Biology:Haplogroup D-M55

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Haplogroup D-M55
Possible time of origin45,357 (95% CI 52,258 - 39,364) ybp[1]

45,200 (95% CI 48,500 <-> 42,000) ybp[2]
Coalescence age21,434 (95% CI 24,812 - 18,513) ybp[3]

21,000 (95% CI 22,800 <-> 19,300) ybp[2]
Possible place of originpossibly Japanese archipelago
AncestorD-M174
Defining mutationsM55, M57, M64.1, M179, P37.1, P41.1, P190, 12f2b
Highest frequenciesJapanese people, Jōmon people, Ainu people、 Ryukyuan people

Haplogroup D-M55 (M64.1/Page44.1) also known as Haplogroup D1a2a is a Y-chromosome haplogroup. It is one of two branches of Haplogroup D1a. The other is D1a1, which is found with high frequency in Tibetans and other Tibeto-Burmese populations and geographical close groups. D is also distributed with low to medium frequency in Central Asia, East Asia, and Mainland Southeast Asia.

Haplogroup D-M55 is found in about 33%[4][5][6][7][8] of present-day Japanese males. It has been found in fourteen of a sample of sixteen or 87.5% of a sample of Ainu males in one study published in 2004[9] and in three of a sample of four or 75% of a sample of Ainu males in another study published in 2005 in which some individuals from the 2004 study may have been retested.[5] It is currently the most common Y-DNA haplogroup in Japan if O1-F265 and O2-M122 (TMRCA approx. 30,000 ~ 35,000 ybp) are considered as separate haplogroups. Haplogroup D-M55 may have been born in Japan at any time between its MRCA with D-Y34637 (found in present-day Onge and Jarawas) about 45,000 years ago and the MRCA of all extant branches of D-M55 about 21,000 years ago.

In 2017 it was confirmed that the Japanese branch of haplogroup D-M55 is distinct and isolated from other branches of haplogroup D since about 50,000 years ago. The split in D1a may have occurred near the Tibetan Plateau.[10]

History

Migration route of haplogroup D
Migration route of Y-DNA haplogroups in East Asia

Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago.[11] According to Michael F. Hammer of the University of Arizona, haplogroup D originated near the Tibetan Plateau and migrated into Japan were it eventually became D-M55.[12] Mitsuru Sakitani said that Haplogroup D1 came from Tibet to northern Kyushu via the Altai Mountains and the Korean Peninsula more than, and Haplogroup D-M55 (D1a2a) was born in the Japanese archipelago.[11]

Recent studies suggest that D-M55 became dominant during the late Jōmon period, shortly before the arrival of the Yayoi, suggesting a population boom and bust.[13]

Frequency

The average frequency in Japanese is about 33%.[4][5][7][8] High frequencies are found in various places in Japan, especially in Hokkaidō, eastern Honshū, southern Kyūshū, and Okinawa.

  • Ainu people: 87.5%（Tajima et al. 2004[9]）
  • Asahikawa (Hokkaido): 63.7% (estimated from Y-STR haplotypes)[7]
  • Chiba: 45.5%[14]
  • Tokyo: 40.4% (21/57 = 36.8% JPT, 23/52 = 44.2%[14])
  • Okinawa: 37.6% (0/7 Hateruma,[15] 1/20 = 5.0% Iriomote,[15] 8/29 = 27.6% Katsuren,[15] 10/32 = 31.3% Yomitan,[15] 16/49 = 32.7% Ishigaki,[16] 13/38 = 34.2% Miyako,[16] 13/36 = 36.1% Haebaru,[16] 7/19 = 36.8% Gushikami,[15] 35/87 = 40.2% Okinawa estimated from Y-STR haplotypes,[7] 38/80 = 47.5% Itoman,[15] 25/45 = 55.6% Okinawa[5])
  • Kanto region: 37.6%[4]
  • Kyushu: 35.0% (8/31 = 25.8% Fukuoka Prefecture,[17] 29/104 = 27.9% Kyushu,[9] 90/300 = 30.0% Nagasaki college students,[8] 39/129 = 30.2% Saga Prefectural Chienkan Senior High School students,[16] 34/102 = 33.3% Fukuoka adult men,[8] 7/21 = 33.3% Nagasaki Prefecture,[17] 13/37 = 35.1% Ōita Prefecture,[17] 95/270 = 35.2% Miyazaki Prefecture,[18] 470/1285 = 36.6% Miyazaki Prefecture,[17] 58/151 = 38.4% Kagoshima Prefecture,[17] 5/11 = 45.5% Saga Prefecture,[17] 22/47 = 46.8% Kumamoto Prefecture[17])
  • Nagoya: 34.3% (estimated from Y-STR haplotypes)[7]
  • Sapporo: 33.9% (100/302 = 33.1% Sapporo college students,[8] 72/206 = 35.0% Sapporo adult men[8])
  • Kawasaki: 33.0%[8]
  • Shizuoka: 32.8%[5]
  • Kanazawa: 32.6% (97/298 = 32.6%,[8] 76/232 = 32.8%[8])
  • Aomori: 31.1% (22/79 = 27.8%,[16] 11/27 = 40.7%[5])
  • Shikoku: 30% (18/70 = 25.7% Tokushima,[5] 9/31 = 29.0% Shikoku,[17] 119/388 = 30.7% Tokushima college students[8]）
  • Micronesia: 1/17 = 5.9％（Hammer et al. 2006[5]）
  • South Korea : 3/75 = 4.0% (Hammer et al. 2006[5]), 12/317 = 3.8% (estimated from Y-STR haplotypes),[7] 8/506 = 1.6% (Kim et al. 2011[19])
  • West Timor: 1/497 = 0.2%（Tumonggor et al. 2014[20]）

