Population Genetics Analysis of the Origin of Modern Japanese


Human settlement of the Japanese archipelago is of significant interest for understanding how human populations migrated from the East Asian continent to isolated islands and shifted lifestyles from hunter‐gathering to farming. The hunter‐gathering Jomon period follows the Palaeolithic period but precedes the agricultural Yayoi period. Three hypotheses have been proposed to model the population history in the Japanese archipelago. Two of these are in contrast with each other, hypothesising that lineages leading to modern Japanese are traced back to a single ancestor of indigenous Jomon (the transformation hypothesis) or migrant Yayoi (the replacement hypothesis) people. The third model postulates a hybridisation lineage or an admixture of the two ancestral populations. Recent advances in high‐throughput technology have enabled the application of genome‐scale data to directly test the three models. Several lines of population genetics studies strongly support the hybridisation hypothesis to explain the origin of modern Japanese.

Key Concepts

  • Prehistory in the Japanese archipelago is characterised by the Jomon and Yayoi cultures.
  • A major cultural transition from the Jomon period to the Yayoi period is a shift in lifestyles from hunter‐gathering to farming.
  • Three demographic models have been proposed to explain the origin of modern Japanese: transformation, replacement and hybridisation.
  • A dual structure hypothesis is based on the hybridisation model and assumes that modern Japanese is admixed between the indigenous Jomon and migrated Yayoi people, and the degree of admixture varies among local populations in the Japanese archipelago.
  • Population genetics analyses have been performed to make inferences about the evolutionary history of modern Japanese.
  • Genomic data, as well as genetic data from a single locus or small number of loci, support the hybridisation hypothesis to explain the origin of modern Japanese.
  • Statistical modelling based on genomic data shows a complex history characterised with the population stratification of the Jomon people in the Japanese archipelago.

Keywords: modern Japanese; Jomon; Yayoi; hunter‐gathering; farming; admixture; population genetics; genome‐wide SNPs

Figure 1. Cultural transition in the Japanese archipelago and three hypotheses on the origin of modern Japanese. The Jomon culture started around 13 000 years ago (13 kya). The Japanese archipelago consists of five major islands including Hokkaido, mainland Japan, Shikoku, Kyushu and Okinawa. The Jomon people widely spread through the islands. Then, the transition occurred around 3 kya when the Yayoi culture migrated through the Korean Peninsula. The main question is how people living during the Jomon or Yayoi period contributed to the formation of modern Japanese. Three hypotheses have been proposed: the transformation, replacement and hybridisation models.
Figure 2. Testing three hypotheses for the origin of modern Japanese by formulating three models using genome‐scale data from three populations. Ainu or Han Chinese in Beijing (CHB) is assumed as direct descendants from the Jomon or Yayoi lineages, respectively. Japanese from Tokyo (JPT) represent modern Japanese. The transformation model does not involve demic diffusion during the spread of the Yayoi culture; therefore, the lineage leading to JPT split from the shared ancestor with the Ainu. By contrast, the replacement model postulates that JPT are descendants of the Yayoi people, so the JPT lineage branches off from the Yayoi lineage. The hybridisation model postulates admixture between the Jomon and Yayoi lineages, so that both of the ancestors contribute to the formation of JPT.
Figure 3. Complex demography inferred from genome‐wide SNP data. The model is essentially the same as the hybridisation model (Figure), but this model includes divergence in the Jomon lineages that occurred after the split between the Jomon and Yayoi lineages but before admixture. One lineage leads to contemporary Ainu living in Hokkaido, whereas the other contributes to the admixture with the Yayoi people. The change in recent migration rates is shown as a thick arrow.


Allentoft ME , Sikora M , Sjogren KG , et al. (2015) Population genomics of Bronze Age Eurasia. Nature 522: 167–172.

Ammerman AJ and Cavalli‐Sforza LL (1984) The Neolithic Transition and the Genetics of Populations in Europe. Princeton, NJ: Princeton University Press.

Brace CL , Brace ML and Leonard WR (1989) Reflections on the face of Japan: a multivariate craniofacial and odontometric perspective. American Journal of Physical Anthropology 78: 93–113.

