A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan

Journal of Human Genetics - Tập 62 Số 2 - Trang 213-221 - 2017
Hideaki Kanzawa‐Kiriyama1, Kirill Kryukov2, Timothy A. Jinam1, Kazuyoshi Hosomichi1, Aiko Saso3, Gen Suwa3, Shintaroh Ueda4, Minoru Yoneda3, Atsushi Tajima5, Ken‐ichi Shinoda6, Ituro Inoue7, Naruya Saitou8
1Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan
2Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
3The University Museum, The University of Tokyo, Tokyo, Japan
4Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
5Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan;
6Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
7Division of Human Genetics, National Institute of Genetics, Mishima, Japan
8Division of Population Genetics, National Institute of Genetics, Mishima, Japan

Tóm tắt

Từ khóa


Tài liệu tham khảo

Japanese Archipelago Human Population Genetics Consortium, Jinam, T., Nishida, N., Hirai, M., Kawamura, S., Oota, H. 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).

Jinam, A. T., Kanzawa-Kiriyama, H., Inoue, I., Tokunaga, K., Omoto, K. & Saitou, N. Unique characteristics of the Ainu population in Northern Japan. J. Hum. Genet. 60, 565–571 (2015).

Hanihara, K. Dual structure model for the population history of the Japanese. Jpn. Rev. 2, 1–33 (1991).

Omoto, K. & Saitou, N. Genetic origins of the Japanese: a partial support for the ‘dual structure hypothesis’. Amer. J. Phys. Anthropol. 102, 437–446 (1997).

Imamura, K. Prehistoric Japan: new perspectives on Insular East Asia, University of Hawaii Press, Honolulu (1996).

Habu, J. Ancient Jomon of Japan. (Cambridge University Press, Cambridge, UK, 2004).

Horai, S., Kondo, R., Murayama, K., Hayashi, S., Koike, H. & Nakai, N. Phylogenetic affiliation of ancient and contemporary humans inferred from mitochondrial DNA. Philos. Trans. Royal Soc. London B Biol. Sci 333, 409–416 (1991).

Shinoda, K. & Kanai, S. Intracemetery genetic analysis at the Nakazuma Jomon site in Japan by mitochondrial DNA sequencing. Anthropol. Sci. 107, 129–140 (1999).

Adachi, N., Shinoda, K., Umetsu, K. & Matsumura, H. Mitochondrial DNA analysis of Jomon skeletons from the Funadomari Site, Hokkaido, and its implication for the origins of Native American. Amer. J. Phys. Anthropol. 138, 255–265 (2009).

Adachi, N., Shinoda, K., Umetsu, K., Kitano, T., Matsumura, H., Fujiyama, R. et al. Mitochondrial DNA analysis of Hokkaido Jomon skeletons: remnants of archaic maternal lineages at the southwestern edge of former Beringia. Amer. 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).

Adachi, N., Sawada, J., Yoneda, M., Kobayashi, K. & Itoh, S. Mitochondrial DNA analysis of the human skeleton of the initial Jomon phase excavated at the Yugura cave site, Nagano, Japan. Anthropol. Sci. 121, 137–143 (2013).

Tanaka, M., Cabrera, V. M., González, A. M., Larruga, J. M., Takeyasu, T., Fuku, N. et al (2004) Mitochondrial genome variation in Eastern Asia and the peopling of Japan. Genome Res. 14, 1832–1850 (2004).

Umetsu, K., Tanaka, M., Yuasa, I., Adachi, N., Miyoshi, A., Kashimura, S. et al. Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations. Electrophoresis 26, 91–98 (2005).

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).

Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010).

Skoglund, P. & Jakobsson, M. Archaic human ancestry in East Asia. Proc. Natl Acad. Sci. USA 108, 18301–18306 (2011).

Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P., Willerslev, E. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012).

Meyer, M., Kircher, M., Gansauge, M., Li, H., Racimo, F., Mallick, S. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J. & Pääbo, S. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).

Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A. et al. Genome sequence of a 45000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).

The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).

Fukushima Prefectural Museum Sanganji Kaizuka (in Japanese). (Fukushima Prefectural Museum, Fukushima, Japan, 1988).

Pairwise alignment of panTro2 and human (hg19) http://hgdownload.cse.ucsc.edu/goldenPath/panTro2/vsHg19/ .

Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S. et al. Worldwide human relationships inferred fro`m genome-wide patterns of variation. Science 319, 1100–1104 (2008).

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

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Amer. J. Hum. Genet. 81, 559–575 (2007).

Sánchez-Quinto, F., Schroeder, H., Ramirez, O., Ávila-Arcos, M. C., Pybus, M., Olalde, I. et al. Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Curr. Biol. 22, 1494–1499 (2012).

Patterson, N., Price, A. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).

Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987).

Bryant, D. & Moulton, V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21, 255–265 (2004).

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y. et al. Ancient admixture in human history. Genetics 112, 1065–1093 (2012) ADMIXTOOLS 1.1 http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html .

