Haplogroup D-M174

Haplogroup D-M174
Possible time of origin 50,000[1] - 60,000[2] years BP
Possible place of origin Asia(Central Asia)[2][3][4]
Ancestor DE
Descendants

D-Z27276(D1a)

D-M55(D1b)
Defining mutations M174, 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.

Origins

Migration of haplogroup D

Haplogroup D-M174 is believed to have originated in Asia some 60,000 years before present.[2][3] 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.[3]

Overview

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.[5]

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),[6] 6/120 = 5.0% D-P47[7]), Kazakhs (1/54 = 1.9% D-M174,[8] 6/1294 = 0.5% D[9]), Nogais (4/76 = 5.3% D-M174 Kara Nogai,[10] 1/87 = 1.1% D-M174 Kuban Nogai[10]), Khalkhas (1/24 = 4.2% D-M174,[8] 3/85 = 3.5% D-M174,[11] 2/149 D-M15 + 2/149 D-P47 = 4/149 = 2.7% D-M174 total[12]), Zakhchin (2/60 = 3.3% D-M174[11]), Uriankhai (1/60 = 1.7% D-M174[11]), and Kalmyks (5/426 = 1.2% D-M174[13]). 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.[14]

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[15] and the Altai[12][6][7]), 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.[16] 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.[16] 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.[17]

Distribution

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.

Subclades

D-M174 (D*) Paragroup

Basal D-M174, without positive-tested subclades, found at high frequencies among Andaman Islanders [18](especially Onge（23/23 = 100%), Jarawa(4/4 = 100%)[19]) and some Tibetan minority tribes in Northeast India (among whom rates vary from zero to 65%).[4][20][21][22]

D-M174(xD-M15, D-P37, D-P47) has been found in approximately 5% of Altaians.[12] 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%).[6]

D-Z27276 (D1a)

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

D-M15 (D1a1)

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.[23]

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][24][25] approximately 12.5% of Tibetans,[2] and approximately 9% of Yi[2][26]) 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)[27] 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.[27]

D-P47 (D1a2a)

Found with high frequency among Pumi,[2] Naxi,[2] and Tibetans,[28][2] with a moderate distribution in Central Asia.[2]

D-M55 (D1b)

Previously known as D-M55, D-M64.1/Page44.1 (D1b) is found with high frequency among Ainu,[29] Japanese,[30] and Ryukyuans.[30]

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.[31] Hammer et al. (2006) found Haplogroup D-P37.1 in 4.0% (3/75) of a sample from South Korea.[12]

Low levels of D-M116.1 (a subclade of D-M55) among males in present-day Timor (0.2% of males),[32] and one individual from "Micronesia",[12] 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

Phylogenetic history

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********DDDDDDDDDD
D-M154IV3G12Eu5H3BD1D1D1D1D1D1D1D1D1D1D1
D-M55********D2D2D2D2D2D2D2D2D2D2
D-P124IV3G11Eu5H2BD2aD2aD2a1a1D2a1a1D2D2D2a1a1D2a1a1D2a1a1removedremoved
D-M116.14IV3G11Eu5H2BD2b*D2aD2aD2aD2aD2aD2aD2aD2aremovedremoved
D-M1254IV3G11Eu5H2BD2b1D2a1D2a1D2a1D2a1D2a1D2a1D2a1D2a1D2a1D2a1
D-M1514IV3G11Eu5H2BD2b2D2a1D2a2D2a2D2a2D2a2D2a2D2a2D2a2D2a2D2a2

