Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the japanese archipelago

Molecular Biology and Evolution

Volumn 31, Issue 11, 2014, Pages 2929-2940

  Sato, Takehiro ^a   Nakagome, Shigeki ^b   Watanabe, Chiaki ^a   Yamaguchi, Kyoko ^a   Kawaguchi, Akira ^a   Koganebuchi, Kae ^c,d   Haneji, Kuniaki ^e   Yamaguchi, Tetsutaro ^f   Hanihara, Tsunehiko ^g   Yamamoto, Ken ^h,i   Ishida, Hajime ^a   Mano, Shuhei ^b   Kimura, Ryosuke ^a   Oota, Hiroki ^g  

^a UNIVERSITY OF THE RYUKYUS   (Japan)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d KITASATO UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCES   (Japan)

^e Haneji Oral Surgery Clinic Medical Corporation Hayamakai   (Japan)

^f SHOWA UNIVERSITY SCHOOL OF DENTISTRY   (Japan)

^g KITASATO UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^h KYUSHU UNIVERSITY   (Japan)

ⁱ KURUME UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

demographic history; genome wide SNPs; Japanese archipelago; population structure; Ryukyu Islanders

Indexed keywords

ARTICLE; EFFECTIVE POPULATION SIZE; GENE FLOW; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DIFFERENCE; GENETIC DISTANCE; GENETIC DRIFT; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; GEOGRAPHIC NAMES; HAPLOTYPE MAP; HOLOCENE; HUMAN; INDIGENOUS PEOPLE; JAPANESE (PEOPLE); MIYAKO; MOLECULAR PHYLOGENY; NEIGHBOR JOINING METHOD; OKINAWA; PHYLOGENY; PLEISTOCENE; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; TAIWANESE; ASIAN CONTINENTAL ANCESTRY GROUP; CLUSTER ANALYSIS; FEMALE; HUMAN GENOME; ISLAND (GEOLOGICAL); JAPAN; MALE; PALEONTOLOGY; PRINCIPAL COMPONENT ANALYSIS; REPRODUCTIVE ISOLATION;

ASIAN CONTINENTAL ANCESTRY GROUP; CLUSTER ANALYSIS; FEMALE; GENETIC DRIFT; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; ISLANDS; JAPAN; MALE; PALEONTOLOGY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; REPRODUCTIVE ISOLATION;

EID: 84910667928     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu230     Document Type: Article

References (54)

1. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655-1664.
2. Asato S. 2003. Prehistory and proto-history in the Ryukyu island chain. History of Okinawa Prefecture 2: archaeology. Naha: Okinawa Prefecture. (in Japanese)
3. Brownin g BL, Browning SR. 2009. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet. 84:210-223.
4. Bryant D, Moulton V . 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 21: 255-265.
5. Diskin SJ, Capasso M, Schnepp RW, Cole KA, Attiyeh EF, Hou C, Diamond M, Carpen ter EL, Winter C, Lee H, et al. 2012. Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma. Nat Genet. 44:1126-1130.
6. Fukumine T, Hanihara T, Nishime A, Ishida H. 2006. Nonmetric cranial variation of early modern human skeletal remains from Kumejima, Okinawa and the peopling of the Ryukyu Islands. Anthropol Sci. 114: 141-151.
7. Fukumizu K, Song L, Gretton A. 2013. Kernel Bayes' rule: Bayesian inference with positive definite kernels. J Mach Learn Res. 14: 3753-3783.
8. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. 2011. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet. 43:1031-1034.
9. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferr ing the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5:e1000695.
10. Haga S, Nakaoka H, Yamaguchi T, Yamamoto K, Kim YI, Samoto H, Ohno T, K atayama K, Ishida H, Park SB, et al. 2013. A genome-wide association study of third molar agenesis in Japanese and Korean populations. J Hum Genet. 58:799-803.
11. Hammer M, Horai S. 1995. Y c hromosomal DNA variation and the peopling of Japan. Am J Hum Genet. 56:951-962.
12. Haneji K, Hanihara T, Sunakawa H, Toma T, Ishida H. 2007. Non-metric dental variation of Sakishima Islanders, Okinawa, Japan: a comparative study among Sakishima and neighboring populations. Anthropol Sci. 115:35-45.
13. Hanihara K. 1991. Dual structuremodel for the population history of the Japanese. Jpn Rev. 2:1-33.
14. Hanihara T 1993 Craniofacial features of southeast Asians and Jomonese: a reconsideration of their microevolution since the Late Pleistocene. Anthropol Sci. 101 25-46.
15. Hashimoto M, Yahagi K, Tsujimoto H, Saito T, and Yoshida K. 2002. Geochemical analysis of Minatogawa Fissure site. In: Gushikami Village Board of Education, editor. Minatogawa Fissure Site. Chapter 8. Gushikami: Gushikami Village. pp. 89-106. (in Japanese
16. Horai S,Murayama K, Hayasaka K,Matsubayashi S, Hattori Y, Fucharoen G, Harihara S, Park KS, Omoto K, Pan IH. 1996. mtDNA polymorphism in East Asian Populations, with special reference to the peopling o f Japan. Am J Hum Genet. 59:579-590.
17. HUGO Pan-Asian SNP Consortium. 2009. Mapping human genetic diversity in Asia. Science 326:1541-1545.
18. Huson DH, Bryant D. 2006. Applicat ion of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267.
19. International HapMap 3 Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
20. Ishida H, Hanihara T, Kondo O, Fukumine T. 2009. Craniometric divergence history of the Japanese populations. Anthropol Sci. 117: 147-156.
21. JinamT, NishidaN,HiraiM, Kawamura S,Oota H, Umetsu K, Kimura R, Ohashi J, Tajima A, Yamamoto T, et al. 2012. The history of human populations in the Japanese Archipelago inferred from genomewide SNP data with a special reference to the Ainu and the Ryukyuan populations. J Hum Genet. 57:787-795.
22. Kass RE, Raftery AE. 1995. Bayes factors. J Am Stat Assoc. 90:773-795.
23. Kishimoto Y. 2003. Nature and antiquity of Rukyu island chain. History of Okinawa Prefecture 2: archaeology. Naha: Okinawa Prefecture. (in Japanese
24. Koganebuchi K, Katsumura T, Nakagome S, Ishida H, Kawamura S, Oota H, Consortium TAADR. 2012. Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders. Anthropol Sci. 120:199-208.
25. Matsukusa H, Oota H, Haneji K, Toma T, Kawamura S, Ishida H . 2010. A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and mainisland Japanese. Am J Phys Anthropol. 142:211-223.
26. Matsumura H. 1994. A microevolutional history of the Japanese people from a dental characteristics perspective. Anthropol Sci. 102:93-118.
27. Matsumura H, Hudson MJ. 2005. Dental perspectives on the population history of Southeast Asia. Am J Phys Anthropol. 127:182-209.
