AA  Vol.1 No.2 , November 2011
Mapping Human Genetic Diversity on the Japanese Archipelago
Abstract: The Japanese people are one of the most important populations for studying the origin and diversification of East Asian populations. As an island population, the Japanese's path of migration is a long-standing controversy. Archeological evidence suggests that there were at least two waves of migration to the Japanese archipelago in prehistory: the Paleolithic and Neolithic Jomonese as well as the Aeneolithic Yayoiese. However, the contributions of these Jomonese and Yayoiese to the contemporary Japanese population remain unclear. In this article, we provide evidence from human genetics as a new approach to addressing this topic. At the beginning, we introduce the history of human migration to the Japanese archipelago, as well as materials and methods human geneticists use. Subsequently, we tested three distinct population expansion models using evidences from recent human genetic studies on the Japanese, East Asian, and Serbian populations. Finally, we conclude that the contemporary main island Japanese are the result of population admixture of Jomonese, Yayoiese, and Han Chinese, which consists with the Admixture model.
Cite this paper: nullDing, Q. , Wang, C. , Farina, S. & Li, H. (2011). Mapping Human Genetic Diversity on the Japanese Archipelago. Advances in Anthropology, 1, 19-25. doi: 10.4236/aa.2011.12004.

[1]   Adachi, N., Shinoda, K. I., Umetsu, K., & Matsumura, H. (2009). Mitochondrial DNA analysis of Jomon skeletons from the Funado- mari site, Hokkaido, and its implication for the origin of Native American. American Journal of Physical Anthropology, 138, 255-265. doi:10.1002/ajpa.20923

[2]   Anderson, S., Bankier, A. T., Barrell, B. G., De Bruijn, M. H. L., Coul- son, A. R., Drouin, J. et al. (1981). Sequence and organization of the human mitochondrial genome. Nature, 290, 457-465. doi:10.1038/290457a0

[3]   Arctander, P. (1999). Mitochondrial recombination? Science, 284, 2090-2091. doi:10.1126/science.284.5423.2089e

[4]   Bowcock, A. M., Ruiz-Linares, A., Tomfohrde, J., Minch, E., Kidd, J. R., & Cavalli-Sforza, L. L. (1994). High resolution of human evolu- tionary trees with polymorphic microsatellites. Nature, 368, 455-457. doi:10.1038/368455a0

[5]   Cavalli-Sforza, L. L., Menozzi, P., & Piazza, A. (1994). The history and geography of human genes. Princeton, NJ: Princeton University.

[6]   Chard, C. S. (1974). Northeast Asia in prehistory. Madison, WI: Uni- versity of Wisconsin Press.

[7]   Deng, W., Shi, B., He, X., Zhang, Z., Xu, J., Li, B. et al. (2004). Evolution and migration history of the Chinese population inferred from Chinese Y-chromosome evidence. Journal of Human Genetics, 49, 339-348. doi:10.1007/s10038-004-0154-3

[8]   Hammer, M. F., & Horai, S. (1995). Y chromosomal DNA variation and the peopling of Japan. American Journal of Human Genetics, 56, 951-962.

[9]   Hammer, M. F., Karafet, T. M., Park, H., Omoto, K., Harinara, S., Stoneking, M., & Horai, S. (2006). Dual origins of the Japanese: Common ground for hunter-gatherer and farmer Y chromosomes. Journal of Human Genetics, 51, 47-58. doi:10.1007/s10038-005-0322-0

[10]   Hanihara, K. (1984). Origins and affinities of Japanese viewed from cranial measurements. Acta Anthropogenetica, 8, 149-158.

[11]   Hanihara, K. (1991). Dual structure model for the population history of Japanese. Japan Review, 2, 1-33.

[12]   Hisao, B., Hajime, S., & Shuichiro N. (1989). Human skeletal remains of Jomon period from Minamitsubo shell-mound site in Ibaraki Prefecture, East Japan. Bulletin of the National Science Museum, Tokyo, Serial D, 15, 1-40.

[13]   Hisao, B., Shuichiro, N., & Seiho, O. (1998). Minatogawa hominid fossils and the evolution of Late Pleistocene humans in East Asia. Anthropological Science, 106, 27-45.

[14]   Horai, S., Murayama, K., Hayasaka. K., Matsubayashi, S., Hattori, Y., Fucharoen, G. et al. (1996). mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan. Ameri- can Journal of Human Genetics, 59, 579-590.

[15]   Howells, W. W. (1966). The Jomon people of Japan: a study by discriminant analysis of Japanese and Ainu crania. Paper of the Peabody Museum of Archeology and Ethnology, Harvard University, 57, 1-4.

