Haplogroup H (Y-DNA)
|Haplogroup H (Y-DNA)|
|Possible time of origin||25,000–45,000 years BP|
|Possible place of origin||South Asia|
|Highest frequencies||South Asia and Romani people|
In human genetics, Haplogroup H (Y-DNA), also known as H-L901/M2939 is a Y-chromosome haplogroup. This haplogroup is found at high frequencies among some populations in South Asia, particularly the subclade H1 (H-M69), including its direct descendant H1a (M52). Outside South Asia, H1a1 (H-M82) – which is a direct descendant of H1A/M-82 – is found commonly in the paternal lineage of Romani people.
Haplogroup H2 (P96) seems to be primarily European, and very ancient. It was recently found in Linear Pottery culture and Neolithic Iberia and may have entered Europe as long ago during the Epipaleolithic. It was founded to have somewhat of a higher average concentration in Western Europe, but was also found amongst many ethnicities of the Near East; most notably Armenians and Iranian peoples; as well as India and other Southern Asia.
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: M69/Page45, M370; – South Asians, Romani and Tajiks
- H2: P96, L279, L281, L284, L285, L286, M282 (formerly known as H* and before that was misclassified under Haplogroup F-M89, as "F3"); – Western Europe: in France, Switzerland, Iberian Peninsula, Germany and the Netherlands. But it is also found in Armenian, Iran, and India. H2 was found in Neolithic Iberia and in Linear Pottery culture.
- H3: Z5857 – South Asians
H-L901/M2939 is believed to have arisen in South Asia between 30,000 and 40,000 years ago. Its probable site of introduction is South Asia, since it is concentrated there. It seems to represent the main Y-Chromosome haplogroup of the paleolithic inhabitants of Indian-Subcontinent. Some individuals in South Asia have also been shown to belong to the much rarer subclade H3 (Z5857).
Haplogroup H-M69 is fairly common among populations of India, Sri Lanka, Nepal and Pakistan with lower frequency in Afghanistan. The highest frequencies of H-M69 are in India, especially in southern India at (32.9%). and H-M52 among Kalash (20.5%) in Pakistan.
Haplogroup H-M69 has been found in:
- 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.
- Sri Lanka – in 25.3% (23/91) of a sample of unspecified ethnic composition and in 10.3% (4/39) of a sample of Sinhalese.
- 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)), in 6% of a sample of Newars (4/66 H-M82) and 25.7% in Tharus of Nepal.
- Pakistan – in 4.1% Burusho, 20.5% Kalash, 4.2% Pashtun, and 6.3% in other Pakistanis. 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.
- Afghanistan – in 6.1% Pashtun.
Haplogroup H-M82 is a major lineage cluster in the Balkan Romani group, accounting for approximately 60% of the total. A 2-bp deletion at M82 locus defining this haplogroup was also reported in one-third of males from traditional Romani populations living in Bulgaria, Spain, and Lithuania (Gresham et al. 2001). 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 Romani 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 and the Middle East
Haplogroup H1 has been found very rarely outside of the Indian subcontinent and the Romani populations, including approximately 12.5% (2 out of 16 individuals) H-M52 in a sample of Tajiks from Dushanbe, 6% (1/17) H-M52 in a sample of Turks, 5% (1/20) H-M69 in a sample of Syrians, 4% (2/45) H-M52 in a sample of Uzbeks from Samarkand, 4% (2/53) H-M52 in a sample of Iranians from Samarkand, 3% (2/70) H-M52 in a sample of Uzbeks from Khorezm, 3% (1/38) H-M82 in a sample of Balkarians, 2.6% (3/117) H-M82 in a sample from southern Iran, 2% (1/41) H-M52 in a sample of Uyghurs from Kazakhstan, 1% (1/92 H-M82) to 2% (1/50 H-M69) of Ukrainians, 2% (1/56) H-M52 in a sample of Uzbeks from Bukhara, 2% (1/57) H-M82 in a sample of Macedonian Greeks, 2% (1/63) H-M52 in a sample of Uzbeks from the Fergana Valley, 0.9% (1/113) H-M82 in a sample of Serbians, 0.6% (3/523) H-M370 in a sample of Turks, and 0.5% (1/201) H-M52 in a sample of Somali immigrants in Denmark.
In the Arabian Peninsula, Haplogroup H-M69 has been found in 4.3% (7/164) of males from the United Arab Emirates (including 4/164 = 2.4% H-M69(xM52,Apt) and 3/164 = 1.8% H-M82), approximately 2% of males from Oman, 1.9% (3/157) of males from Saudi Arabia (including 2/157 = 1.3% H-M69(xM52) and 1/157 = 0.6% H-M82), and 1.4% (1/72 H-M82) of males from Qatar.
East and Southeast Asia
At the easternmost extent of its distribution, Haplogroup H-M69 has been found in Thais from northern Thailand (1/17 = 5.9% H-M69), Balinese (19/551 = 3.45% H-M69), Tibetans (3/156 = 1.9% H-M69(xM52, APT)), 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.
