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In population genetics, research has been made to study the genetic origins of the modern Japanese people in Japan.

Hideko Hosokawa's family in traditional folk dress, kimono, in 1957
A Japanese family, showing a range of ages
Two girls walking at the Shibuya Crossing

Y-chromosome DNA

It has been noted since as early as 1995 that the distribution of Y-chromosome DNA markers among Japanese males differs significantly from the males of neighboring populations: "The Y Alu polymorphic (YAP) element is present in 42% of the Japanese and absent in the Taiwanese, confirming the irregular distribution of this polymorphism in Asia."[1]

In 1999, a study by Tatiana M. Karafet et al. aimed at identifying the nearest Old World relatives of indigenous American Y-DNA lineages included a sample of 118 Japanese, of whom 55 or 47% were found to belong to DE-YAP(xE-SRY4064), 54 or 46% were found to belong to K-M9(xTat, SRY9138, P-DYS257), 6 or 5.1% were found to belong to C-RPS4Y, 2 or 1.7% were found to belong to P-DYS257, and 1 or 0.8% were found to belong to BT-SRY10831.1(xC-RPS4Y, DE-YAP, K-M9).[2]

A comprehensive study of worldwide Y-DNA diversity (Underhill et al. 2000) included a sample of 23 males from Japan, of whom eight (35%) belonged to haplogroup D-M174 (including one D-M15, one D-M55(xM116.2), five D-M125, and one D-M151), six (26%) belonged to O-M175(xM122, M119, M95), five (22%) belonged to O-M122 (including two O-M122(xM7, M164, M159, M121, M134), two O-M134(xM117/M133), and one O-M117/M133(xM162)), three (13%) belonged to C-M130 (including one C-M130(xM38, M48/M77/M86, M93, M8/M105/M131), one C-M93, and one C-M8/M105/M131), and one (4.3%) belonged to N-M128.[3]

Among 259 males from Japan (70 from Tokushima, 61 from Shizuoka, 53 from Kyūshū, 45 from Okinawa, 26 from Aomori, and 4 Ainus) whose Y-DNA has been examined in a 2005 study by Michael F. Hammer, ninety (34.7%) belong to haplogroup D-M55, eighty-two (31.7%) belong to haplogroup O-P31 (including 22% O-47z, 7.7% O-M176(x47z), and 1.9% O-M95(xM111)), fifty-two (20.1%) belong to haplogroup O-M122, fourteen (5.4%) belong to haplogroup C-M8, ten (3.9%) belong to haplogroup NO-M214(xO-M175) (including 2.3% NO-M214(xO-M175, N-LLY22g), 1.2% haplogroup N-LLY22g(xM128, P43, M178), and 0.4% haplogroup N-M178), and eight (3.1%) belong to haplogroup C-M217 (including 1.9% haplogroup C-M217(xM86) and 1.2% haplogroup C-M86).[4] The patrilines belonging to D-P37.1 were found in all the Japanese samples, but were more frequently found in the Ainu (75.0%) and Okinawa (55.6%) samples and less frequently found in the Tokushima (25.7%) and Kyūshū samples (26.4%).[4] Haplogroups O-M175 and C-M8 were not found in the small Ainu sample of four individuals, and C-M217 was not found in the Okinawa sample of 45 individuals.[4] Haplogroup N was detected in samples of Japanese from Aomori (2/26 N-LLY22g(xM128, P43, M178)), Shizuoka (1/61 N-LLY22g(xM128, P43, M178)), and Tokushima (1/70 N-M178), but was not found in the Kyūshū, Okinawa, or Ainu samples.[4] This study, and others, report that Y-chromosome patrilines crossed from the Asian mainland into the Japanese archipelago, and continue to make up a large proportion of the Japanese male lineage.[5] If focusing haplogroup O-P31 in those researches, the patrilines derived from its subclade O-SRY465 are frequently found in both Japanese (mean 32%,[6] with frequency in various samples ranging from 26%[7][8] to 36%[9]) and Koreans (mean 30%,[10] with frequency in various samples ranging from 19%[7][11] to 40%[9]). According to the research, these patrilines have undergone extensive genetic admixture with the Jōmon period populations previously established in Japan.[4]

A 2007 study by Nonaka et al. reported that among a total of 263 healthy unrelated Japanese male individuals born in 40 of the 47 prefectures of Japan, but especially Tokyo (n=51), Chiba (n=45), Kanagawa (n=14), Saitama (n=13), Shizuoka (n=12), and Nagano (n=11), the frequencies of the D2, O2b, and O3 lineages were 38.8%, 33.5%, and 16.7%, respectively, which constituted approximately 90% of the Japanese population. Haplogroup diversity for the binary polymorphisms was calculated to be 86.3%.[12]