Brace CL and Hunt KD (1990) A nonracial craniofacial perspective on human variation: A(ustralia) to Z(uni). American Journal of Physical Anthropology 82: 341–360.

Cavalli‐Sforza LL , Menozzi P and Piazza A (1994) The History and Geography of Human Genes. Princeton, NJ: Princeton University Press.

Chard CS (1974) Northeast Asia in Prehistory. Madiwon, WI: University of Wisconsin Press.

Craig OE , Saul H , Lucquin A , et al. (2013) Earliest evidence for the use of pottery. Nature 496: 351–354.

Dodo Y , Doi N and Kondo O (1998) Ainu and Ryukyuan cranial nonmetric variation: evidence which disputes the Ainu‐Ryukyu common origin theory. Anthropological Science 106: 99–120.

Dodo Y and Ishida H (1990) Population history of Japan as reviewed from cranial nonmetric variation. Journal of the Anthropological Society of Nippon 98: 269–287.

Dodo Y and Kawakubo Y (2002) Cranial affinities of the Epi‐Jomon inhabitants in Hokkaido, Japan. Anthropological Science 110: 1–32.

Fukase H , Wakebe T , Tsurumoto T , et al. (2012a) Geographic variation in body form of prehistoric Jomon males in the Japanese archipelago: its ecogeographic implications. American Journal of Physical Anthropology 149: 125–135.

Fukase H , Wakebe T , Tsurumoto T , et al. (2012b) Facial characteristics of the prehistoric and early‐modern inhabitants of the Okinawa islands in comparison to the contemporary people of Honshu. Anthropological Science 120: 23–32.

Fukumine T , Hanihara T , Nishime A and Ishida H (2006) Nonmetric cranial variation of early modem human skeletal remains from Kumejima, Okinawa and the peopling of the Ryukyu Islands. Anthropological Science 114: 141–151.

Green RE , Krause J , Briggs AW , et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710–722.

Haak W , Lazaridis I , Patterson N , et al. (2015) Massive migration from the steppe was a source for Indo‐European languages in Europe. Nature 522: 207–211.

Habu J (2004) Ancient Jomon of Japan. Berkeley, CA: Cambridge University Press.

Hammer MF and Horai S (1995) Y chromosomal DNA variation and the peopling of Japan. American Journal of Human Genetics 56: 951–962.

Hammer MF , Karafet TM , Park H , et al. (2006) Dual origins of the Japanese: common ground for hunter‐gatherer and farmer Y chromosomes. Journal of Human Genetics 51: 47–58.

Hanihara K (1991) Dual structure model for the population history of Japanese. Japan Review 2: 1–33.

Hanihara K (1998) Reanalysis of local variations in the Ainu crania. Anthropological Science 106: 1–15.

Hanihara T and Ishida H (2009) Regional differences in craniofacial diversity and the population history of Jomon Japan. American Journal of Physical Anthropology 139: 311–322.

Hasebe K (1940) The ancient Japanese. Journal of Anthropological Society of Nippon 55: 27–34 (in Japanese).

Horai S , Murayama K , Hayasaka K , et al. (1996) mtDNA polymorphism in East Asian Populations, with special reference to the peopling of Japan. American Journal of Human Genetics 59: 579–590.

Howells WW (1966) The Jomon People of Japan: a Study by Discriminant Analysis of Japanese and Ainu Crania. Papers of the Peabody Museum of Archaeology and Ethnology, Harvard University 57:1–43.

Imamura K (1996) Prehistoric Japan: New Perspective on Insular East Asia. London: UCL Press Ltd.

Jeong C , Nakagome S and Di Rienzo A (2016) Deep history of East Asian populations revealed through genetic analysis of the Ainu. Genetics 202(1): 261–272.

Jinam T , Nishida N , Hirai M , et al. (2012) 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. Journal of Human Genetics 57: 787–795.

Kingman JFC (1982) On the genealogy of large populations. Journal of Applied Probability 19A: 27–43.

Kiyono K (1949) Kodaijinkotsu No Kenkyu Ni Motozuku Nihonjinshuron (in Japanese), pp. 1–602. Tokyo: Iwanami Shoten.

Koganebuchi K , Katsumura T , Nakagome S , et al. (2012) Autosomal and Y‐chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders. Anthropological Science 120: 199–208.

