Haplogroup D-M55 Explained

D-M55
Origin-Date:45,357 (95% CI 52,258 - 39,364) ybp[1]

45,200 (95% CI 48,500 <-> 42,000) ybp[2]
Origin-Place:possibly Japanese archipelago
Tmrca:21,434 (95% CI 24,812 - 18,513) ybp[3]

21,000 (95% CI 22,800 <-> 19,300) ybp
Ancestor:D-M174
Mutations:M55, M57, M64.1, M179, P37.1, P41.1, P190, 12f2b
Members:Japanese 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] 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[7] 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. 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.

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.[8]

History

Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago.[9] 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.[10] Mitsuru Sakitani said that Haplogroup D1 came from Tibet to northern Kyushu via the Altai Mountains and the Korean Peninsula more than 50,000 years ago, and Haplogroup D-M55 (D1a2a) was born in the Japanese archipelago.[9]

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.[11]

Frequency

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

87.5%（Tajima et al. 2004）

45.5%[12]

40.4% (21/57 = 36.8% JPT, 23/52 = 44.2%)

37.6% (0/7 Hateruma,[13] 1/20 = 5.0% Iriomote, 8/29 = 27.6% Katsuren, 10/32 = 31.3% Yomitan, 16/49 = 32.7% Ishigaki,[14] 13/38 = 34.2% Miyako, 13/36 = 36.1% Haebaru, 7/19 = 36.8% Gushikami, 35/87 = 40.2% Okinawa estimated from Y-STR haplotypes, 38/80 = 47.5% Itoman, 25/45 = 55.6% Okinawa)

37.6%[15]

35.0% (8/31 = 25.8% Fukuoka Prefecture, 29/104 = 27.9% Kyushu, 90/300 = 30.0% Nagasaki college students, 39/129 = 30.2% Saga Prefectural Chienkan Senior High School students, 34/102 = 33.3% Fukuoka adult men, 7/21 = 33.3% Nagasaki Prefecture, 13/37 = 35.1% Ōita Prefecture, 95/270 = 35.2% Miyazaki Prefecture,[16] 470/1285 = 36.6% Miyazaki Prefecture,[17] 58/151 = 38.4% Kagoshima Prefecture, 5/11 = 45.5% Saga Prefecture, 22/47 = 46.8% Kumamoto Prefecture)

34.3% (estimated from Y-STR haplotypes)

33.9% (100/302 = 33.1% Sapporo college students, 72/206 = 35.0% Sapporo adult men)

33.0%

32.8%

32.6% (97/298 = 32.6%, 76/232 = 32.8%)

31.1% (22/79 = 27.8%, 11/27 = 40.7%)

30% (18/70 = 25.7% Tokushima,[18] 9/31 = 29.0% Shikoku, 119/388 = 30.7% Tokushima college students）

1/17 = 5.9％（Hammer et al. 2006[18] ）

3/75 = 4.0% (Hammer et al. 2006[18]), 12/317 = 3.8% (estimated from Y-STR haplotypes), 8/506 = 1.6% (Kim et al. 2011[19])

