Haplogroup H (Y-DNA)

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Haplogroup H (Y-DNA)
Y haplo H.png
haplogroup H map
Possible time of origin~48,500 ybp
Possible place of originSouth Asia or West Asia
DescendantsH1 (L902/M3061);
H2 (P96);
H3 (Z5857)
Defining mutationsL901/M2939
Highest frequenciesSouth Asians and Romani people

Haplogroup H (Y-DNA), also known as H-L901/M2939 is a Y-chromosome haplogroup.

The primary branch H1 (H-M69) and its subclades is one of the most predominant haplogroups amongst populations in South Asia, particularly its descendant H1a1 (M52). A primary branch of H-M52, H1a1a (H-M82), is found commonly among the Romani people, who originated in South Asia and migrated into the Middle East and Europe, around the beginning of the 2nd millennium CE and the Khmer people who got under influence from Indian populations.[1] The much rarer primary branch H3 (Z5857) is also concentrated in South Asia.

However, the primary branch H2 (P96) seems to have been found in sparse levels primarily in Europe and West Asia since prehistory. It has been found in remains from the Linear Pottery culture and Neolithic Iberia.[2][3] H2 likely entered Europe during the Neolithic with the spread of agriculture.[3] Its present distribution is made up of various individual cases spread out throughout Europe and West Asia today.[4]


H-L901/M2939 is a direct descendant of Haplogroup GHIJK. There are, in turn, three direct descendants of H-L901/M2939 – their defining SNPs are as follows:

  • H1 (L902/M3061)
    • H1a previously haplogroup H1 (M69/Page45, M370)
    • H1b B108, Z34961, Z34962, Z34963, Z34964
  • H2 previously haplogroup F3,[5] (P96, L279, L281, L284, L285, L286, M282)
    • H2a FGC29299/Z19067
    • H2b Z41290
    • H2c Y21618, Z19080
  • H3 (Z5857)
    • H3a (Z5866)
    • H3b (Z13871)

Ancient distribution[edit]

H-L901/M2939 is believed to have split from HIJK 48,500 years before present.[6] Its probable site of introduction is South Asia, since it is highly concentrated there. It seems to represent the main Y-Chromosome haplogroup of the paleolithic inhabitants of the Indian Subcontinent.


With limited ancient DNA testing in South Asia, accordingly there is a limited amount of ancient samples for H1a, despite it being a populous and well distributed haplogroup today. The first set of ancient DNA from South Asia was published in March 2018.[7] 65 samples were collected from the Swat Valley of northern Pakistan, 2 of which belonged to H1a.[7]

H1a ancient samples
Date Subclade Location Country Culture Accompanying haplogroups Source
1100-900 BC H1a1 Gogdara, Swat Valley Pakistan Udegram Iron Age E1b1b1b2, E1b1b1b2a [7]
1000-800 BC H1a1 Barikot, Swat Valley Pakistan Barikot Iron Age [7]


The earliest sample of H2 is found in the Pre-Pottery Neolithic B culture of the Levant 10,000 years ago.[8] From ancient samples. it is clear that H2 also has a strong association with the spread of agriculture from Anatolia into Europe, and is commonly found with haplogroup G2a.[9] H2 was found in Neolithic Anatolia, as well as in multiple later Neolithic cultures of Europe, such as the Vinča culture in Serbia,[10] and the Megalith culture of Western Europe.[10]

H2 ancient samples
Date Location Country Culture Accompanying haplogroups Source
7300-6750 BC Motza Israel Levantine Neolithic (PPNB) E1b1b1, T1a1, T1a2a (PPNB from Jordan) [8]
6500-6200 BC Barcin site, Yenişehir Valley Turkey Anatolian Neolithic G2a, I2C, C1a, J2a [11]
6500-6200 BC Barcin site, Yenişehir Valley Turkey Anatolian Neolithic G2a, I2C, C1a, J2a [11]
5832–5667 BC Старчево Serbia Vinca [10]
5702–5536 BC Старчево Serbia Vinca [10]
5400-5000 BC Szemely Hungary Vinča G2a2a, G2a2b2a1a [10]
3900–3600 BC La Mina site, Soria Spain Megalithic I2a2a1 [10]
3336-3028 BC Dzhulyunitsa Bulgaria Bulgaria_BA G2a2a1a2 [12]
2899–2678 BC El Portalon cave Spain Pre-Bell Beaker I2a2a [2]
2470-2060 BC Budapest-Bekasmegyer Hungary Kurgan Bell Beaker R1b1a1a2a1a2b1 [13]

