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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.

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. ^ https://discover.familytreedna.com/y-dna/D-Z3660/scientific?section=tmrca
  2. ^ a b YFull Haplogroup YTree v7.02.01 as of March 15, 2019.
  3. ^ https://discover.familytreedna.com/y-dna/D-M64/scientific?section=tmrca
  4. ^ a b c Katoh, Toru; Munkhbat, Batmunkh; Tounai, Kenichi; et al. (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. ^ a b c d e f g h i 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. ^ a b c d e f 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. hdl:10130/491. PMID 17274803. S2CID 1041367.
  8. ^ a b c d e f g h i j 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. doi:10.1537/ase.140709.
  9. ^ a b c Tajima, Atsushi; et al. (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. ^ a b 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" (PDF). Archived from the original (PDF) on 2009-03-04. Retrieved 2017-09-29.{{cite web}}: CS1 maint: archived copy as title (link)
  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". Scientific Reports. 9 (1): 8556. Bibcode:2019NatSR...9.8556W. doi:10.1038/s41598-019-44473-z. ISSN 2045-2322. PMC 6572846. PMID 31209235.
  14. ^ a b Naitoh S, Kasahara-Nonaka I, Minaguchi K, Nambiar P (April 2013). "Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree". Journal of Human Genetics. 58 (4): 195–201. doi:10.1038/jhg.2012.159. PMID 23389242.
  15. ^ a b c d e f Shinka, Toshikatsu; Tomita, Keiko; Toda, Tatsushi; Kotliarova, Svetlana E.; Lee, Juwon; Kuroki, Yoko; Jin, Dong Kyu; Tokunaga, Katsushi; Nakamura, Hideki; Nakahori, Y. (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. S2CID 9593881.
  16. ^ a b c d e 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.
  17. ^ a b c d e f g h 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; 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. doi:10.1186/2041-2223-2-10. PMC 3087676. PMID 21463511.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  20. ^ Tumonggor, Meryanne K; Karafet, Tatiana M; Downey, Sean; et al. (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. PMC 4521296. 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". Evolutionary Human Sciences. 2. doi:10.1017/ehs.2020.7. ISSN 2513-843X.
  23. ^ "2019-2020 Haplogroup D Tree".
  24. ^ Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC, Underhill PA, Pierson M, Frame IG, Hagelberg E (January 2003). "Genetic affinities of the Andaman Islanders, a vanishing human population". Current Biology. 13 (2): 86–93. doi:10.1016/S0960-9822(02)01336-2. PMID 12546781. S2CID 12155496.
  25. ^ "D YTree". Archived from the original on 2019-08-31. Retrieved 2019-09-02.
  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.; 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. 212 (4): 1421–1428. doi:10.1534/genetics.119.302368. ISSN 0016-6731. PMC 6707464. PMID 31196864.
  28. ^ Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!". DNAeXplained - Genetic Genealogy. Retrieved 2019-07-08.
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