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 a 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. Web site: Welcome to FamilyTreeDNA Discover .
  2. YFull Haplogroup YTree v7.02.01 as of March 15, 2019.
  3. Web site: Welcome to FamilyTreeDNA Discover .
  4. YOUICHI SATO, TOSHIKATSU SHINKA, ASHRAF A. EWIS, AIKO YAMAUCHI, TERUAKI IWAMOTO, YUTAKA NAKAHORI of genetic variation in the Y chromosome of modern Japanese males.
  5. Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms. N.. Takezaki. K.. Minaguchi. Nonaka, I.. Annals of Human Genetics. February 2, 2007. 17274803. 10.1111/j.1469-1809.2006.00343.x. 71. Pt 4. 480–95. 10130/491. 1041367. free.
  6. Sato Y, Shinka T, Ewis AA, Yamauchi A, Iwamoto T, Nakahori Y . 2014. Overview of genetic variation in the Y chromosome of modern Japanese males . Anthropological Science . 122 . 3. 131–136 . 10.1537/ase.140709 . free.
  7. Tajima . Atsushi . etal . 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 . 10.1007/s10038-004-0131-x . 14997363 . free .
  8. 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.
  9. 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)
  10. Web site: Archived copy . 2017-09-29 . 2009-03-04 . https://web.archive.org/web/20090304162550/http://www.eva.mpg.de/genetics/pdf/Japan.pdf . dead .
  11. 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. Scientific Reports. en. 9. 1. 8556. 10.1038/s41598-019-44473-z. 2045-2322. free. 31209235. 6572846. 2019NatSR...9.8556W.
  12. Naitoh S, Kasahara-Nonaka I, Minaguchi K, Nambiar P . Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree . Journal of Human Genetics . 58 . 4 . 195–201 . April 2013 . 23389242 . 10.1038/jhg.2012.159 . free .
  13. 10.1007/s100380050151 . Genetic variations on the y chromosome in the Japanese population and implications for modern human y chromosome lineage . 1999 . Shinka . Toshikatsu . Tomita . Keiko . Toda . Tatsushi . Kotliarova . Svetlana E. . Lee . Juwon . Kuroki . Yoko . Jin . Dong Kyu . Tokunaga . Katsushi . Nakamura . Hideki . Nakahori . Y. . Journal of Human Genetics . 44 . 4 . 240–245 . 10429363 . 9593881 . free .
  14. A study of the geographic distribution of y chromosomal and mitochondrial DNA haplogroups in Japanese population by Super Science High School Consortium (SSH) . 10.1537/asj.161018 . 2016 . Totsuka . Shoji . Sato . Youichi . Tanaka . Masashi . Anthropological Science (Japanese Series) . 124 . 2 . 85–91 .
  15. Katoh . Toru . Munkhbat . Batmunkh . Tounai . Kenichi . etal . 2005 . Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis . Gene . 346 . 63–70 . 10.1016/j.gene.2004.10.023 . 15716011 .
  16. 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.
  17. 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. 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 . 10.1007/s10038-005-0322-0 . 16328082 . free .
  19. Kim . Soon-Hee . Kim . Ki-Cheol . Shin . Dong-Jik . Jin . Han-Jun . Kwak . Kyoung-Don . Han . Myun-Soo . Song . Joon-Myong . Kim . Won . Kim . Wook . 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 . 10.1186/2041-2223-2-10 . 21463511 . 3087676 . free .
  20. Tumonggor . Meryanne K . Karafet . Tatiana M . Downey . Sean . etal . 2014 . Isolation, contact and social behavior shaped genetic diversity in West Timor . Journal of Human Genetics . 59 . 9. 494–503 . 10.1038/jhg.2014.62 . free . 25078354 . 4521296 .
  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 http://anthrop-meeting.sakura.ne.jp/70/pdf/ittupan_proceeding%20.pdf (in Japanese)
  22. Boer. Elisabeth de. Yang. Melinda A.. Kawagoe. Aileen. Barnes. Gina L.. 2020. Japan considered from the hypothesis of farmer/language spread. Evolutionary Human Sciences. en. 2. e13 . 10.1017/ehs.2020.7. 37588377 . 10427481 . 2513-843X. free.
  23. Web site: 2019-2020 Haplogroup D Tree.
  24. Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC, Underhill PA, Pierson M, Frame IG, Hagelberg E . Genetic affinities of the Andaman Islanders, a vanishing human population . Current Biology . 13 . 2 . 86–93 . January 2003 . 12546781 . 10.1016/S0960-9822(02)01336-2 . 12155496 . free .
  25. Web site: D YTree . 2019-09-02 . 2019-08-31 . https://web.archive.org/web/20190831121238/https://www.yfull.com/tree/D/ . dead .
  26. http://www.isogg.org/tree/ISOGG_HapgrpD.html 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.. Haber. Marc. 2019-06-13. A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa. Genetics. en. 1421–1428. 10.1534/genetics.119.302368. 0016-6731. 31196864. free. 212. 4. 6707464.
  28. Web site: Exciting New Y DNA Haplogroup D Discoveries!. Estes. Roberta. 2019-06-21. DNAeXplained - Genetic Genealogy. en-US. 2019-07-08.

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