Haplogroup D-M174

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Haplogroup D-M174
Geographic distributions of Y chromosome haplogroups D-M174 in East Asia.png
Possible time of origin50,000[1] - 60,000[2] years BP

65,200 [95% CI 62,100 <-> 68,300] ybp[3]
Coalescence age46,300 [95% CI 43,500 <-> 49,100] ybp[3]
Possible place of originAsia(Central Asia)[2][4][5]
AncestorDE
DescendantsD-Z27276(D1a) D-M55(D1b)
Defining mutationsM174, IMS-JST021355, PAGES00003

In human genetics, Haplogroup D-M174 is a Y-chromosome haplogroup. Both D-M174 and E lineages also exhibit the single-nucleotide polymorphism M168 which is present in all Y-chromosome haplogroups except A and B, as well as the YAP+ unique-event polymorphism, which is unique to Haplogroup DE. This haplogroup is found primarily in East Asia, though it is also found regularly with low frequency in Central Asia and Southeast Asia, and it has also been found sporadically in Europe and Western Asia.

Origins[edit]

Migration of haplogroup D

Haplogroup D-M174 is believed to have originated in Asia some 60,000 years before present.[2][4] While haplogroup D-M174 along with haplogroup E contains the distinctive YAP polymorphism (which indicates their common ancestry), no haplogroup D-M174 chromosomes have been found anywhere outside of Asia.[4]

Overview[edit]

It is found today at high frequency among populations in Tibet, the Japanese archipelago, and the Andaman Islands, though curiously not as much in the rest of India. The Ainu of Japan are notable for possessing almost exclusively Haplogroup D-M174 chromosomes. Haplogroup D-M174 chromosomes are also found at low to moderate frequencies among the Bai, Dai, Han, Hui, Manchu, Miao, Tujia, Xibe, Yao, and Zhuang of China and among several minority populations of Sichuan and Yunnan that speak Tibeto-Burman languages and reside in close proximity to the Tibetans, such as the Jingpo, Jino, Mosuo, Naxi, Pumi, Qiang, and Yi.[6]

Haplogroup D is also found in populations of China proper and Korea, but with much lower frequency than in populations of Tibet and Japan. A study published in 2011 found D-M174 in 2.49% (43/1729) of Han Chinese males, with frequencies of this haplogroup tending to be higher than average toward the north and toward the west of the country (5/56 = 8.9% D-M174 Shaanxi Han, 13/221 = 5.9% D-M174 Gansu Han, 6/136 = 4.4% D-M174 Yunnan Han, 1/27 = 3.7% D-M174 Guangxi Han, 2/61 = 3.3% D-M174 Hunan Han, 2/62 = 3.2% D-M174 Sichuan Han).[7] In another study of Han Chinese Y-DNA published in 2011, Haplogroup D-M174 was observed in 1.94% (7/361) of a sample of unrelated Han Chinese male volunteers at Fudan University in Shanghai, with the origins of most of the volunteers being traced back to East China (Jiangsu, Zhejiang, Shanghai, and Anhui).[8] In Korea, Haplogroup D-M174 has been observed in 3.8% (5/133) of a sample from Daejeon,[9] 3/85 = 3.5% of a sample from Seoul,[10] 3.3% (3/90) of a sample from Jeolla,[11] 2.4% (2/84) of a sample from Gyeongsang,[11] 2.3% (13/573) of another sample from Seoul,[9] 1.4% (1/72) of a sample from Chungcheong,[11] 1.1% (1/87) of a sample from Jeju,[11] and 0.9% (1/110) of a third sample from Seoul-Gyeonggi.[11] In other studies, haplogroup D-M174 has been observed in 6.7% (3/45)[12] and 4.0% (3/75)[13] of samples from Korea without any further specification of the area of sampling. Little high-resolution data regarding the phylogenetic position of Han Chinese and Korean members of Y-DNA Haplogroup D has been published, but the available data suggests that most Han Chinese members of Haplogroup D should belong to clades found frequently among Tibetans (and especially the D-M15 clade, also found among speakers of some Lolo-Burmese and Hmong-Mien languages), whereas most Korean members of Haplogroup D should belong to the D-M55 clade, which is found frequently among Ainu, Ryukyuan, and Japanese people.[13][11][3]

