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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. The much rarer primary branch H3 (Z5857) is also concentrated in South Asia.
H-L901/M2939 is believed to have split from HIJK 48,500 years before present. 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. 65 samples were collected from the Swat Valley of northern Pakistan, 2 of which belonged to H1a.
H-M69 is common among populations of Bangladesh, India, Sri Lanka, and Nepal, with lower frequency in Afghanistan and Pakistan. The highest frequencies of H-M69 are in India, in both Dravidian and Indo Aryan castes (32.9%)., in Bangladesh (35.71%), and H-M52 among Kalash (20.5%) in Pakistan.
Haplogroup H is typically found among Indo-Aryan, Dravidian and Tribal (Indian as well as Pakistani Kalash) populations in the Indian subcontinent. In Europe it is mostly found among Romani, who belong predominantly (between 7% and 50%) to the H1a (M82) subclade.
South India - 27.2% (110/405) of a sample of unspecified ethnic composition. Another study has found haplogroup H-M69 in 26.4% (192/728) of an ethnically diverse pool of samples from various regions of India.
Gujarat - 20.69% (12/58)among Gujaratis in USA. 13.8% (4/29) among unspesified Gujaratis in India. 26% (13/50)among Dawoodi Bohra. 27.27 (6/22) among Bhils.
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, 44.4% (8/18) among Chamar, 16.13% (5/31) among UP Brahmins, 10.53% (2/19) among Himachal Brahmin, 10.2% (5/49) in J&K Kashmiri Gujars, 9.8% (5/51) in J&K Kashmiri Pandits, 18.3% (9/49) among New Delhi Hindus, 14.81% (4/27) among Bihar Paswan.
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). 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.
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. 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. 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.
Central Asia - 12.5% (2/16) H-M52 in a sample of Tajiks from Dushanbe, 5.19% (7/135) H-M69 in a sample of Salar from Qinghai, 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, 4.65% (6/129) H-M69 in a sample of Mongols from Qinghai, 4.44% (2/45) H-M52 in a sample of Uzbeks from Samarkand, 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, 2.86% (2/70) H-M52 in a sample of Uzbeks from Khorezm, 2.44% (1/41) H-M52 in a sample of Uyghurs from Kazakhstan, 1.79% (1/56) H-M52 in a sample of Uzbeks from Bukhara, 1.71% (3/175) H-M69 in a sample of Hui from the Changji area, Xinjiang, 1.59% (1/63) H-M52 in a sample of Uzbeks from the Fergana Valley, 1.56% (1/64) H1 in a sample of Uyghurs from Qarchugha Village, Yuli (Lopnur) County, Xinjiang, 1.32% (1/76) H2 in a sample of Uyghurs from Horiqol Township, Awat County, Xinjiang, 0.99% (1/101) H-M69 in a sample of Kazakhs from the Hami area, Xinjiang.
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; 2/290 = 0.7% H-M52 Northern Thai; 2/75 = 2.7% H-M69(xM52) and 1/75 = 1.3% H-M52(xM82) general population of Thailand), Balinese (19/551 = 3.45% H-M69),Tibetans (3/156 = 1.9% H-M69(xM52, APT)),Filipinos from southern Luzon (1/55 = 1.8% H-M69(xM52)), Bamars from Myanmar (1/59 = 1.7% H-M82, with the relevant individual having been sampled in Bago Region),Chams from Binh Thuan, Vietnam (1/59 = 1.7% H-M69), and Mongolians (1/149 = 0.7% H-M69). The subclade H-M39/M138 has been observed in the vicinity of Cambodia, including one instance in a sample of six Cambodians and one instance in a sample of 18 individuals from Cambodia and Laos. A genome study about Khmer people resulted in an average amount of 16,5% of Khmer belonging to y-DNA H.
H1b is defined by the SNPs - B108, Z34961, Z34962, Z34963, and Z34964. Only discovered in 2015, H1b was detected in a single sample from an individual in Myanmar. 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. Formerly named F3, H2 was reclassified as belonging to haplogroup H due to sharing the marker M3035 with H1. While being found in numerous ancient samples, H2 has only been found scarcely in modern populations across West Eurasia.
H3 (Z5857) like H1, is also mostly centered in South Asia. albeit at much lower frequencies.
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*. In consumer testing, it has been found principally among South Indians and Sri Lankans, and other areas of Asia such as Arabia as well.
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.
^Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187-91. doi:10.1002/humu.22468. PMID24166809.
^ abcdNarasimhan VM, Patterson NJ, Moorjani P, Lazaridis I, Mark L, Mallick S, Rohland N, Bernardos R, Kim AM, Nakatsuka N, Olalde I (2018-03-31). "The Genomic Formation of South and Central Asia". bioRxiv10.1101/292581.
^ abMathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, Sirak K (2015-10-10). "Eight thousand years of natural selection in Europe". bioRxiv10.1101/016477.
^Mathieson I, Alpaslan-Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N, Mallick S, Olalde I, Broomandkhoshbacht N, Candilio F, Cheronet O, Fernandes D (2017-05-09). "The Genomic History Of Southeastern Europe". bioRxiv10.1101/135616.
^ abcKarafet TM, Lansing JS, Redd AJ, Reznikova S, Watkins JC, Surata SP, et al. (February 2005). "Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders". Human Biology. 77 (1): 93-114. doi:10.1353/hub.2005.0030. hdl:1808/13586. PMID16114819. S2CID7953854.
^ abUnderhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, et al. (November 2000). "Y chromosome sequence variation and the history of human populations". Nature Genetics. 26 (3): 358-61. doi:10.1038/81685. PMID11062480. S2CID12893406.
^Ferri G, Tofanelli S, Alù M, Taglioli L, Radheshi E, Corradini B, et al. (September 2010). "Y-STR variation in Albanian populations: implications on the match probabilities and the genetic legacy of the minority claiming an Egyptian descent". International Journal of Legal Medicine. 124 (5): 363-70. doi:10.1007/s00414-010-0432-x. PMID20238122. S2CID1433895.
^ abPamjav H, Zalán A, Béres J, Nagy M, Chang YM (May 2011). "Genetic structure of the paternal lineage of the Roma people". American Journal of Physical Anthropology. 145 (1): 21-9. doi:10.1002/ajpa.21454. PMID21484758.
^ abRegueiro M, Stanojevic A, Chennakrishnaiah S, Rivera L, Varljen T, Alempijevic D, Stojkovic O, Simms T, Gayden T, Herrera RJ (January 2011). "Divergent patrilineal signals in three Roma populations". American Journal of Physical Anthropology. 144 (1): 80-91. doi:10.1002/ajpa.21372. PMID20878647.
^Gusmão A, Gusmão L, Gomes V, Alves C, Calafell F, Amorim A, Prata MJ (March 2008). "A perspective on the history of the Iberian gypsies provided by phylogeographic analysis of Y-chromosome lineages". Annals of Human Genetics. 72 (Pt 2): 215-27. doi:10.1111/j.1469-1809.2007.00421.x. PMID18205888. S2CID36365458.
^ abcdeLu Yan (2011), "Genetic Mixture of Populations in Western China." Shanghai: Fudan University, 2011: 1-84. (Doctoral dissertation in Chinese?, "", :?,2011: 1-84.)
^ abcLIU Shuhu, NIZAM Yilihamu, RABIYAMU Bake, ABDUKERAM Bupatima, and DOLKUN Matyusup, "A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP." Acta Anthropologica Sinica, 2018, 37(1): 146-156.
^van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau MH (February 2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187-91. doi:10.1002/humu.22468. PMID24166809. S2CID23291764.