Abstract
The demographic history of the Japanese archipelago was shaped by major episodes of migration and admixture, most notably the transition approximately 3,000 years ago from the Jomon period, a long-established hunter-gatherer tradition, to the Yayoi period, when migrants from the Eurasian continent introduced agriculture and new technologies. However, the timing, extent, and regional variability of the admixture between continental migrants and indigenous Jomon populations remain poorly understood. Northwestern Kyushu has drawn particular attention because skeletal analyses have indicated that Yayoi individuals from this region retain Jomon-like morphological features. However, their genetic background remains unclear. Here, we report whole genome sequences from four Northwestern Kyushu Yayoi individuals excavated from Nagasaki Prefecture, Japan. The two individuals retained nearly full Jomon ancestry, demonstrating that unadmixed Jomon descendants persisted alongside the admixed populations until the transitional phase between the Early and Middle Yayoi periods. The other two individuals showed clear evidence of an admixture, and genetic analyses indicated that gene flow between migrants and the indigenous Jomon population had already begun in this region approximately 2.5–2.6 kya. These findings suggest that the admixture in northwestern Kyushu occurred gradually rather than through a single large-scale migration event at the onset of the Yayoi period, offering new insights into the complex demographic dynamics that shaped the genetic landscape of ancient Japan.
Data availability
The fastq-format raw sequencing reads and BAM-format genome files of Shomura, Neshiko 11, Neshiko 13, and Neshiko 16 were deposited in the DDBJ Sequence Read Archive under the BioProject accession number PRJDB35646 (https://ddbj.nig.ac.jp/resource/bioproject/PRJDB35646).
References
Habu, J. Ancient Jomon of Japan (Cambridge Univ. Press, 2004).
Kanzawa-Kiriyama, H. et al. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J. Hum. Genet. 62, 213–221 (2017).
Kanzawa-Kiriyama, H. et al. Late Jomon male and female genome sequences from the funadomari site in Hokkaido. Japan Anthropol Sci. 127, 83–108 (2019).
Gakuhari, T. et al. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Commun. Biol. 3, 437 (2020).
Crema, E. R., Stevens, C. J. & Shoda, S. Bayesian analyses of direct radiocarbon dates reveal geographic variations in the rate of rice farming dispersal in prehistoric Japan. Sci. Adv. 8, eadc9171 (2022).
Hudson, M. & Barnes, G. L. Yoshinogari. A Yayoi settlement in Northern Kyushu. Monumenta Nipponica. 46, 211–235 (1991).
Daifuku, H. The early cultures of the Island of Kyushu, Japan. Southwest. J. Anthropol. 5, 253–271 (1949).
Hanihara, K. Dual structure model for the population history of the Japanese. Nichibunken Jpn Rev. 2, 1–33 (1991).
Kim, Y. J. & Jin, H. J. Dissecting the genetic structure of Korean population using genome-wide SNP arrays. Genes Genomics. 35, 355–363 (2013).
Wang, Y., Lu, D., Chung, Y. J. & Xu, S. Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations. Hereditas 155, 1–12 (2018).
Jeon, S. et al. Korean genome project: 1094 Korean personal genomes with clinical information. Sci. Adv. 6, eaaz7835 (2020).
Kim, J. et al. Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago. J. Hum. Genet. 70, 47–57 (2025).
Naito, Y. On the human skeletons of Yayoi period excavated at the sites in North-Western Kyushu. J. Anthropol. Soc. Nippon. 79, 236–248 (1971). (in Japanese).
Saiki, K., Wakebe, T. & Nagashima, S. Cranial nonmetrical analyses of the Yayoi people in the Northwestern Kyushu area. Anthropol. Sci. 108, 27–44 (2000).
Watanabe, T., Saiki, K., Okamoto, K. & Wakebe, T. Metrical and nonmetrical analyses of modern female Crania in the Northwestern Kyushu area. Anthropol. Sci. 112, 147–159 (2004).
Kanaseki, T. The physical characteristics of Japanese in the Yayoi-period. Proc. 15th Gen. Assembly Jpn Med. Congr. 1, 167–174 (1959). (in Japanese).
Kaifu, Y. Differences in mandibular morphology of the Jomon people from Kanto and the Yayoi people from Northern Kyushu and Yamaguchi. Anthropol. Sci. 103, 291–308 (1995).
Shinoda, K. I., Kanzawa-Kiriyama, H., Kakuda, T. & Adachi, N. Genetic characteristics of Yayoi people in Northwestern kyushu: ancient genome analysis of human bones excavated from Shimomotoyama rock shelter, Sasebo, Nagasaki prefecture, Japan. Anthropol. Sci. (Jpn Ser). 127, 25–43 (2019). (in Japanese).
Matsushita, M., Mizuno, F. & Matsushita, T. Yayoi human skeletal remains from a stone coffin adjacent to the Shomura site, Iki City, Nagasaki Prefecture. Bull. Doigahama Site Anthropol. Museum. 18, 49–463 (2023). (in Japanese).
