Haplogroup D-M55

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%  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 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.

History
Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago. 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. 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 33%. 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, 470/1285 = 36.6% Miyazaki Prefecture, 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).

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).

Phylogenetic tree
By ISOGG tree（Version: 14.151）.


 * D1b (M55, M57, M64.1/Page44.1, M179/Page31, M359.1/P41.1, P37.1, P190, 12f2.2) - Japan (Mainlands Japanese people、Ainu people、Ryukyuan people)
 * D1b1 (M116.1)
 * D1b1a (M125)
 * D1b1a1 (P42)
 * D1b1a1a (P12_1, P12_2, P12_3)
 * D1b1a2 (IMS-JST022457)
 * D1b1a2a (P53.2)
 * D1b1a2b (IMS-JST006841/Page3)
 * D1b1a2b1 (CTS3397)
 * D1b1a2b1a (Z1500)
 * D1b1a2b1a1 (Z1504, CTS8093) - Japan(Aichi prefecture)
 * D1b1a2b1a1a (FGC6373) - Japan(Hiroshima prefecture)
 * D1b1a2b1a1a1 (L137.3) - Japan(Shizuoka prefecture)
 * D1b1a2b1a1a1a (Z40625)
 * D1b1a2b1a1a1b (CTS217)
 * D1b1a2b1a1a1c (Z38475)
 * D1b1a2b1a1a2 (FGC6372)
 * D1b1a2b1a1a3 (CTS10649)
 * D1b1a2b1a1a4 (Z40609)
 * D1b1a2b1a1b (Z40614)
 * D1b1a2b1a1c (Z31543)
 * D1b1a2b1a1d (FGC30021)
 * D1b1a2b1a1e (Z31548)
 * D1b1a2b1a1f (Z31553)
 * D1b1a2b1a1g (CTS6223)
 * D1b1a2b1a1h (CTS4093)
 * D1b1a2b1a1i (Z40687)
 * D1b1a2b1a1i1 (Z35641)
 * D1b1a2b1a1i2 (Z40688)
 * D1b1a2b1a1j (CTS5058)
 * D1b1a2b1a1k (FGC34008)
 * D1b1a2b1a2 (CTS266)
 * D1b1a2b1a3 (Z40672)
 * D1b1a2b1b (CTS1372)
 * D1b1a2b2 (CTS5581)
 * D1b1a3 (CTS10972)
 * D1b1a3a (Z31538)
 * D1b1a3b (CTS232)
 * D1b1b (P120)
 * D1b1c (CTS6609)
 * D1b1c1 (CTS1897/Z1574)
 * D1b1c1a (CTS11032) - Japan(Aichi prefecture)
 * D1b1c1a1 (CTS218/V1105/Z1527)
 * D1b1c1a1a (CTS6909)
 * D1b1c1a1a1 (CTS6969)
 * D1b1c1a1a2 (CTS9770)
 * D1b1c1a1b (CTS3033)
 * D1b1c1a1b1 (M2176)
 * D1b1c1a1b2 (CTS2472)
 * D1b1c1a1c (M151)
 * D1b1c1a2 (F8521.3)
 * D1b1c1b (CTS1964)
 * D1b1c1b1 (CTS974)
 * D1b1c1b2 (CTS722)
 * D1b1c1c (Z30644) - Japan(Fukushima prefecture)
 * D1b1c1c1 (CTS4292)
 * D1b1c1c1a (Z31517)
 * D1b1c1c1b (CTS1798)
 * D1b1c1c2 (Z31512)
 * D1b1c1d (CTS5641) - Japan(Kyoto prefecture)
 * D1b1c1e (CTS429)
 * D1b1c2 (CTS103)
 * D1b1c2a (Z42462)
 * D1b2 (CTS131)
 * D1b2a (CTS220) - Japan (a Jomon man from Rebun Island)
 * D1b2a1 (CTS10495)
 * D1b2a1a (Z31507)
 * D1b2a1b (CTS624)
 * D1b2a2 (CTS11285) - Japan(Osaka prefecture)
 * D1b2a2a (PH2316) - Japan(Iwate prefecture)
 * D1b2a2a1 (Z38287)
 * D1b2a2a1a (Z38284)
 * D1b2a2a2 (Z38289) - Japan(Hyogo prefecture)
 * D1b2a2b (CTS288)
 * D1b2a2b1 (CTS1815)
 * D1b2a2b2 (Z40665)
 * D1b2b (CTS68)