28. Matsu'ura S. 1999. A chronological review of Pleistocene human remains from the Japanese Archipelago. In: Omoto K, editor. Interdisciplinary perspectives on the origins of the Japanese. Kyoto: International Research Center for Japanese Studies. p. 181-197.
29. Naito Y. 1976. People in Okinawa prefecture from the point of view of somatometry. In: Association of Nine Learned Societies, editor. OKINAWA-Nature-Culture-Society. Tokyo: Kobundo. p. 77-86. (in Japanese
30. Nakagawa R, Doi N, Nishioka Y, Nunami S, Yamauchi H, Fujita M, Yamazaki S, Yamamoto M, Katagiri C, Mukai H, et al. 2010. Pleistocene human remains from Shiraho-Saonetabaru Cave on Ishigaki Island, Okinawa, Japan, and their radiocarbon dating. Anthropol Sci. 118:173-183.
31. Nakagome S, Fukumizu K, Mano S. 2013. Kernel approximate Bayesian computation in population genetic inferences. Stat Appl Genet Mol Biol. 12:667-678.
32. Nakamura M, Nishida N, Kawashima M, Aiba Y, Tanaka A, Yasunami M, Nakamura H, Komori A, Nakamuta M, Zeniya M, et al. 2012. Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population. Am J Hum Genet. 91:721-728.
33. Nei M. 1972. Genetic distance between populations. Am Nat. 106: 283-292.
34. Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S 2011 PanSNPdb: the Pan-Asian SNP genotyping database PLoS One 6 e21451.
35. Novembre J, Stephens M. 2008. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 40: 646-649.
36. Omoto K, Misawa S, Ishimoto G. 1976. People in Okinawa prefecture from the point of view of genetic markers which is associated with blood. In: Association of Nine Learned Societies, editor. OKINAWA-Nature-Culture-Soci ety. Tokyo: Kobundo. p. 93-111. (in Japanese
37. Omoto K, Saitou N. 1997. Genetic origins of the Japanese: a partial support for the dual structure hypothesis. Am J Phys Anthropol. 102:437-446.
38. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. 2012. Ancient admixture in human history. Genetics 192:1065-1093.
39. Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet. 2:e190.
40. Pickrell JK, Pritchard JK. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8: e1002967.
41. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, et al. 2007. PLINK: a tool set for whole-geno me association and population-based linkage analyses. Am J Hum Genet. 81:559-575.
42. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. 2002. Genetic structure of human populations. Science 298:2381-2385.
43. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
44. Sa kura H. 1985. Pleistocene human fossil remains from Pinza-Abu (Goat Cave), Miyako Island, Okinawa, Japan. In: Okinawa Prefecture editor. Reports on Excavation of the Pinza-Abu Cave. Naha: Okinawa Prefecture. p. 161-176. (in Japanese).
45. Shi Y, Zhao H, Cao Y, Yang D, Li Z, Zhang B, Liang X, Li T, Chen J, Shen J, et al. 2012. Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. Nat Genet. 44:1020-1025.
46. Steffens M, Leu C, Ruppert AK, Zara F, Striano P, Robbiano A, Capovilla G, Tinuper P, Gambardella A, Bianchi A, et al. 2012. Genome-wide association analysis of genetic gen eralized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32. HumMol Genet. 21:5359-5372.
47. Suzuki H. 1975. Discoveries of the fossil man from Okinawa Island. J Anthrop Soc Nippon. 83:113-124. (in Japanese with English abstract
48. Tajima A, Hayami M, Tokunaga K, Juji T, Matsuo M, Marzuki S, Omoto K, Horai S. 2004. Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages. J Hum Genet. 49: 187-193.
49. Tajima A, Pan IH, Fucharoen G, F ucharoen S, Matsuo M, Tokunaga K, Juji T, Hayami M, Omoto K, Horai S. 2002. Three major lineages of Asian Y chromosomes: implications for the peopling of east and southeast Asia. Hum Genet. 110:80-88.
50. Takamiya H. 2006. An unusual case? Hunter-gatherer adaptations to an island environment: a case study from Okinawa, Japan. J Island Coast Archaeol. 1:49-66.
51. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
52. Toma T, Hanihara T, Sunakawa H, Haneji K, Ishida H. 2007. Metric dental diversity of Ryukyu Islanders: a comparative study among Ryukyu and other Asian populations. Anthropol Sci. 115: 119-131.
53. Wigginton JE, Cutler DJ, Abecasis GR. 2005. A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet. 76:887-893.
54. Yamaguchi-Kabata Y, Nakazono K, Takahashi A, Saito S, Hosono N, Kubo M, Nakamura Y, Kamatani N. 2008. Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies. Am J Hum Genet. 83:445-456.