Matsushita, T. Yayoi-period human skeletal remains from the Nezushi site. Hirado City History: Nat. Archaeological, 405–441 (Hirado City, 1996). (in Japanese).
Matsushita, M. & Matsushita, T. Yayoi human skeletal remains from the Neshiko site, Hirado City, Nagasaki Prefecture. Hirado Bull. 5, 1–46 (2017). (in Japanese).
DeNiro, M. J. Postmortem preservation and alteration of in vivo bone collagen isotope ratios in relation to palaeodietary reconstruction. Nature 317, 806–809 (1985).
Yoneda, M. et al. Isotopic evidence of inland-water fishing by a Jomon population excavated from the Boji site, Nagano, Japan. J. Archaeol. Sci. 31, 97–107 (2004).
Arneborg, J. et al. Change of diet of the Greenland Vikings determined from stable carbon isotope analysis and 14 C dating of their bones. Radiocarbon 41, 157–168 (1999).
Reimer, P. J. et al. The IntCal20 Northern hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725–757 (2020).
Heaton, T. J. et al. Marine20—the marine radiocarbon age calibration curve (0–55,000 cal BP). Radiocarbon 62, 779–820 (2020).
Kong, G. S. & Lee, C. W. Marine reservoir corrections (∆R) for Southern coastal waters of Korea. The sea. J. Korean Soc. Oceanogr. 10, 124–128 (2005). (in Korean).
Sakamoto, M. & Takigami, M. Recalibration of the radiocarbon ages of the ‘Yaponesia genome’ using IntCal20 and Marine20. Res. Bull. Natl. Museum Japanese History. 237, 173–186 (2022). (in Japanese).
Nohira, C., Maruyama, S. & Minaguchi, K. Phylogenetic classification of Japanese MtDNA assisted by complete mitochondrial DNA sequences. Int. J. Legal Med. 124, 7–12 (2010).
Kim, S. H. et al. High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in korea: a genetic perspective on the peopling of Korea. Investig Genet. 2, 1–11 (2011).
Adachi, N. et al. Mitochondrial DNA analysis of Hokkaido Jomon skeletons: remnants of archaic maternal lineages at the Southwestern edge of former Beringia. Am. J. Phys. Anthropol. 146, 346–360 (2011).
Kanzawa-Kiriyama, H., Saso, A., Suwa, G. & Saitou, N. Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan. Anthropol. Sci. 121, 89–103 (2013).
Mizuno, F. et al. Diversity in matrilineages among the Jomon individuals of Japan. Ann. Hum. Biol. 50, 324–331 (2023).
Tajima, A. et al. Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages. J. Hum. Genet. 49, 187–193 (2004).
Hammer, M. F. et al. Dual origins of the japanese: common ground for hunter-gatherer and farmer Y chromosomes. J. Hum. Genet. 51, 47–58 (2006).
Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867–2873 (2010).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based Estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Robbeets, M. et al. Triangulation supports agricultural spread of the Transeurasian languages. Nature 599, 616–621 (2021).
Cooke, N. P. et al. Ancient genomics reveals tripartite origins of Japanese populations. Sci. Adv. 7, eabh2419 (2021).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Narasimhan, V. M. et al. The formation of human populations in South and central Asia. Science 365, eaat7487 (2019).
Shoda, S. Y. Radiocarbon and archaeology in Japan and korea: what has changed because of the Yayoi dating controversy? Radiocarbon 52, 421–427 (2010).
Sakamoto, M., Hakozaki, M., Nakatsuka, T. & Ozaki, H. Radiocarbon dating of tree rings from the beginning and end of the Yayoi period, Japan. Radiocarbon 66, 1991–1999 (2024).
Skoglund, P. et al. Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 344, 747–750 (2014).
Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652–655 (2017).
Olalde, I. et al. The genomic history of the Iberian Peninsula over the past 8000 years. Science 363, 1230–1234 (2019).
Watanabe, Y. & Ohashi, J. Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations. Iscience 26, 106130 (2023).
Jinam, T. et al. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J. Hum. Genet. 57, 787–795 (2012).
Tokanai, F. et al. Present status of YU-AMS system. Radiocarbon 55, 251–259 (2013).
Ramsey, C. B. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).
Kato, K., Tokanai, F., Anshita, M., Sakurai, H. & Ohashi, M. S. Automated sample combustion and CO2 collection system with IRMS for 14 C AMS in Yamagata University, Japan. Radiocarbon 56, 327–331 (2014).
Mizuno, F. et al. A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing. Ann. Hum. Biol. 47, 555–559 (2020).
Mizuno, F. et al. Population dynamics in the Japanese Archipelago since the pleistocene revealed by the complete mitochondrial genome sequences. Sci. Rep. 11, 12018 (2021).