Teo, Y. Y., Sim, X., Ong, R. T., Tan, A. K., Chen, J., Tantoso, E. et al. Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations. Genome. Res. 19, 2154–2162 (2009).

Saitou, N. A genetic affinity of human populations. Hum. Evol 10, 17–33 (1995).

Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

Turner, C. G. II Late Pleistocene and Holocene population history of East Asia based on dental variation. Amer. J. Phys. Anthropol. 73, 305–321 (1987).

Turner, C. G. II Major features of sundadonty and sinodonty, including suggestions about East Asian microevolution, population history, and late Pleistocene relationships with Australian Aboriginals. Amer. J. Phys. Anthropol. 83, 295–317 (1990).

Yamaguchi, B. Establishment of Japanese (in Japanese), Misuzu Shobo, Tokyo, Japan, (1999).

Matsumura, H. Non-metric dental trait variation among local sites and regional groups of the Neolithic Jomon period, Japan. Anthropol. Sci. 115, 25–33 (2007).

Matsumura, H., Ishida, H., Amano, T., Ono, H. & Yoneda, M. Biological affinities of Okhotsk-culture people with East Siberians and Arctic people based on dental characteristics. Anthropol. Sci. 117, 121–132 (2009).

Hanihara, T. & Ishida, H. Regional difference in craniofacial diversity and the population history of Jomon Japan. Amer. J. Phys. Anthropol 139, 311–322 (2009).

Nakashima, A., Ishida, H., Shigematsu, M., Goto, M. & Hanihara, T. Nonmetric cranial variation of Jomon Japan: Implications for the evolution of Eastern Asian diversity. Amer. J. Hum. Biol. 22, 782–790 (2010).

Horai, S., Murayama, K., Hayasaka, K., Matsubayashi, S., Hattori, Y., Fucharoen, G. et al. mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan. Am. J. Hum. Genet. 59, 579–590 (1996).

Hammer, M. F. & Horai, S. Y Chromosomal DNA variation and the peopling of Japan. Am. J. Hum. Genet. 56, 951–962 (1995).

Tajima, A., Hayami, M., Tokunaga, K., Juji, T., Matsuo, M., Marzuki, S. 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., Karafet, T. M., Park, H., Omoto, K., Harihara, S., Stoneking, M. et al. Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes. J. Hum. Genet. 51, 47–58 (2006).

Nakagome, S., Sato, T., Ishida, H., Hanihara, T., Yamaguchi, T., Kimura, R. et al. The Asian DNA Repository Consortium. Model-based verification of hypotheses on the origin of modern Japanese revisited y Bayesian inference based on genome-wide SNP data. Mol. Biol. Evol. 32, 1533–1543 (2015).

Jinam, T. A., Kanzawa-Kiriyama, H. & Saitou, N. Human genetic diversity in the Japanese Archipelago: dual structure and beyond. Genes Genet. Syst. 60, 565–571 (2015).

Kozintsev, A. G. Ainu, Japanese, their ancestors and neighbors cranioscopic data. J. Anthropol. Soc. Nippon 98, 247–267 (1990).

Kozintsev, A. G. Prehistoric and recent populations of Japan: multivariate analysis of cranioscopic data. Arctic Anthropol. 29, 104–111 (1992).

Ishida, H. Metric and nonmetric cranial variation of the pre-historic Okhotsk people. Anthropol. Sci. 104, 233–258 (1996).

Komesu, A., Hanihara, T., Amano, T., Ono, H., Yoneda, M., Dodo, Y. et al. Nonmetric cranial variation in human skeleton remains associated with Okhotsk culture. Anthropol. Sci. 116, 33–47 (2008).

Sato, T., Amano, T., Ono, H., Ishida, H., Kodera, H., Matsumura, H. et al. Mitochondrial DNA haplogrouping of the Okhotsk people based on analysis of ancient DNA: an intermediate of gene flow from the continental Sakhalin people to the Ainu. Anthropol. Sci. 117, 171–180 (2009).

Kaburagi, M., Ushida, H., Goto, M. & Hanihara, T. Comparative studies of the Ainu, their ancestors, and neighbors: assessment based on metric and nonmetric dental data. Anthropol. Sci. 118, 95–106 (2010).

Kazuta, H., Sato, T., Dodo, Y., Matsumura, H., Amano, T., Ishisa, H. et al. Genotype frequencies of the ABCC11 gene in 2000–3000-year-old human bones from the Epi-Jomon and Jomon sites in Hokkaido, Japan. Anthropol. Sci. 119, 81–86 (2011).

Dodo, Y., Kawakubo, Y., Sawada, J. & Ishida, H. The Ainu and their neighbors as seen from the perspective of nonmetric cranial trait variation: I. The Hokkaido Ainu as a population among East and Northeast Asian peoples. (in Japanese) Anthropol. Sci. (Japanese series) 120, 1–13 (2012).

Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

He, Y., Wang, W. R., Xu, S. & Jin, L., Pan-Asia SNP Consortium Paleolithic contingent in modern Japanese: estimation and inference using genome-wide data. Sci. Rep 2, 355 (2012).

Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I. et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011).