Mathieson I , Lazaridis I , Rohland N , et al. (2015) Genome‐wide patterns of selection in 230 ancient Eurasians. Nature 528: 499–503.

Matsukusa H , Oota H , Haneji K , et al. (2010) A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main‐island Japanese. American Journal of Physical Anthropology 142: 211–223.

Matsumura H (1994) Microevolutional history of the Japanese people from a dental characteristics perspective. Anthropological Science 102: 93–118.

Matsumura H and Hudson MJ (2005) Dental perspectives on the population history of Southeast Asia. American Journal of Physical Anthropology 127: 182–209.

Mizoguchi Y (1986) Contributions of prehistoric Far East populations to the population of modern Japan: a Q‐mode path analysis based on cranial measurements. In: Akazawa T and Aikens CM (eds) Prehistoric Hunter Gatherers in Japan, pp. 107–136. Tokyo: University of Tokyo Press.

Nakagome S , Alkorta‐Aranburu G , Amato R , et al. (2015a) Estimating the ages of selection signals from different epochs in human history. Molecular Biology and Evolution. DOI: 10.1093/molbev/msv256.

Nakagome S , Sato T , Ishida H , et al. (2015b) Model‐based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome‐wide SNP data. Molecular Biology and Evolution 32: 1533–1543.

Nakashima A , Ishida H , Shigematsu M , Goto M and Hanihara T (2010) Nonmetric cranial variation of Jomon Japan: implications for the evolution of eastern Asian diversity. American Journal of Human Biology 22: 782–790.

Nei M (1995) The origins of human populations: genetic, linguistic and archeological data. In: Brenner S and Hanihara K (eds) The Origin and Past of Modern Humans as Viewed from DNA, pp. 71–91. Singapore: World Scientific.

Omoto K and Saitou N (1997) Genetic origins of the Japanese: a partial support for the dual structure hypothesis. American Journal of Physical Anthropology 102: 437–446.

Reich D , Green RE , Kircher M , et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053–1060.

Suzuki H (1969) Microevolutionary changes in the Japanese population for the prehistoric age to the present day. Journal of the Faculty of Science, the University of Tokyo, Section V 3: 279–308.

Suzuki H (1981) Racial history of the Japanese. In: Schwidetzkys I (ed) Lieferung Asien I: Japan, Indonesien, Ozeanien, pp. 7–69. Vol 8 in: Abbie A, Saller K, Schwidetzkys I (eds) Rassengeschichte der Menschhiet. Munich: R Oldenbourg.

Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437–460.

Takamiya H and Obata H (2002) Peopling of western Japan, focusing of Kyushu. Shikoku, and Ryukyu archipelago. Radiocardon 44: 495–502.

Tanaka M , Cabrera VM , Gonzalez AM , et al. (2004) Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Research 14: 1832–1850.

The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299–1320.

Turner CG 2nd. (1976) Dental evidence on the origins of the Ainu and Japanese. Science 193: 911–913.

Turner CG 2nd. (1987) Late Pleistocene and Holocene population history of East Asia based on dental variation. American Journal of Physical Anthropology 73: 305–321.

Watanabe T , Saiki K , Okamoto K and Wakebe T (2004) Metrical and nonmetrical analyses of modem female crania in the northwestern Kyushu area. Anthropological Science 112: 147–159.

Yamaguchi B (1982) A review of the osteological characteristics of the Jomon population in prehistoric Japan. Journal of the Anthropological Society of Nippon 90: 77–90.

Yamaguchi‐Kabata Y , Nakazono K , Takahashi A , et al. (2008) Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population‐based association studies. American Journal of Human Genetics 83: 445–456.

Further Reading

Kaifu Y , Izuho M , Goebel T , Sato H and Ono A (2015) Emergence and Diversity of Modern Human Behavior in Paleolithic Asia. College Station, TX: Texas A&M University Press.

Rosenberg NA and Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380–390.

Stoneking M and Delfin F (2010) The human genetic history of East Asia: weaving a complex tapestry. Current Biology 20: R188–R193.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Nakagome, Shigeki, and Oota, Hiroki(Mar 2016) Population Genetics Analysis of the Origin of Modern Japanese. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0026516]