Haplogroup D Y-DNA has been found (albeit with low frequency) among modern populations of the Eurasian steppe, such as Southern Altaians (6/96 = 6.3% D-M174(xM15),[14] 6/120 = 5.0% D-P47[15]), Kazakhs (1/54 = 1.9% D-M174,[12] 6/1294 = 0.5% D[16]), Nogais (4/76 = 5.3% D-M174 Kara Nogai,[17] 1/87 = 1.1% D-M174 Kuban Nogai[17]), Khalkhas (1/24 = 4.2% D-M174,[12] 3/85 = 3.5% D-M174,[10] 2/149 D-M15 + 2/149 D-P47 = 4/149 = 2.7% D-M174 total[13]), Zakhchin (2/60 = 3.3% D-M174[10]), Uriankhai (1/60 = 1.7% D-M174[10]), and Kalmyks (5/426 = 1.2% D-M174[18]). It also has been found among linguistically similar (Turkic- or Mongolic-speaking) modern populations of the desert and oasis belt south of the steppe, such as Yugurs, Bao’an, Monguors, Uyghurs, and Uzbeks. In commercial testing, members have been found as far west as Romania in Europe and Iraq in Western Asia.[19]

Unlike haplogroup C-M217, Haplogroup D-M174 is not found in the New World; it is not present in any modern Native American (North, Central or South) populations. While it is possible that it traveled to the New World like Haplogroup C-M217, those lineages apparently became extinct.

Haplogroup D-M174 is also remarkable for its rather extreme geographic differentiation, with a distinct subset of Haplogroup D-M174 chromosomes being found exclusively in each of the populations that contains a large percentage of individuals whose Y-chromosomes belong to Haplogroup D-M174: Haplogroup D-M15 among the Tibetans (as well as among other East Asian and Southeast Asian populations that display low frequencies of Haplogroup D-M174 Y-chromosomes), Haplogroup D-M55 among the various populations of the Japanese Archipelago and with low frequency among Koreans, Haplogroup D-P99 among the inhabitants of Tibet and some other parts of central Eurasia (e.g. Mongolia[20] and the Altai[13][14][15]), and paragroup D-M174 without tested positive subclades (probably another monophyletic branch of Haplogroup D) among the Andaman Islanders. Another type (or types) of paragroup D-M174 without tested positive subclades is found at a very low frequency among the Turkic and Mongolic populations of Central Asia, amounting to no more than 1% in total. This apparently ancient diversification of Haplogroup D-M174 suggests that it may perhaps be better characterized as a "super-haplogroup" or "macro-haplogroup."

In one study, the frequency of Haplogroup D-M174 without tested positive subclades found among Thais was 10%.[2] Su et al. (2000) found DE-YAP/DYS287(xM15) in 11.1% (5/45) of a set of three samples from Thailand (including 20% (4/20) North Thai, 20% (1/5) So, and 0% (0/20) Northeast Thai) and in 16.7% (1/6) of a sample from Guam.[21] Meanwhile, the authors found D-M15 in 15% of a pair of samples of Yao (including 30% (3/10) Yao Jinxiu and 0% (0/10) Yao Nandan), 14.3% (2/14) of a sample of Yi, 3.8% (1/26) of a sample of Cambodians, and 3.6% (1/28) of a sample of Zhuang.[21] Dong et al. (2002) found DE-YAP Y-chromosomes in 12.5% (2/16) of a sample of Jingpo from Luxi City, Yunnan, 10.0% (2/20) of a sample of Dai from Luxi City, Yunnan, and 1.82% (1/55) of a sample of Nu from Gongshan and Fugong counties of Yunnan.[22]

Distribution[edit]

The Haplogroup D-M174 Y-chromosomes that are found among populations of the Japanese Archipelago (haplogroup D-M55 a.k.a. haplogroup D2) are particularly distinctive, bearing a complex of at least five individual mutations along an internal branch of the Haplogroup D-M174 phylogeny, thus distinguishing them clearly from the Haplogroup D-M174 chromosomes that are found among the Tibetans and Andaman Islanders and providing evidence that Y-chromosome Haplogroup D-M55 was the modal haplogroup in the ancestral population that developed the prehistoric Jōmon culture in the Japanese islands.