Research publications

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

Phylogenetic trees

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)[33]
        • 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[39][40]
                • D1b1a2a (P53.2)
                • D1b1a2b (IMS-JST006841/Page3)
                  • D1b1a2b1 (CTS3397)
                    • D1b1a2b1a (Z1500)
                      • D1b1a2b1a1 (Z1504, CTS8093) - Minamoto clan[39][41]
                        • D1b1a2b1a1a (FGC6373) - Japanese (Hiroshima)[37]
                          • D1b1a2b1a1a1 (L137.3) - Japanese (Shizuoka)[37]
                            • 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)[37]
                  • 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)[37]
                  • D1b1c1c1 (CTS4292)
                    • D1b1c1c1a (Z31517)
                    • D1b1c1c1b (CTS1798)
                  • D1b1c1c2 (Z31512)
                • D1b1c1d (CTS5641) - Japanese (Kyoto)[37]
                • D1b1c1e (CTS429)
              • D1b1c2 (CTS103)
                • D1b1c2a (Z42462)
          • D1b2 (CTS131)
            • D1b2a (CTS220) - Jōmon man (Rebun Island)[42]
              • D1b2a1 (CTS10495)
                • D1b2a1a (Z31507)
                • D1b2a1b (CTS624)
              • D1b2a2 (CTS11285) - Japanese (Osaka, Kumamoto)[37][43]
                • D1b2a2a (PH2316) - Japanese (Iwate)[37]
                  • D1b2a2a1 (Z38287)
                    • D1b2a2a1a (Z38284)
                  • D1b2a2a2 (Z38289) - Japanese (Hyōgo)[37]
                • D1b2a2b (CTS288)
                  • D1b2a2b1 (CTS1815)
                  • D1b2a2b2 (Z40665)
            • D1b2b (CTS68)
      • D2 (L1366, L1378, M226.2) - Philippines (Mactan, Luzon)[44]
        • D2a (FGC8848)
        • D2b (FGC8940)

