Haplogroup D-M55

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Haplogroup D-M55
Possible time of origin35,000-40,000YBP[1]

44,600 [95% CI 41,400 <-> 47,800] ybp[2]
Coalescence age21,100 [95% CI 19,000 <-> 23,300] 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%[3][4][5][6][7] 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[8] 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.[4] 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. It is considered that Haplogroup D-M55 was born in Japan 38,000-37,000 years before present.[1]

Recently it was confirmed that the Japanese branch of haplogroup D-M55 is distinct and isolated from other D-branches since more than 53,000 years ago. The split in D1a probably happened near the Tibetan Plateau.[9]

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.[10] 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.[11] 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.[10]

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.[12]

Frequency[]

The average frequency in Japanese is about 33%.[3][4][6][7] High frequencies are found in various places in Japan, especially in Hokkaidō, eastern Honshū, and Okinawa.

  • Ainu people：87.5%（Tajima et al. 2004[8]）
  • Asahikawa (Hokkaido): 63.7% (estimated from Y-STR haplotypes)[6]
  • Okinawa：55.6%[4]
  • Kanto region: 48.2%[6]
  • Okinawa: 40.2% (estimated from Y-STR haplotypes)[6]
  • Aomori：38.5%[4]
  • Kanto region: 37.6%[3]
  • Nagoya: 34.3% (estimated from Y-STR haplotypes)[6]
  • Shizuoka：32.8%[4]
  • Kyushu：26.4%[4]
  • Tokushima：25.7%[4]（Hammer et al. 2006[4]）
  • Micronesia：9.5％（Hammer et al. 2006[4]）
  • South Korea: 4.0% (Hammer et al. 2006[4]), 3.8% (estimated from Y-STR haplotypes),[6] 1.6% (Kim et al. 2011[13])
  • Timor Island：0.2%（Meryanne et al. 2014[14]）

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).[15]

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).[16]

Phylogenetic tree[]

By ISOGG tree（Version: 14.151）.[17]

References[]

  1. ^ a b Shi, Hong; Zhong, Hua; Peng, Yi; Dong, Yong-li; Qi, Xue-bin; Zhang, Feng; Liu, Lu-Fang; Tan, Si-jie; Ma, Runlin Z; Xiao, Chun-Jie; Wells, R Spencer; Jin, Li; Su, Bing (October 29, 2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biology. 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782. open access
  2. ^ a b YFull Haplogroup YTree v7.02.01 as of March 15, 2019.
  3. ^ 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.
  4. ^ a b c d e f g h i j k 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.
  5. ^ 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.
  6. ^ a b c d e f g 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.
  7. ^ a b Harayama, Yuta; Kamei, Sayako; Sato, Noriko; Hayashi, Tokutaro; Shiozaki, Tetsuya; Ota, Masao; Asamura, Hideki (2014-01-01). "Analysis of Y chromosome haplogroups in Japanese population using short amplicons and its application in forensic analysis". Legal Medicine. 16 (1): 20–25. doi:10.1016/j.legalmed.2013.10.005. hdl:10091/17954. ISSN 1344-6223. PMID 24262653.
  8. ^ a b 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.
  9. ^ 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.
  10. ^ 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)
  11. ^ http://www.eva.mpg.de/genetics/pdf/Japan.pdf
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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)
  16. ^ 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.
  17. ^ "2019-2020 Haplogroup D Tree".
  18. ^ 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.
  19. ^ Y-Full
  20. ^ Y-DNA Haplogroup D and its Subclades - 2014
  21. ^ 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.
  22. ^ Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!". DNAeXplained - Genetic Genealogy (in American English). Retrieved 2019-07-08.
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