Modern distribution[edit]


South Asia[edit]

H-M69 is common among populations of Bangladesh, India, Sri Lanka, and Nepal, with lower frequency in Afghanistan and Pakistan.[14] The highest frequencies of H-M69 are in India, in both Dravidian and Indo Aryan castes (32.9%).,[1][15] in Bangladesh (35.71%),[16] and H-M52 among Kalash (20.5%) in Pakistan.[17][18]

Haplogroup H is typically found among Indo-Aryan, Dravidian and Tribal(Indian Tribals and Pakistani Kalash tribe) populations in the Indian subcontinent, with highest concentration in India]( West India and South India in particular) and Bangladesh. In Europe it is found almost exclusively among the Gypsies (Romani), who belong predominantly (between 15% and 50%) to the H1a (M82) subclade of Indian origin. The highest frequencies of haplogroup H among non-Romani Europeans are found in regions with large Romani populations, such as Romania, Slovakia, the southern Balkans, and Andalusia, suggesting that these lineages are also of Romani origin.[citation needed]

Haplogroup H-M69 has been found in:

  • Bangladesh - 35.71% (15/42).[16]
  • South India – 27.2% (110/405) of a sample of unspecified ethnic composition.[19][20] Another study has found haplogroup H-M69 in 26.4% (192/728) of an ethnically diverse pool of samples from various regions of India.[1]
  • Maharashtra - 33.3% of a sample of (68/204).[21]
  • Gujarat - 20.69% (12/58)among Gujaratis in USA.[16] 13.8% (4/29) among unspesified Gujaratis in India.[22] 26% (13/50)among Dawoodi Bohra.[23] 27.27 (6/22) among Bhils.[24]
  • North India - According to a study(Trivedi2007) it is found 24.5% (44/180) in both Caste and tribal population of North India. Most frequently found : 20.7% (6/29) among Rajputs,[1] 44.4% (8/18) among Chamar,[1] 16.13% (5/31) among UP Brahmins,[24] 10.53% (2/19) among Himachal Brahmin,[24] 10.2% (5/49) in J&K Kashmiri Gujars,[24] 9.8% (5/51) in J&K Kashmiri Pandits,[24] 18.3% (9/49) among New Delhi Hindus,[25] 14.81% (4/27) among Bihar Paswan.[24]
  • Sri Lanka – in 25.3% (23/91) of a sample of unspecified ethnic composition[19][20] and in 10.3% (4/39) of a sample of Sinhalese.[18]
  • Nepal – one study has found Haplogroup H-M69 in approximately 12% of a sample of males from the general population of Kathmandu (including 4/77 H-M82, 4/77 H-M52(xM82), and 1/77 H-M69(xM52, APT)) and 6% of a sample of Newars (4/66 H-M82).[26] In another study, Y-DNA that belongs to Haplogroup H-M69 has been found in 25.7% (5/37 = 13.5% H-M69 from a village in Morang District, 9/57 = 15.8% H-M69 from a village in Chitwan District, and 30/77 = 39.0% H-M69 from another village in Chitwan District) of Tharus in Nepal.[27]
  • Pakistan – in 4.1% Burusho, 20.5% Kalash, 4.2% Pashtun, and 6.3% in other Pakistanis.[1][17] Another study has found haplogroup H-M69 in approximately 8% (3/38) of a sample of Burusho (also known as Hunza), including 5% (2/38) H-M82(xM36, M97, M39/M138) and 3% (1/38) H-M36.[28]
  • Afghanistan – in 6.1% Pashtun,[14] in 7.1% Tajik.[14]

Roma people[edit]

Haplogroup H-M82 is a major lineage cluster in the Roma, especially Balkan Roma, among whom it accounts for approximately as high as 60% of males.[29] A 2-bp deletion at M82 locus defining this haplogroup was also reported in one-third of males from traditional Roma populations living in Bulgaria, Spain, and Lithuania.[30] High prevalence of Asian-specific Y chromosome haplogroup H-M82 supports their Indian origin and a hypothesis of a small number of founders diverging from a single ethnic group in India (Gresham et al. 2001).