See also

Genetics

Y-DNA D subclades

Y-DNA backbone tree

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

  1. 1 2 "Y-DNA Haplogroup D-M174 and its Subclades - 2017".
  2. 1 2 3 4 5 6 7 8 9 10 11 12 Shi H, Zhong H, Peng Y, et al. (2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biol. 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782.
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  5. ↑ Y染色体单倍群D在東亞的分布及其意義
  6. 1 2 3 Kharkov, V. N.; Stepanov, V. A.; Medvedeva, O. F.; Spiridonova, M. G.; Voevoda, M. I.; Tadinova, V. N.; Puzyrev, V. P. (2007). "Gene pool differences between Northern and Southern Altaians inferred from the data on Y-chromosomal haplogroups". Russian Journal of Genetics. 43 (5): 551–562. doi:10.1134/S1022795407050110.
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  13. ↑ Boris Malyarchuk, Miroslava Derenko, Galina Denisova, Sanj Khoyt, Marcin Woźniak, Tomasz Grzybowski, and Ilya Zakharov, "Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels." Journal of Human Genetics (2013) 58, 804–811; doi:10.1038/jhg.2013.108; published online 17 October 2013.
  14. ↑ Y-DNA D Haplogroup Project at Family Tree DNA
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  16. 1 2 Bing Su, Li Jin, Peter Underhill, Jeremy Martinson, Nilmani Saha, Stephen T. McGarvey, Mark D. Shriver, Jiayou Chu, Peter Oefner, Ranajit Chakraborty, and Ranjan Deka, "Polynesian origins: Insights from the Y chromosome." PNAS (July 18, 2000), vol. 97, no. 15, 8225–8228.
  17. ↑ DONG Yongli, SHI Hong, LI Weixiang, YANG Jie, ZENG Weimin, LI Kaiyuan, and XIAO Chunjie, "Study of polymorphism at the YAP locus in seven Yunnan ethnic minority populations in the great gorge of the Salween River and downstream areas" (original title in Chinese: "怒江大峡谷及下游地区7个云南少数民族YAP位点的多态性研究"), Acta Anthropologica Sinica, Vol. 21, No. 3 (August, 2002).
  18. ↑ Hong Shi, Hua Zhong, Yi Peng, Yong-Li Dong, Xue-Bin Qi, Feng Zhang, Lu-Fang Liu, Si-Jie Tan, Runlin Z Ma, Chun-Jie Xiao, R Spencer Wells, Li Jin and Bing Su:Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biology 2008 6:45
  19. ↑ Kumarasamy et al.(2003)Genetic Affinities of the Andaman Islanders, a Vanishing Human Population Current Biology Volume 13, Issue 2, Pages 86–93 doi:10.1016/S0960-9822(02)01336-2
  20. ↑ Cordaux, R.; Weiss, G; Saha, N; Stoneking, M (2004). "The Northeast Indian Passageway: A Barrier or Corridor for Human Migrations?". Molecular Biology and Evolution. 21 (8): 1525–33. doi:10.1093/molbev/msh151. PMID 15128876.
  21. ↑ Chandrasekar, A.; Saheb, S. Y.; Gangopadyaya, P.; Gangopadyaya, S.; Mukherjee, A.; Basu, D.; Lakshmi, G. R.; Sahani, A. K.; et al. (2007). "YAP insertion signature in South Asia". Annals of Human Biology. 34 (5): 582–6. doi:10.1080/03014460701556262. PMID 17786594.
  22. ↑ Reddy BM, Langstieh BT, Kumar V, Nagaraja T, Reddy AN, et al. (2007). Awadalla P, ed. "Austro-Asiatic Tribes of Northeast India Provide Hitherto Missing Genetic Link between South and Southeast Asia". PLoS ONE. 2 (11): e1141. doi:10.1371/journal.pone.0001141. PMC 2065843. PMID 17989774.
  23. ↑ Peter A. Underhill, Peidong Shen, Alice A. Lin et al., "Y chromosome sequence variation and the history of human populations," Nature Genetics • Volume 26 • November 2000
  24. ↑ Xue, Y.; Zerjal, T; Bao, W; Zhu, S; Shu, Q; Xu, J; Du, R; Fu, S; et al. (2005). "Male Demography in East Asia: A North-South Contrast in Human Population Expansion Times". Genetics. 172 (4): 2431–9. doi:10.1534/genetics.105.054270. PMC 1456369. PMID 16489223.
  25. ↑ Wang, Chuan-Chao, Ling-Xiang Wang, Rukesh Shrestha, Manfei Zhang, Xiu-Yuan Huang, Kang Hu, Li Jin, and Hui Li. "Genetic Structure of Qiangic Populations Residing in the Western Sichuan Corridor." PLoS ONE,2014 9(8): e103772.
  26. ↑ Wen Bo; Xie Xuanhua; Gao Song; et al. (2004). "Analyses of Genetic Structure of Tibeto-Burman Populations Reveals Sex-Biased Admixture in Southern Tibeto-Burmans". American Journal of Human Genetics. 74 (856–865): 2004. doi:10.1086/386292. PMC 1181980. PMID 15042512.
  27. 1 2 Cai, X; Qin, Z; Wen, B; Xu, S; Wang, Y; et al. (2011). "Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes". PLoS ONE. 6 (8): e24282. doi:10.1371/journal.pone.0024282. PMC 3164178. PMID 21904623.
  28. ↑ Dongsheng Lu et al. Ancestral Origins and Genetic History of Tibetan Highlanders, August 25, 2016
  29. ↑ Tajima, Atsushi; 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.
  30. 1 2 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.
  31. ↑ Soon-Hee Kim, Ki-Cheol Kim, Dong-Jik Shin, Han-Jun Jin, Kyoung-Don Kwak, Myun-Soo Han, Joon-Myong Song, Won Kim, and Wook Kim, "High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea." Investigative Genetics 2011, 2:10. http://www.investigativegenetics.com/content/2/1/10
  32. ↑ Tumonggor, Karafet et al., 2014, "Isolation, contact and social behavior shaped genetic diversity in West Timor", Journal of Human Genetics Vol. 59, No. 9 (September), pp. 494–503
  33. ↑ YFull
  34. 1 2 Y-DNA D Haplogroup Project
  35. 1 2 Pille Hallast, Chiara Batini, Daniel Zadik, et al. (2014), "The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades." Molecular Biology and Evolution Advance Access publication December 2, 2014. doi:10.1093/molbev/msu327
  36. 1 2 Yan S, Wang C-C, Zheng H-X, Wang W, Qin Z-D, et al. (2014), "Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers." PLoS ONE 9(8): e105691. doi:10.1371/journal.pone.0105691.
  37. 1 2 3 4 5 6 7 8 9 JAPAN Y-DNA Project
  38. 1 2 3 4 5 6 YFull Haplogroup YTree v6.02 at 02 April 2018. Accessed July 7, 2018.
  39. 1 2 famous Y dna by haplogroup
  40. ↑ List of haplogroups of famous/notable people Most of Japanese males share their paternal Y-dna lineages with the Imperial Family.
  41. ↑ List of haplogroups of famous/notable people
  42. ↑ 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
  43. ↑ ysearch DNA of Kimura (D-CTS11285)
  44. ↑ Y-DNA Haplogroup D and its Subclades - 2014
  • Underhill PA, Kivisild T (2007). "Use of y chromosome and mitochondrial DNA population structure in tracing human migrations". Annu. Rev. Genet. 41: 539–64. doi:10.1146/annurev.genet.41.110306.130407. PMID 18076332.
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