Ancient DNA

A Jōmon period man excavated from Funadomari remains (about 3,800 - 3,500 YBP) in Rebun Island in Hokkaido belongs to Haplogroup D1a2a2a(D-CTS220).[21]

The analysis of an Jōmon sample (Ikawazu) and an ancient sample from the Tibetan Plateau (Chokhopani, Ch) found only partially shared ancestry, suggesting a positive genetic bottleneck regarding the spread of haplogroup D from an ancient population related to the Tibetan Chokhopani sample (and modern Tibeto-Burmese groups).[22]

Phylogenetic tree

By ISOGG tree（Version: 14.151）.[23]

References

  1. ↑ "Welcome to FamilyTreeDNA Discover". https://discover.familytreedna.com/y-dna/D-Z3660/scientific?section=tmrca. 
  2. ↑ 2.0 2.1 YFull Haplogroup YTree v7.02.01 as of March 15, 2019.
  3. ↑ "Welcome to FamilyTreeDNA Discover". https://discover.familytreedna.com/y-dna/D-M64/scientific?section=tmrca. 
  4. ↑ 4.0 4.1 4.2 Katoh, ToruExpression error: Unrecognized word "etal". (2005). "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. 
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 Hammer, Michael F.; Karafet, Tatiana M.; Park, Hwayong; Omoto, Keiichi; Harihara, Shinji; Stoneking, Mark; Horai, Satoshi (2006). "Dual origins of the Japanese: Common ground for hunter-gatherer and farmer Y chromosomes". Journal of Human Genetics 51 (1): 47–58. doi:10.1007/s10038-005-0322-0. PMID 16328082. 
  6. ↑ YOUICHI SATO, TOSHIKATSU SHINKA, ASHRAF A. EWIS, AIKO YAMAUCHI, TERUAKI IWAMOTO, YUTAKA NAKAHORI Overview of genetic variation in the Y chromosome of modern Japanese males.
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 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): 480–95. doi:10.1111/j.1469-1809.2006.00343.x. PMID 17274803. 
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 "Overview of genetic variation in the Y chromosome of modern Japanese males". Anthropological Science 122 (3): 131–136. 2014. doi:10.1537/ase.140709. 
  9. ↑ 9.0 9.1 9.2 Tajima, Atsushi (2004). ""(March 2, 2004). "Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages". Journal of Human Genetics 49 (4): 187–193. doi:10.1007/s10038-004-0131-x. PMID 14997363. 
  10. ↑ Mondal, Mayukh & Bergström, Anders & Xue, Yali & Calafell, Francesc & Laayouni, Hafid & Casals, Ferran & Majumder, Partha & Tyler-Smith, Chris & Bertranpetit, Jaume. (2017). Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Human Genetics. 136. 10.1007/s00439-017-1800-0.
  11. ↑ 11.0 11.1 崎谷満『DNA・考古・言語の学際研究が示す新・日本列島史』（勉誠出版　2009年）(in Japanese)
  12. ↑ "Archived copy". http://www.eva.mpg.de/genetics/pdf/Japan.pdf. 
  13. ↑ Ohashi, Jun; Tokunaga, Katsushi; Hitomi, Yuki; Sawai, Hiromi; Khor, Seik-Soon; Naka, Izumi; Watanabe, Yusuke (2019-06-17). "Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period" (in en). Scientific Reports 9 (1): 8556. doi:10.1038/s41598-019-44473-z. ISSN 2045-2322. PMID 31209235. Bibcode: 2019NatSR...9.8556W. 
  14. ↑ 14.0 14.1 "Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree". Journal of Human Genetics 58 (4): 195–201. April 2013. doi:10.1038/jhg.2012.159. PMID 23389242. 