It is suggested that the majority of D-M174 Y-chromosome carriers migrated from Central Asia to East Asia. One group migrated into the Andaman Islands and mixed with the native Negrito population, thus forming the today Andamanese people (probably a male-only migration). Another group stayed in modern Tibet and southern China (today Tibeto-Burman peoples) and another group migrated to Japan, possibly via the Korean Peninsula (Jōmon people).[23][24]

Subclades[edit]

D-M174 (D*) Paragroup[edit]

Basal D-M174, without positive-tested subclades, found at high frequencies among Andaman Islanders [25](especially Onge(23/23 = 100%), Jarawa(4/4 = 100%)[26]) and some Tibetan minority tribes in Northeast India (among whom rates vary from zero to 65%).[5][27][28][29]

D-M174(xD-M15, D-P37, D-P47) has been found in approximately 5% of Altaians.[13] Kharkov et al. have found haplogroup D-M174(xD-M15) in 6.3% (6/96) of a pool of samples of Southern Altaians from three different localities, particularly in Kulada (5/46 = 10.9%) and Kosh-Agach (1/7 = 14%), though they have not tested for any marker of the subclade D-M55 or D-P99. Kharkov et al. also have reported finding haplogroup DE-M1(xD-M174) Y-DNA in one Southern Altaian individual from Beshpeltir (1/43 = 2.3%).[14]

D-Z27276 (D1a)[edit]

Haplogroup D-Z27276 is the common ancestor of D-M15 and D-P99.

D-M15 (D1a1)[edit]

D-M15 was first reported to have been found in a sample from Cambodia and Laos (1/18 = 5.6%) and in a sample from Japan (1/23 = 4.3%) in a preliminary worldwide survey of Y-DNA variation in extant human populations.[30]

Subsequently, Y-DNA that belongs to Haplogroup D-M15 has been found frequently among Tibeto-Burman-speaking populations of Southwestern China (including approximately 23% of Qiang,[2][31][32] approximately 12.5% of Tibetans,[2] and approximately 9% of Yi[2][33]) and among Yao people inhabiting northeastern Guangxi (6/31 = 19.4% Lowland Yao, 5/41 = 12.2% Native Mien, 3/41 = 7.3% Lowland Kimmun)[34] with a moderate distribution throughout Central Asia, East Asia, and continental Southeast Asia (Indochina).[2]

A study published in 2011 has found D-M15 in 7.8% (4/51) of a sample of Hmong Daw and in 3.4% (1/29) of a sample of Xinhmul from northern Laos.[34]

D-P47 (D1a2a)[edit]

Found with high frequency among Pumi,[2] Naxi,[2] and Tibetans,[35][2] with a moderate distribution in Central Asia.[2]

D-M55 (D1b)[edit]

Previously known as D-M55, D-M64.1/Page44.1 (D1b) is found with high frequency among Ainu,[36] Japanese,[37] and Ryukyuans.[37]

Kim et al. (2011) found Haplogroup D-M55 in 2.0% (1/51) of a sample of Beijing Han and in 1.6% (8/506) of a pool of samples from South Korea, including 3.3% (3/90) from the Jeolla region, 2.4% (2/84) from the Gyeongsang region, 1.4% (1/72) from the Chungcheong region, 1.1% (1/87) from the Jeju region, 0.9% (1/110) from the Seoul-Gyeonggi region, and 0% (0/63) from the Gangwon region.[11] Hammer et al. (2006) found Haplogroup D-P37.1 in 4.0% (3/75) of a sample from South Korea.[13]

Low levels of D-M116.1 (a subclade of D-M55) among males in present-day Timor (0.2% of males),[38] It's found in 9.5% of males from Micronesia(Hammer et al. 2006[39],[13] is believed to reflect recent admixture from Japan. That is, D-M116.1 (D1b1) is generally believed to be a primary subclade of D-M64.1 (D1b), possibly as a result of the Japanese military occupation of South East Asia during World War II.

Phylogenetics[edit]

Phylogenetic history[edit]

Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree. This led to considerable confusion. In 2002, the major research groups came together and formed the Y-Chromosome Consortium (YCC). They published a joint paper that created a single new tree that all agreed to use. Latter, a group of citizen scientists with an interest in population genetics and genetic genealogy formed a working group to create an amateur tree aiming at being above all timely. The table below brings together all of these works at the point of the landmark 2002 YCC Tree. This allows a researcher reviewing older published literature to quickly move between nomenclatures.