Important studies show a limited introgression of the typical Roma Y-chromosome haplogroup H1 in several European groups, including approximately 0.61% in Gheg Albanians, 2.48% in Tosk Albanians and 0.9% in Serbians.[31]

H1a in Roma populations
Population n/Sample size Percentage Source
Bulgarian Roma 98/248 39.5 [30]
Hungarian Roma 34/107 31.8 [32]
Kosovar Roma 25/42 59.5 [33]
Lithuanian Roma 10/20 50 [30]
Macedonian Roma 34/57 59.6 [29]
Portuguese Roma 21/126 16.7 [34]
Serbian Roma 16/46 34.8 [33]
Slovakian Roma 19/62 30.65 [32]
Spanish Roma 5/27 18.5 [30]

Europe, Caucasus, Central Asia & Middle East[edit]

Haplogroup H1a is found at much lower levels outside of the Indian subcontinent and the Romani populations but is still present in other populations:

  • Europe - 0.9% (1/113) H-M82 in a sample of Serbians,[29] 2% (1/57) H-M82 in a sample of Macedonian Greeks,[25] 1% (1/92 H-M82)[25] to 2% (1/50 H-M69)[35] of Ukrainians, H1a2a in 1.3% (1/77) of a sample of Greeks.[17]
  • Caucasus- 2.6% (1/38) H-M82 in a sample of Balkarians,[25]
  • Central Asia - 12.5% (2/16) H-M52 in a sample of Tajiks from Dushanbe,[36] 5.19% (7/135) H-M69 in a sample of Salar from Qinghai,[37] 5.13% (2/39) H (including 1/39 H(xH1,H2) and 1/39 H1) in a sample of Uyghurs from Darya Boyi Village, Yutian (Keriya) County, Xinjiang,[38] 4.65% (6/129) H-M69 in a sample of Mongols from Qinghai,[37] 4.44% (2/45) H-M52 in a sample of Uzbeks from Samarkand,[36] 3.56% (17/478) H-M69 and 0.84% (4/478) F-M89(xG-M201, H-M69, I-M258, J-M304, L-M20, N-M231, O-M175, P-M45, T-M272) in a sample of Uyghurs from the Hotan area, Xinjiang,[37] 2.86% (2/70) H-M52 in a sample of Uzbeks from Khorezm,[36] 2.44% (1/41) H-M52 in a sample of Uyghurs from Kazakhstan,[36] 1.79% (1/56) H-M52 in a sample of Uzbeks from Bukhara,[36] 1.71% (3/175) H-M69 in a sample of Hui from the Changji area, Xinjiang,[37] 1.59% (1/63) H-M52 in a sample of Uzbeks from the Fergana Valley,[36] 1.56% (1/64) H1 in a sample of Uyghurs from Qarchugha Village, Yuli (Lopnur) County, Xinjiang,[38] 1.32% (1/76) H2 in a sample of Uyghurs from Horiqol Township, Awat County, Xinjiang,[38] 0.99% (1/101) H-M69 in a sample of Kazakhs from the Hami area, Xinjiang.[37]
  • West Asia- 6% (1/17) H-M52 in a sample of Turks,[35][36] 5% (1/20) H-M69 in a sample of Syrians,[35] 4% (2/53) H-M52 in a sample of Iranians from Samarkand,[36] 2.6% (3/117) H-M82 in a sample from southern Iran,[39] 4.3% (7/164) of males from the United Arab Emirates,[40] 2% of males from Oman,[41] 1.9% (3/157) of males from Saudi Arabia,[42] 1.4% (1/72 H-M82) of males from Qatar,[40] and 0.6% (3/523) H-M370 in another sample of Turks.[43]

East & South-East Asia[edit]

At the easternmost extent of its distribution, Haplogroup H-M69 has been found in Thais from Thailand (1/17 = 5.9% H-M69 Northern Thailand;[44] 2/290 = 0.7% H-M52 Northern Thai;[45] 2/75 = 2.7% H-M69(xM52) and 1/75 = 1.3% H-M52(xM82) general population of Thailand[46]), Balinese (19/551 = 3.45% H-M69),[20] Tibetans (3/156 = 1.9% H-M69(xM52, APT)),[26] Filipinos from southern Luzon (1/55 = 1.8% H-M69(xM52)[46]), Bamars from Myanmar (1/59 = 1.7% H-M82, with the relevant individual having been sampled in Bago Region),[47] Chams from Binh Thuan, Vietnam (1/59 = 1.7% H-M69),[44] and Mongolians (1/149 = 0.7% H-M69).[19] The subclade H-M39/M138 has been observed in the vicinity of Cambodia, including one instance in a sample of six Cambodians[1] and one instance in a sample of 18 individuals from Cambodia and Laos.[28] A genome study about Khmer people resulted in an average amount of 16,5% of Khmer belonging to y-DNA H.[1]