Poznik et al. (2016) have reported that the males in the JPT (Japanese in Tokyo, Japan) sample[13] of the 1000 Genomes Project are 20/56 = 36% D2-M179, 18/56 = 32% O2b-M176, 10/56 = 18% O3-M122, 4/56 = 7.1% C1a1-M8, 2/56 = 3.6% O2a-K18, and 2/56 = 3.6% C2-M217.[14]

In a project approved by the Ethics Committee of Tokai University School of Medicine, Ochiai et al. (2016) have reported finding D-M174 (rs2032602 T>C) in 24/59 (40.7%), O-M268 (rs13447443 A>G) in 21/59 (35.6%), C-M130 (rs35284970 C>T) in 8/59 (13.6%), O-P198 (rs17269816 T>C) in 4/59 (6.8%), N-M231 (rs9341278 G>A) in 1/59 (1.7%), and O-P186(xM268, P198) (rs16981290 C>A, rs13447443 A, rs17269816 T) in 1/59 (1.7%) of a sample obtained through buccal swabs from Japanese male volunteers (n = 59) who had given informed consent to participate in the study.[15]

Mitochondrial DNA

According to an analysis of the 1000 Genomes Project's sample of Japanese collected in the Tokyo metropolitan area, the mtDNA haplogroups found among modern Japanese include D (42/118 = 35.6%, including 39/118 = 33.1% D4 and 3/118 = 2.5% D5), B (16/118 = 13.6%, including 11/118 = 9.3% B4 and 5/118 = 4.2% B5), M7 (12/118 = 10.2%), G (12/118 = 10.2%), N9 (10/118 = 8.5%), F (9/118 = 7.6%), A (8/118 = 6.8%), Z (4/118 = 3.4%), M9 (3/118 = 2.5%), and M8 (2/118 = 1.7%).[16]

Single-nucleotide polymorphism

A 2011 SNP consortium study done by the Chinese Academy of Sciences and Max Planck Society consisting of 1719 DNA samples determined that Koreans and Japanese clustered near to each other, confirming the findings of an earlier study that Koreans and Japanese are related. However, the Japanese were found to be genetically closer to South Asian populations as evident by a genetic position that is significantly closer towards South Asian populations on the principal component analysis (PCA) chart. Some Japanese individuals are also genetically closer to Southeast Asian and Melanesian populations when compared to other East Asians such as Koreans and Han Chinese, indicating possible genetic interactions between Japanese and these populations.[17]

A 2008 study about genome-wide SNPs of East Asians by Chao Tian et al. reported that Japanese along with other East Asians such as Joseon Koreans and Han Chinese are genetically distinguishable from Southeast Asians and that the Japanese are related to Koreans, who in turn are more closely related to Han Chinese. However, the Japanese are relatively genetically distant from Han Chinese, compared to Koreans.[18]

Data tables

Template:Lee1965Table12
Template:OmotoSaitou1997Table1
Template:Kang1997Table2
Template:Watanabe2004Table6
Template:Nakaoka2013Table2
Template:GenographicProjectJapanese

