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%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. 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 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 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.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.

History

Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago.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) According to Michael F. Hammer of the University of Arizona, haplogroup D originated near the Tibetan Plateau and migrated into Japan where it eventually became D-M55. 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.

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.

Frequency The average frequency in Japanese is about 30%. 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） Asahikawa (Hokkaido): 63.7% (estimated from Y-STR haplotypes) Chiba: 45.5% Tokyo: 40.4% (21/57 = 36.8% JPT, 23/52 = 44.2%) Okinawa: 37.6% (0/7 Hateruma, 1/20 = 5.0% Iriomote, 8/29 = 27.6% Katsuren, 10/32 = 31.3% Yomitan, 16/49 = 32.7% Ishigaki, 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) Kanto region: 37.6% Kyushu: 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,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. 470/1285 = 36.6% Miyazaki Prefecture,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 58/151 = 38.4% Kagoshima Prefecture, 5/11 = 45.5% Saga Prefecture, 22/47 = 46.8% Kumamoto Prefecture) Nagoya: 34.3% (estimated from Y-STR haplotypes) Sapporo: 33.9% (100/302 = 33.1% Sapporo college students, 72/206 = 35.0% Sapporo adult men) Kawasaki: 33.0% Shizuoka: 32.8% Kanazawa: 32.6% (97/298 = 32.6%, 76/232 = 32.8%) Aomori: 31.1% (22/79 = 27.8%, 11/27 = 40.7%) Shikoku: 30% (18/70 = 25.7% Tokushima, 9/31 = 29.0% Shikoku, 119/388 = 30.7% Tokushima college students） Micronesia: 1/17 = 5.9%（Hammer et al. 2006） South Korea: 3/75 = 4.0% (Hammer et al. 2006), 12/317 = 3.8% (estimated from Y-STR haplotypes), 8/506 = 1.6% (Kim et al. 2011) West Timor: 1/497 = 0.2%（Tumonggor et al. 2014）

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).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)

The analysis of a Jōmon sample (Ikawazu) and an ancient sample from the Tibetan Plateau (Chokhopani) 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).

Phylogenetic tree By ISOGG Tree (Version: 14.151).

DE (YAP) D (CTS3946) D1 (M174/Page30, IMS-JST021355, Haplogroup D-M174) D1a (CTS11577) D1a1 (F6251/Z27276) D1a1a (M15) Tibet D1a1b (P99) Tibet, Mongol, Central Asia D1a2(Z3660) D1a2a (M64.1/Page44.1, M55) Japan(Yamato people、Ryukyuan people、Ainu people) D1a2b (Y34637) Andaman Islands（Onge people, Jarawa people） D1b (L1378) PhilippinesY-DNA Haplogroup D and its Subclades - 2014 D2 (A5580.2) Nigeria, African American, Saudi Arabia, Syria

References