  15. ↑ 15.0 15.1 15.2 15.3 15.4 15.5 Shinka, Toshikatsu; Tomita, Keiko; Toda, Tatsushi; Kotliarova, Svetlana E.; Lee, Juwon; Kuroki, Yoko; Jin, Dong Kyu; Tokunaga, Katsushi et al. (1999). "Genetic variations on the y chromosome in the Japanese population and implications for modern human y chromosome lineage". Journal of Human Genetics 44 (4): 240–245. doi:10.1007/s100380050151. PMID 10429363. 
  16. ↑ 16.0 16.1 16.2 16.3 16.4 Totsuka, Shoji; Sato, Youichi; Tanaka, Masashi (2016). "A study of the geographic distribution of y chromosomal and mitochondrial DNA haplogroups in Japanese population by Super Science High School Consortium (SSH)". Anthropological Science (Japanese Series) 124 (2): 85–91. doi:10.1537/asj.161018. https://www.jstage.jst.go.jp/article/asj/124/2/124_161018/_article/-char/ja/. 
  17. ↑ 17.0 17.1 17.2 17.3 17.4 17.5 17.6 17.7 Hirofumi Nohara, Ikuko Maeda, Rinnosuke Hisazumi, Taketo Uchiyama, Hiroko Hirashima, Masahito Nakata, Rika Ohno, Tetsuro Hasegawa, and Kenshi Shimizu (2021), "Geographic distribution of Y-STR haplotypes and Y-haplogroups among Miyazaki Prefecture residents." Japanese Journal of Forensic Science and Technology, Vol. 26, Issue 1, p. 17-27. https://doi.org/10.3408/jafst.778
  18. ↑ Y Seo, Y Takami, T Nakayama, and K Takahama, "Y chromosome DNA polymorphisms and their haplotypes in a Japanese population." Leg Med (Tokyo) 1999 Sep;1(3):145-9. doi: 10.1016/s1344-6223(99)80027-3.
  19. ↑ Kim, Soon-Hee; Kim, Ki-Cheol; Shin, Dong-Jik; Jin, Han-Jun; Kwak, Kyoung-Don; Han, Myun-Soo; Song, Joon-Myong; Kim, Won et al. (2011). "High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea". Investigative Genetics 2011 (2): 10. doi:10.1186/2041-2223-2-10. PMID 21463511. 
  20. ↑ Tumonggor, Meryanne KExpression error: Unrecognized word "etal". (2014). "Isolation, contact and social behavior shaped genetic diversity in West Timor". Journal of Human Genetics 59 (9): 494–503. doi:10.1038/jhg.2014.62. PMID 25078354. 
  21. ↑ 神澤ほか(2016)「礼文島船泊縄文人の核ゲノム解析」第70回日本人類学大会 [1](in Japanese)
  22. ↑ Boer, Elisabeth de; Yang, Melinda A.; Kawagoe, Aileen; Barnes, Gina L. (2020). "Japan considered from the hypothesis of farmer/language spread" (in en). Evolutionary Human Sciences 2: e13. doi:10.1017/ehs.2020.7. ISSN 2513-843X. PMID 37588377. 
  23. ↑ "2019-2020 Haplogroup D Tree". https://docs.google.com/spreadsheets/d/1QBUFZl03X92qNN61lQ8VtIKwbBMeuBzvqXQ47IQPBps/edit#gid=437997455. 
  24. ↑ "Genetic affinities of the Andaman Islanders, a vanishing human population". Current Biology 13 (2): 86–93. January 2003. doi:10.1016/S0960-9822(02)01336-2. PMID 12546781. 
  25. ↑ "D YTree". https://www.yfull.com/tree/D/. 
  26. ↑ Y-DNA Haplogroup D and its Subclades - 2014
  27. ↑ Tyler-Smith, Chris; Xue, Yali; Thomas, Mark G.; Yang, Huanming; Arciero, Elena; Asan; Connell, Bruce A.; Jones, Abigail L. et al. (2019-06-13). "A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa" (in en). Genetics 212 (4): 1421–1428. doi:10.1534/genetics.119.302368. ISSN 0016-6731. PMID 31196864. 
  28. ↑ Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!" (in en-US). https://dna-explained.com/2019/06/21/exciting-new-y-dna-haplogroup-d-discoveries/. 



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