
The genomics community has long acknowledged the lack of diversity in datasets used for research, prompting various stakeholders to confront this issue. In response, the Global Alliance for Genomics and Health (GA4GH) formulated a policy framework that recognizes the multiplicity of perspectives on diversity and proposed a systemic approach for more optimal data diversity. Given the importance of the research context, assessing this policy's applicability within countries where diversity is less discussed is important. This study investigated the feasibility of implementing the GA4GH policy in Japan, a nation with a smaller genetic diversity than many Western countries. As the proportion of East Asian genomic research is limited internationally, focusing on the Japanese genome contributes to enhancing diversity. Meanwhile, labelling findings as "Japanese" can inadvertently reinforce perceptions of homogeneity and overlook ethnic minorities. Regions and socioeconomic status are also recognized as substantial factors of diversity within academia, yet concerns persist among the public regarding the heritability of stigmatized conditions. Social inclusion of sexual minorities has begun in Japan, but research surveys generally still use binary sex and gender categories, which underscores the need for additional variables. This study found that both academia and the public need to confront the overemphasis on homogeneity within Japanese society and hesitancy in addressing genetic factors. By doing so, more inclusive and diverse datasets can advance the field both ethically and scientifically. Perhaps the most important impact of the GA4GH policy will be to draw greater attention to the complex diversity challenges ahead in Japan.
Collapse
Affiliation(s)
- Momoko Sato
- Graduate School of Interdisciplinary Information Studies, The University of Tokyo, Tokyo, Japan
- Center for Integrative Medical Sciences, Laboratory for Biomedical Ethics and Co-design, RIKEN, Yokohama, Japan
| | - Kaori Muto
- Center for Integrative Medical Sciences, Laboratory for Biomedical Ethics and Co-design, RIKEN, Yokohama, Japan
- The Institute of Medical Science, Department of Public Policy, The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Center for Integrative Medical Sciences, Laboratory for Genotyping Development, RIKEN, Yokohama, Japan
| | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| |
Collapse
|
4
|
Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience 2024; 27:110050. [PMID: 38883821 PMCID: PMC11176660 DOI: 10.1016/j.isci.2024.110050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
Collapse
Affiliation(s)
- Niall P. Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
5
|
Liu X, Koyama S, Tomizuka K, Takata S, Ishikawa Y, Ito S, Kosugi S, Suzuki K, Hikino K, Koido M, Koike Y, Horikoshi M, Gakuhari T, Ikegawa S, Matsuda K, Momozawa Y, Ito K, Kamatani Y, Terao C. Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing. SCIENCE ADVANCES 2024; 10:eadi8419. [PMID: 38630824 PMCID: PMC11023554 DOI: 10.1126/sciadv.adi8419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant-based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components. Second, we identified unreported loss-of-function (LoF) variants and observed that for specific genes, LoF variants appeared to be restricted to a more limited set of transcripts than would be expected by chance, with PTPRD as a notable example. Third, we identified 44 archaic segments linked to complex traits, including a Denisovan-derived segment at NKX6-1 associated with type 2 diabetes. Most of these segments are specific to East Asians. Fourth, we identified candidate genetic loci under recent natural selection. Overall, our work provided insights into genetic characteristics of the Japanese population.
Collapse
Affiliation(s)
- Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sadaaki Takata
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Ishikawa
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shuji Ito
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Department of Orthopedic Surgery, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Shunichi Kosugi
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kunihiko Suzuki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinao Koike
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Medical Sciences, Tokyo, Japan
| | - Kochi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| |
Collapse
|