Rohland, N. et al. Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs. Genome Res. 32, 2068–2078 (2022).
Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes. 9, 1–7 (2016).
Andrews, S. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The sequence alignment/map format and samtools. Bioinformatics 25, 2078–2079 (2009).
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. & Orlando, L. mapDamage2. 0: fast approximate bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
Jun, G., Wing, M. K., Abecasis, G. R. & Kang, H. M. An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res. 25, 918–925 (2015).
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinform. 15, 1–13 (2014).
Zhang, F. et al. Ancestry-agnostic Estimation of DNA sample contamination from sequence reads. Genome Res. 30, 185–194 (2020).
Okonechnikov, K., Conesa, A. & García-Alcalde, F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 32, 292–294 (2016).
McKenna, A. et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013). (2013).
Schönherr, S., Weissensteiner, H., Kronenberg, F. & Forer, L. Haplogrep 3-an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 51, W263–W268 (2023).
Chen, H., Lu, Y., Lu, D. & Xu, S. Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data. BMC Bioinform. 22, 1–15 (2021).
Mallick, S. et al. The Allen ancient DNA resource (AADR) a curated compendium of ancient human genomes. Sci. Data. 11, 182 (2024).
Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012 (2020).
Mallick, S. et al. The Simons genome diversity project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).
Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, s13742–s13015 (2015).
Raghavan, M. et al. Upper palaeolithic Siberian genome reveals dual ancestry of native Americans. Nature 505, 87–91 (2014).
Fu, Q. et al. The genetic history of ice age Europe. Nature 534, 200–205 (2016).
Yang, M. A. et al. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Curr. Biol. 27, 3202–3208 (2017).
Moreno-Mayar, J. V. et al. Terminal pleistocene Alaskan genome reveals first founding population of native Americans. Nature 553, 203–207 (2018).
Sikora, M. et al. The population history of Northeastern Siberia since the pleistocene. Nature 570, 182–188 (2019).
Ning, C. et al. Ancient genomes from Northern China suggest links between subsistence changes and human migration. Nat. Commun. 11, 2700 (2020).
Yang, M. A. et al. Ancient DNA indicates human population shifts and admixture in Northern and Southern China. Science 369, 282–288 (2020).
Wang, C. C. et al. Genomic insights into the formation of human populations in East Asia. Nature 591, 413–419 (2021).
Gelabert, P. et al. Northeastern Asian and Jomon-related genetic structure in the three kingdoms period of Gimhae, Korea. Curr. Biol. 32, 3232–3244 (2022).
Lee, D. N. et al. Genomic detection of a secondary family burial in a single Jar coffin in early medieval Korea. Am. J. Biol. Anthropol. 179, 585–597 (2022).
Dimitromanolakis, A., Paterson, A. D. & Sun, L. Fast and accurate shared segment detection and relatedness Estimation in un-phased genetic data via TRUFFLE. Am. J. Hum. Genet. 105, 78–88 (2019).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68 (2015).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Harney, É., Patterson, N., Reich, D. & Wakeley, J. Assessing the performance of qpadm: a statistical tool for studying population admixture. Genetics 217, iyaa045 (2021).
Acknowledgements
We would like to thank Michiko Hayashi for her valuable experimental contributions, and Twist Bioscience (Japan office) for their technical assistance during the experiments.
Funding
This work was supported in part by grants from JSPS KAKENHI (Grant Numbers 24H01582 and 19H05737 to FM; 23H04838 to IN; 18H02514, 19H05341, 21H00336, 21H04779, 21H04983, 22H00421, and 23H04840 to JO) and AMED (Grant Number JP20km0405211 to JO).
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T.M. and M.M. provided the archaeological materials and associated information. F.T conducted the radiocarbon dating analyses. F.M. and S.U. extracted DNA from the skeletal remains. F.M. performed whole-genome sequencing. K.K. supported the experimental procedures and advised on the handling of ancient DNA. J.K., F.M., I.N., and S.U. organized and curated the archaeological and genetic data. J.K. performed statistical analyses. J.K. drafted most of the manuscript. F.T. wrote the radiocarbon dating section. F.M. wrote the sequencing analysis section. J.O. provided revisions and editorial inputs. F.M. and J.O. conceived of and supervised the study. All the authors have read and approved the final version of the manuscript.
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The analysis of human remains from the Shomura site was approved by the Board of Education of Iki City, Nagasaki Prefecture, Japan. The analysis of human remains from the Neshiko site was approved by the Board of Education of Hirado City, Nagasaki Prefecture, Japan.
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Kim, J., Mizuno, F., Matsushita, T. et al. Ancient genomes reveal early-stage admixture and genetic diversity in the Northwestern Kyushu Yayoi. Sci Rep (2026). https://doi.org/10.1038/s41598-026-34996-7
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DOI: https://doi.org/10.1038/s41598-026-34996-7
