Haplogroup D-M55

Haplogroup D-M55 also known as Haplogroup D1a2 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 Tibet and also distributed sparsely in Central Asia, East Asia, and Mainland Southeast Asia.

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
Ancestor(Grandparent) D
Defining mutationsM55, M57, M64.1, M179, P37.1, P41.1, P190, 12f2b
Highest frequenciesJōmon people and Koban culture;
today: Ainu people、Ryukyuan people

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.[9] D1a2 was also found among ancient populations in Russia and Georgia.[10]

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 in Central Asia, while some others suggest an instant split during the origin of haplogroup D itself, as the Japanese branch has five unique mutations not found in any other D-branch.[11]

History
Migration route of haplogroup D considered most likely by Haber et al. 2019

Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago.[12] Michael F. Hammer of the University of Arizona said: "The ancestors of the Jōmon people were in Central Asia about 50,000 years ago. They continued to migrate eastwards and arrived in Japan by the southern Korean and Ryukyuan route and the northern Okhotsk route (Sakhalin and Hokkaido) about 30,000 ago, and D1b was born in the Japanese archipelago.[13] "Mitsuru Sakitani said that Haplogroup D1 came from Central Asia to northern Kyushu via the Altai Mountains and the Korean Peninsula more than 40,000 years before present, and Haplogroup D-M55 (D1b) was born in the Japanese archipelago.[12]

Recent studies suggest that D-M55 was the majority lineage of the Jōmon people at a frequency of about 70%.[14]

Frequency

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

  • 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[16])
  • Timor Island：0.2%（Meryanne et al. 2014[17]）

Ancient DNA

A Jōmon man excavated from Funadomari remains (about 3,800 - 3,500 YBP) in Rebun Island in Hokkaido belongs to Haplogroup D1b2a(D-CTS220).[18] This discovery proved the hypothesis that Haplogroup D-M55 is a Jōmon lineage.

A study published in the “Journal for archeological science” by Boulygina et al. 2020 analyzed ancient Koban burials and found a high number of lineage D1a2 (D-M55) which is common among the Ainu people in Japanand southeastern Russia.[10]

Phylogenetic tree

By ISOGG tree（Version: 14.151）.[19]

References
  1. 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.
  2. YFull Haplogroup YTree v7.02.01 as of March 15, 2019.
  3. 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. 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. 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.
  7. 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. ISSN 1344-6223. PMID 24262653.
  8. 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. 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 (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.
  10. Boulygina, Eugenia; Tsygankova, Svetlana; Sharko, Fedor; Slobodova, Natalia; Gruzdeva, Natalia; Rastorguev, Sergey; Belinsky, Andrej; Härke, Heinrich; Kadieva, Anna; Demidenko, Sergej; Shvedchikova, Tatiana (2020-06-01). "Mitochondrial and Y-chromosome diversity of the prehistoric Koban culture of the North Caucasus". Journal of Archaeological Science: Reports. 31: 102357. doi:10.1016/j.jasrep.2020.102357. ISSN 2352-409X.
  11. 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.
  12. 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)
  13. http://www.eva.mpg.de/genetics/pdf/Japan.pdf
  14. 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. doi:10.1038/s41598-019-44473-z. ISSN 2045-2322. PMC 6572846. PMID 31209235.
  15. Tajima, A.; et al. (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.
  16. 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. "High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea". Investigative Genetics. 2011 (2): 10.
  17. 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: 494–503. doi:10.1038/jhg.2014.62. PMC 4521296. PMID 25078354.
  18. 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 (in Japanese)
  20. 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.
  21. Y-Full
  22. Y-DNA Haplogroup D and its Subclades - 2014
  23. 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: genetics.302368.2019. doi:10.1534/genetics.119.302368. ISSN 0016-6731. PMC 6707464. PMID 31196864.
  24. Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!". DNAeXplained - Genetic Genealogy. Retrieved 2019-07-08.
Phylogenetic tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1 [χ 4]
A1a A1b
A1b1 BT
B CT
DE CF
D E C F
F1  F2  F3  GHIJK
G HIJK
IJK H
IJ K
I   J     LT [χ 5]       K2 [χ 6]
L     T    K2a [χ 7]        K2b [χ 8]     K2c     K2d K2e [χ 9]  
K-M2313 [χ 10]     K2b1 [χ 11] P [χ 12]
NO   S [χ 13]  M [χ 14]    P1     P2
N O Q R
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