[16]   Jobling, M. A., & Tyler-Smith, C. (2003). The human Y chromosome: an evolutionary marker comes of age. Nature Reviews Genetics, 4, 598-612. doi:10.1038/nrg1124

[17]   Karafet, T. M., Mendez, F. L., Mellerman, M. B., Underhill, P. A., Zegura, S. L., & Hammer, M. F. (2008). New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroups tree. Genome Research, 18, 830-838. doi:10.1101/gr.7172008

[18]   Karafet, T. M., Zegura, S. L., Posukh, O., Osipova, L., Bergen, A., Long, J. et al. (1999). Ancestral Asian sources(s) of New World Y-chromo- some founder haplotypes. American Journal of Human Genetics, 64, 817-831. doi:10.1086/302282

[19]   Ke, Y., Bing, S., Song, X., Lu, D., Chen, L., Li, H. et al. (2001). African origin of modern humans in East Asia: A tale of 12,000 Y chromosomes. Science, 292, 1151-1153. doi:10.1126/science.1060011

[20]   Kivisild, T., Tolk, H.V., Parik, J., Wang, Y., Papiha, S. S., Bandelt, H. J., & Villems, R. (2002). The emerging limbs and twigs of the East Asian mtDNA tree. Molecular Biology and Evolution, 19, 1737- 1751.

[21]   Koyama, S. (1978). Jomon subsistence and population. Senri Ethno- logical Studies, 2, 1-65.

[22]   Lee, H. Y., Yoo, J. E., Park, M. J., Chung, U., Kim, C. Y., & Shin, K. J. (2006). East Asian mtDNA haplogroup determination in Koreans: haplogroup-level coding region SNP analysis and subhaplogroup- level control region sequence analysis. Electrophoresis, 27, 4408- 4418. doi:10.1002/elps.200600151

[23]   Maruyama, S., Minaguchi, K., & Saitou, N. (2003). Sequence polymer- phisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese populations. Internal Journal of Legal Medicine, 117, 218-225. doi:10.1007/s00414-003-0379-2

[24]   Matsu’ura, S., & Kondo, M. (2010). Relative chronology of the Minatogawa and the Upper Minatogawa series of human remains from Okinawa Island, Japan. Anthropological Science, Advance Publication.

[25]   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 T. Akazawa & C. M. Aikens (Eds), Prehis- toric hunter-gatherers in Japan, No. 27 (pp. 107-136). Tokyo: Uni- versity of Tokyo Press.

[26]   Nei, M. (1995). The origins of human population: genetic, linguistic, and archeological data. In S. Brenner & K. Hanihara, (Eds.), The origin and past of modern humans as viewed from DNA (pp. 77-91). Singapore and London: World Scientific.

[27]   Omoto, K., & Saitou, N. (1997). Genetic origins of the Japanese: A partial support for the dual structure hypothesis. American Journal of Physical Anthropology, 102, 437-446. doi:10.1002/(SICI)1096-8644(199704)102:4<437::AID-AJPA1>3.0.CO;2-P

[28]   Pakendorf, B., & Stoneking, S. (2005). Mitochondrial DNA and human evolution. Annual Review Genomics Human Genetics, 6, 165-183. doi:10.1146/annurev.genom.6.080604.162249

[29]   Shinoda, K. (2003). DNA analysis of the Jomon skeletal remains ex- cavated from Shimo-Ohta shell midden, Chiba prefecture (in Japanese). Report for Sohnan Research Instutite for Cultual Properties, 50, 201- 205.

[30]   Shinoda, K., & Kanai, S. (1999). Intracemetry genetic analysis at the Nakazuma Jomon site in Japan by mitochondrial DNA sequencing. Anthropological Science, 107, 129-140.

[31]   Sokal, R. R., & Thomson, B. A. (1998). Spatial genetic structure of human population in Japan. Human Biology, 70, 1-22.

[32]   Starikovskaya, E. B., Sukernik, R. I., Derbeneva, O. A., Volodko, N. V., Ruiz-Pesini, E., Torroni, A., et al. (2005). Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of native American haplogroups. Annual Human Gene- tics, 69, 67-89. doi:10.1046/j.1529-8817.2003.00127.x

[33]   Stumpf, M. P. H., & Goldstein, D. B. (2001). Genealogical and evolu- tionary inference with the human Y chromosome. Science, 291, 1738-1742. doi:10.1126/science.291.5509.1738

[34]   Suzuki, H. (1981). Racial history of the Japanese. In I. Schwidetzky, (Ed.), Rassengeschichte der Menschheit, 8 (pp. 7-69). Munich: Lie- ferung Oldenbourg.