H1b is defined by the SNPs - B108, Z34961, Z34962, Z34963, and Z34964.[48] Only discovered in 2015, H1b was detected in a single sample from an individual in Myanmar.[49] Due to only being classified recently, there are currently no studies recording H1b in modern populations.


H2 (H-P96), which is defined by seven SNPs – P96, M282, L279, L281, L284, L285, and L286 – is the only primary branch found mainly outside South Asia.[48] Formerly named F3, H2 was reclassified as belonging to haplogroup H due to sharing the marker M3035 with H1.[50] While being found in numerous ancient samples, H2 has only been found scarcely in modern populations across West Eurasia.[2]

H2 in modern populations
Region Population n/Sample size Percentage Source
Central Asia Dolan 1/76 1.3 [51]
West Asia UAE 1/164 0.6 [52]
West Asia South Iran 2/117 1.7 [53]
West Asia Armenia 5/900 0.6 [54]
Southern Europe Sardinia 2/1194 0.2 [55]


H3 (Z5857) like H1, is also mostly centered in South Asia. albeit at much lower frequencies.[49]

Like other branches of H, due to it being newly classified it is not explicitly found in modern population studies. Samples belonging to H3 were likely labeled under F*.[49] In consumer testing, it has been found principally among South Indians and Sri Lankans, and other areas of Asia such as Arabia as well.[6]

The following gives a summary of most of the studies which specifically tested for the subclades H1a1a (H-M82) and H2 (H-P96), formerly F3, showing its distribution in different part of the world.[56]

Continent/subcontinental region Country &/or ethnicity Sample size H1a1a (M82) freq. (%) Source
East/Southeast Asia Cambodia 6 16.67 Sengupta et al. 2006
East/Southeast Asia Cambodia/Laos 18 5.56 Underhill et al. 2000
South Asia Nepal 188 4.25 Gayden et al. 2007
South Asia Afghanistan 204 3.43 Haber et al. 2012
South Asia Malaysian Indians 301 18.94 Pamjav et al. 2011
South Asia Terai-Nepal 197 10.66 Fornarino et al. 2009
South Asia Hindu New Delhi 49 10.2 Fornarino et al. 2009
South Asia Andhra Pradesh Tribals 29 27.6 Fornarino et al. 2009
South Asia Chenchu Tribe India 41 36.6 Kivisild et al. 2003
South Asia Koya Tribe India 41 70.7 Kivisild et al. 2003
South Asia West Bengal India 31 9.6 Kivisild et al. 2003
South Asia Konkanastha Brahmin India 43 9.3 Kivisild et al. 2003
South Asia Gujarat India 29 13.8 Kivisild et al. 2003
South Asia Lambadi India 35 8.6 Kivisild et al. 2003
South Asia Punjab India 66 4.5 Kivisild et al. 2003
South Asia Sinhalese Sri Lanka 39 10.3 Kivisild et al. 2003
South Asia Northwest India 842 14.49 Rai et al.2012
South Asia South India 1845 20.05 Rai et al.2012
South Asia Central India 863 14.83 Rai et al.2012
South Asia North India 622 13.99 Rai et al.2012
South Asia East India 1706 8.44 Rai et al.2012
South Asia West India 501 17.17 Rai et al.2012
South Asia Northeast India 1090 0.18 Rai et al.2012
South Asia Andaman Island 20 0 Thangaraj et al. 2003
Middle East and North Africa Saudi Arabia 157 0.64 Abu-Amero et al. 2009
Middle East and North Africa Turkish 523 0.19 Cinnioglu et al. 2004
Middle East and North Africa Iran 150 2 Abu-Amero et al. 2009
Middle East and North Africa Iran 938 1.2 Grugni et al. 2012

See also[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
F1  F2  F3  GHIJK
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


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