See also

  1. ^ Michael F. Hammer and Satoshi Horai, "Y Chromosomal DNA Variation and the Peopling of Japan." American Journal of Human Genetics 56:951-962, 1995. Received September 22, 1994; accepted for publication January 19, 1995.
  2. ^ T. M. Karafet, S. L. Zegura, O. Posukh, et al., "Ancestral Asian Source(s) of New World Y-Chromosome Founder Haplotypes." American Journal of Human Genetics 64:817–831, 1999. Received July 16, 1998; accepted for publication January 13, 1999; electronically published February 19, 1999.
  3. ^ Peter A. Underhill, Peidong Shen, Alice A. Lin, et al., "Y chromosome sequence variation and the history of human populations." Nature Genetics, Volume 26, November 2000.
  4. ^ a b c d e Hammer, Michael F. (2005). "Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes" (PDF). The Japan Society of Human Genetics and Springer-Verlag. 51 (1). Springer Science+Business Media via Max Planck Institute for Evolutionary Anthropology: 47–58. doi:10.1007/s10038-005-0322-0. PMID 16328082. Archived from the original (PDF) on 2007-07-28. Retrieved January 19, 2007.
  5. ^ Travis, John (February 15, 1997). "Jomon genes: using DNA, researchers probe the genetic origins of modern Japanese - Cover Story". Science News. BNET. Archived from the original on January 22, 2011. Retrieved January 22, 2011. {{cite web}}: Unknown parameter |deadurl= ignored (|url-status= suggested) (help)
  6. ^ 238/744 = 32.0% O2b-SRY465 in a pool of all Japanese samples of Xue et al. (2006), Katoh et al. (2004), Han-Jun Jin et al. (2009), Nonaka et al. (2007), and all non-Ainu and non-Okinawan Japanese samples of Hammer et al. (2006).
  7. ^ a b Han-Jun Jin; Kyoung-Don Kwak; Michael F. Hammer; Yutaka Nakahori; Toshikatsu Shinka; Ju-Won Lee; Feng Jin; Xuming Jia; Chris Tyler-Smith; Wook Kim (2003). "Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans". Human Genetics. 114 (1): 27–35. doi:10.1007/s00439-003-1019-0. PMID 14505036.
  8. ^ Jin, Han-Jun; Tyler-Smith, Chris; Kim, Wook (2009). "The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers". PLoS ONE. 4 (1): e4210. doi:10.1371/journal.pone.0004210. PMC 2615218. PMID 19148289.{{cite journal}}: CS1 maint: unflagged free DOI (link) Open access icon
  9. ^ a b Katoh, Toru; Munkhbat, Batmunkh; Tounai, Kenichi; Mano, Shuhei; Ando, Harue; Oyungerel, Ganjuur; Chae, Gue-Tae; Han, Huun; Jia, Guan-Jun; Tokunaga, Katsushi; Munkhtuvshin, Namid; Tamiya, Gen; Inoko, Hidetoshi (2004). "Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis". Gene. 346: 63–70. doi:10.1016/j.gene.2004.10.023. PMID 15716011.
  10. ^ 202/677 = 29.8% O2b-SRY465 in a pool of all ethnic Korean samples of Hammer et al. (2006), Xue et al. (2006), Katoh et al. (2004), Wook Kim et al. (2007), and Han-Jun Jin et al. (2009).
  11. ^ Kim, Wook; Yoo, Tag-Keun; Kim, Sung-Joo; Shin, Dong-Jik; Tyler-Smith, Chris; Jin, Han-Jun; Kwak, Kyoung-Don; Kim, Eun-Tak; Bae, Yoon-Sun (January 24, 2007). "Lack of Association between Y-Chromosomal Haplogroups and Prostate Cancer in the Korean Population". PLoS ONE. 2 (1): e172. doi:10.1371/journal.pone.0000172. PMC 1766463. PMID 17245448.{{cite journal}}: CS1 maint: unflagged free DOI (link) Open access icon
  12. ^ Nonaka, I.; Minaguchi, K.; Takezaki, N. (February 2, 2007). "Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms". Annals of Human Genetics. 71 (Pt 4). John Wiley & Sons: 480–95. doi:10.1111/j.1469-1809.2006.00343.x. PMID 17274803.
  13. ^ The JPT sample is considered "as generally representative of the majority population in Japan". See Matsuda, Ichiro. "Japanese in Tokyo, Japan - Population Description". Camden, NJ: Coriell Institute for Medical Research.
  14. ^ Poznik, G. David; Xue, Yali; Mendez, Fernando L.; et al. (2016). "", "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–599. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036. {{cite journal}}: Explicit use of et al. in: |last4= (help)
  15. ^ Ochiai, Eriko; Minaguchi, Kiyoshi; Nambiar, Phrabhakaran; et al. (2016). "Evaluation of Y chromosomal SNP haplogrouping in the HID-Ion AmpliSeqTM Identity Panel". Legal Medicine. 22: 58–61. doi:10.1016/j.legalmed.2016.08.001. PMID 27591541. {{cite journal}}: Explicit use of et al. in: |last4= (help)
  16. ^ Zheng, H-X; Yan, S; Qin, Z-D; Wang, Y; Tan, J-Z; et al. (2011). "Major Population Expansion of East Asians Began before Neolithic Time: Evidence of mtDNA Genomes". PLoS ONE. 6 (10): e25835. doi:10.1371/journal.pone.0025835. PMC 3188578. PMID 21998705. {{cite journal}}: Explicit use of et al. in: |last6= (help)CS1 maint: unflagged free DOI (link)
  17. ^ "Identification of Close Relatives in the HUGO Pan-Asian SNP Database". PLoS ONE. 29 December 2011. Retrieved 30 May 2016.
  18. ^ Tian, Chao; Kosoy, Roman; Lee, Annette; Ransom, Michael; Belmont, John W.; Gregersen, Peter K.; Seldin, Michael F. (December 5, 2008). "Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays". PLoS ONE. 3 (12). Public Library of Science: e3862. doi:10.1371/journal.pone.0003862. PMC 2587696. PMID 19057645. Retrieved May 7, 2011.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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