[35]   Suzuki, H. (1982). Skulls of the Minatogawa man. In H. Suzuki & Hanihara, K. (Eds.), The Minatogawa man: The upper Pleistocene man from the island of Okinawa, No. 19 (pp. 7-49). Tokyo: Univer- sity of Tokyo Press.

[36]   Tajima, A., Hayami, M., Tokunaga, K., Juji, T., Matsuo, M., Marzuki, S., Omoto, K., et al. (2004). Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages. Journal of Human Genetics, 49, 187-193. doi:10.1007/s10038-004-0131-x

[37]   Tajima, A., Pan, I. H., Fucharoen, G., Fucharoen, S., Matsuo, M., Tokunaga, K. et al. (2002). Three major lineages of Asian Y chromo- somes: implications for the peopling of east and Southeast Asia. Human Genetics, 110, 80-88. doi:10.1007/s00439-001-0651-9

[38]   Tanaka, M., Cabrera, V. M., Gonzalez, A. M., Larruga, J. M., Takeyasu, T., Fuku, N., et al. (2004). Mitochondrial genome variation in Eastern Asia and the peopling of Japan. Genome Research, 14, 1832- 1850. doi:10.1101/gr.2286304

[39]   Thangaraj, K., Singh, L., Reddy, A. G., Rao, V. R., Sehgal, S. C., Underhill, P. A. et al. (2004). Genetic affinities of the Andaman Islanders, a vanishing human population. Current Biology, 13, 86-93. doi:10.1016/S0960-9822(02)01336-2

[40]   The HUGO Pan-Asian SNP Consortium (2009). Mapping human genetic diversity in Asia. Science, 326, 1541-1545. doi:10.1126/science.1177074

[41]   Tu, J. F., & Yip, V. F. (1993). Ethnic groups in China. Beijing and New York: Science Press.

[42]   Tuner, C. G. (1976). Dental evidence on the origins of the Ainu and Japanese. Science, 193, 911-913. doi:10.1126/science.781841

[43]   Umetsu, K., Tanaka, M., Yuasa, I., Adachi, N., Miyoshi, A., Kashimura, S. et al. (2005). Multiplex ampli?ed product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations. Electrophoresis, 26, 91-98. doi:10.1002/elps.200406129

[44]   Underhill, P. A., Jin, L., Lin, A. A., Mehdi, S. Q., Jenkins, T., Vollrath, D. et al. (1997). Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chroma- tography. Genome Research, 7, 996-1005.

[45]   Vigilant, L., Stoneking, M., Harpending, H., Hawkes K., & Wilson A. C. (1991). African population and the evolution of human mito- chondrial DNA. Science, 253, 1503-1507. doi:10.1126/science.1840702

[46]   Wang, C. C., Yan, S., & Li, H. (2010). Surnames and the Y chromo- somes (in Chinese). Communication on Contemporary Anthropology, 4, 26-33. doi:10.4236/coca.2010.41005

[47]   Wen, B., Xie, X., Gao, S., Li, H., Shi, H., Song, X. et al. (2004). Analyses of genetic structure of Tibeto-Burman population reveals sex-biased admixture in southern Tibeto-Burmans. American Journal of Human Genetics, 74, 856-865. doi:10.1086/386292

[48]   Yamaguchi-Kabata, Y., Nakazono, K., Takahashi, A., Saito, S., Hosono, N., Nakamura, Y., & Kamatani, N. (2009). Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effect on population-based association studies. American Journal of Human Genetics, 83, 445-456. doi:10.1016/j.ajhg.2008.08.019

[49]   Yan, S., Wang, C. C., Li, H., Li, S. L., Jin, L., & The Genographic Consortium (2011). An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. European Journal of Human Genetics, 19, 1013-1015. doi:10.1038/ejhg.2011.64

[50]   Yao, Y. G., Kong, Q. P., Bandelt, H. J., Kivisild, T., & Zhang, Y. P. (2002). Phylogenetic differentiation of mitochondrial DNA in Han Chinese. American Journal of Human Genetics, 70, 635-651. doi:10.1086/338999

[51]   Yao, Y. G., Lu, X. M., Luo, H. R., Li, W. H., & Zhang, Y. P. (2000). Gene admixture in the Silk Road region of China: Evidence from mtDNA and melanocortin 1 receptor polymorphism. Genes & Gene- tic Systems, 75, 173-178. doi:10.1266/ggs.75.173

[52]   Zhang, F., Su, B., Zhang, Y. P., & Jin, L. (2007). Genetic studies of human diversity in East Asia. Philosophical Transactions of the Royal Society B, 362, 987-995. doi:10.1098/rstb.2007.2028