Original Article

Journal of Human Genetics (2006) 51, 47–58; doi:10.1007/s10038-005-0322-0

Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes

Michael F Hammer1,2, Tatiana M Karafet1, Hwayong Park3, Keiichi Omoto4, Shinji Harihara5, Mark Stoneking6 and Satoshi Horai7

  1. 1Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA
  2. 2Anthropology Department, University of Arizona, Tucson, AZ, 85721, USA
  3. 3Korea Institute of Oriental Medicine, Daejon, South Korea
  4. 4International Research Centre for Japanese Studies, Kyoto, Japan
  5. 5Department of Biological Sciences, University of Tokyo, Tokyo, Japan
  6. 6Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
  7. 7The Graduate Institute for Advanced Studies, Hayama, Japan

Correspondence: Michael F Hammer, Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA. Fax: +1-520-621-9247. E-mail: mfh@u.arizona.edu

Dedicated to the memory of Satoshi Horai

Received 11 August 2005; Accepted 26 September 2005; Published online 18 November 2005.



Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture from Korea beginning approx2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan approx20,000 and approx12,000 years ago, respectively, while haplogroup O-47z began its expansion only approx4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.


Japanese populations, Y-SNPs, Y-STRs, Jomon, Yayoi, Paleolithic, Neolithic, Migrations


These links to content published by NPG are automatically generated.