YCC 2002/2008 (Shorthand) (α) (β) (γ) (δ) (ε) (ζ) (η) YCC 2002 (Longhand) YCC 2005 (Longhand) YCC 2008 (Longhand) YCC 2010r (Longhand) ISOGG 2006 ISOGG 2007 ISOGG 2008 ISOGG 2009 ISOGG 2010 ISOGG 2011 ISOGG 2012
D-M174 * * * * * * * * D D D D D D D D D D
D-M15 4 IV 3G 12 Eu5 H3 B D1 D1 D1 D1 D1 D1 D1 D1 D1 D1 D1
D-M55 * * * * * * * * D2 D2 D2 D2 D2 D2 D2 D2 D2 D2
D-P12 4 IV 3G 11 Eu5 H2 B D2a D2a D2a1a1 D2a1a1 D2 D2 D2a1a1 D2a1a1 D2a1a1 removed removed
D-M116.1 4 IV 3G 11 Eu5 H2 B D2b* D2a D2a D2a D2a D2a D2a D2a D2a removed removed
D-M125 4 IV 3G 11 Eu5 H2 B D2b1 D2a1 D2a1 D2a1 D2a1 D2a1 D2a1 D2a1 D2a1 D2a1 D2a1
D-M151 4 IV 3G 11 Eu5 H2 B D2b2 D2a1 D2a2 D2a2 D2a2 D2a2 D2a2 D2a2 D2a2 D2a2 D2a2

Research publications[edit]

The following research teams per their publications were represented in the creation of the YCC tree.

Phylogenetic trees[edit]

This phylogenetic tree of haplogroup D-M174 subclades is based on the ISOGG 2017 tree (ver.12.168).[1]

  • DE
    • D (M174/Page30, IMS-JST021355)
      • D*
      • D1 (CTS11577) - Onge, Jarawa (Andaman Islands)[40]
        • D1a (Z27276)
        • D1b (M55, M57, M64.1/Page44.1, M179/Page31, M359.1/P41.1, P37.1, P190, 12f2.2) - Japanese (Yamato, Ainu, Ryukyuan)
          • D1b1 (M116.1)
            • D1b1a (M125)
              • D1b1a1 (P42)
                • D1b1a1a (P12_1, P12_2, P12_3)
              • D1b1a2 (IMS-JST022457) - Emperor of Japan[46][47]
                • D1b1a2a (P53.2)
                • D1b1a2b (IMS-JST006841/Page3)
                  • D1b1a2b1 (CTS3397)
                    • D1b1a2b1a (Z1500)
                      • D1b1a2b1a1 (Z1504, CTS8093) - Minamoto clan[46][48]
                        • D1b1a2b1a1a (FGC6373) - Japanese (Hiroshima)[44]
                          • D1b1a2b1a1a1 (L137.3) - Japanese (Shizuoka)[44]
                            • 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) - Japanese (Aichi)[44]
                  • 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) - Japanese (Fukushima)[44]
                  • D1b1c1c1 (CTS4292)
                    • D1b1c1c1a (Z31517)
                    • D1b1c1c1b (CTS1798)
                  • D1b1c1c2 (Z31512)
                • D1b1c1d (CTS5641) - Japanese (Kyoto)[44]
                • D1b1c1e (CTS429)
              • D1b1c2 (CTS103)
                • D1b1c2a (Z42462)
          • D1b2 (CTS131)
            • D1b2a (CTS220) - Jōmon man (Rebun Island)[49]
              • D1b2a1 (CTS10495)
                • D1b2a1a (Z31507)
                • D1b2a1b (CTS624)
              • D1b2a2 (CTS11285) - Japanese (Osaka, Kumamoto)[44][50]
                • D1b2a2a (PH2316) - Japanese (Iwate)[44]
                  • D1b2a2a1 (Z38287)
                    • D1b2a2a1a (Z38284)
                  • D1b2a2a2 (Z38289) - Japanese (Hyōgo)[44]
                • D1b2a2b (CTS288)
                  • D1b2a2b1 (CTS1815)
                  • D1b2a2b2 (Z40665)
            • D1b2b (CTS68)
      • D2 (L1366, L1378, M226.2) - Philippines (Mactan, Luzon)[51]
        • D2a (FGC8848)
        • D2b (FGC8940)

See also[edit]

Genetics[edit]

Y-DNA D subclades[edit]

Y-DNA backbone tree[edit]

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

References[edit]

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  40. ^ YFull
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  46. ^ a b famous Y dna by haplogroup
  47. ^ List of haplogroups of famous/notable people Most of Japanese males share their paternal Y-dna lineages with the Imperial Family.
  48. ^ List of haplogroups of famous/notable people
  49. ^ 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
  50. ^ ysearch DNA of Kimura (D-CTS11285)
  51. ^ Y-DNA Haplogroup D and its Subclades - 2014

External links[edit]