Haplogroup H2 (P96)
The H-P96 lineage is defined by seven SNPs. They are P96, M282, L279, L281, L284, L285, and L286. H-P96 defines the H-P96 subclade. H2 (P96) was found in Neolithic Iberia. There is somewhat of a concentration of H-P96 in Western Europe: in France, Switzerland, Germany and the Netherlands. But it is also found in Armenia, Iran, and India. It is hypothesized that Haplogroup H2 may have been one of the original patrilineal lineages of the earliest Europeans; and may indicate that ancient Europeans once shared a common ancestor with the Proto-Dravidian peoples of the Southern Indian Subcontinent.
This phylogenetic tree of haplogroup subclades is based on the ISOGG Y-DNA Haplogroup H and its Subclades tree – 2016.
- H-M69 (H1) (M69, M370)
- H-M52 (H1a) (M52)
- H-M82 (H1a1) (M82)
- H-M36 (H1a1a1) (M36, M197)
- H-M97 (H1a1b) (M97)
- H-M39 (H1a1c) (M39, M138)
- H-M2914/Z4382 H1a1d
- H-Z5871 H1a1d1
- H-Z4361 H1a1d2
- H-Z4469 (H1a2)
- H-Z4487 H1a2a
- H-Z4417 H1a2a1
- H-Z4487 H1a2a
- H-M82 (H1a1) (M82)
- H-L588 (H1b)
- H-APT (H1b1) (APT)
- H-P80 (H1b1a) (P80, P314)
- H-P266 (H1b1b) (P266)
- H-Z14258 (H1b2)
- H-Z5868 H1b2a
- H-P254 (H1c) (P254)
- H-M52 (H1a) (M52)
- H-P96 (H2) (P96, M282; formerly known as Haplogroup F3 and H-M282.)
- H-Z5857 (H3)
- H-Z5866 (H3a)
- H-Z5864 (H3a1)
- H-Z5863 (H3a2)
- H-Z5865 (H3a2a)
- H-Z5860 (H3a2a1)
- H-Z5862 (H3a2a2)
- H-Z5858 (H3a2b)
- H-Z5865 (H3a2a)
- H-Z13871 (H3b)
- H-Z5859 (H3b1)
- H-Z5866 (H3a)
Distribution of H1a1-M82 and H2-P96
The following gives a summary of most of the studies which specifically tested for M82 and P96, showing its distribution in different part of the world.
|Region/Ethnicity||Country/Population||Size||H1a freq. (%)||H2 freq. (%)||Reference|
|East/Southeast Asia||Tibet||156||0||Gayden et al. 2007|
|East/Southeast Asia||Cambodia||6||16.67||Sengupta et al. 2006|
|East/Southeast Asia||Cambodia/Laos||18||5.56||Underhill et al. 2000|
|East/Southeast Asia||Japan||23||0||Sengupta et al. 2006|
|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||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|
|North Asia||Siberia||18||0||Sengupta et al. 2006|
|Middle East and North Africa||Qatar||72||1.39||Cadenas et al. 2008|
|Middle East and North Africa||United Arab Emirates||164||1.84||Cadenas et al. 2008|
|Middle East and North Africa||Yemen||62||0||Cadenas et al. 2008|
|Middle East and North Africa||Saudi Arabia||157||0.64||Abu-Amero et al. 2009|
|Middle East and North Africa||Oman||121||0||Abu-Amero et al. 2009|
|Middle East and North Africa||Egypt||147||0||Abu-Amero et al. 2009|
|Middle East and North Africa||Somalia||201||0||Abu-Amero et al. 2009|
|Middle East and North Africa||Lebanese||916||0||Abu-Amero et al. 2009|
|Middle East and North Africa||Jordan||146||0||Abu-Amero et al. 2009|
|Middle East and North Africa||Iraq||203||0||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|
|Caucasus||Caucasians||1789||0||Yunusbayev et al. 2011|
|Caucasus||Georgians||66||0||Battaglia et al. 2009|
|Caucasus||Balkarians||38||2.6||Battaglia et al. 2009|
|Europe||Slovakian Romani||62||30.65||Pamjev et al. 2011|
|Europe||Portuguese Romani||126||16.67||Gusmao et al. 2008|
|Europe||Kosovo, Belgrade, Vojvodina Romani||88||43.18||Regueiro et al. 2011|
|Europe||Bulgarian Romani||248||39.52||Gresham et al. 2001|
|Europe||Spanish Romani||27||18.52||Gresham et al. 2001|
|Europe||Croatian Romani||377||20.16||Battaglia et al. 2009|
|Europe||Macedonian Romani (Skopje)||257||13.23||Peričić et al. 2005|
|Europe||Hungarian Romani||424||16.98||Pamjav et al. 2011|
|Europe||Lithuanian Romani||20||50||Gresham et al. 2001|
|Europe||Greeks||92||0||Battaglia et al. 2009|
|Europe||Macedonian Greeks||57||2||Battaglia et al. 2008|
|Europe||Albanians||55||0||Battaglia et al. 2009|
|Europe||Bosniaks||324||0||Battaglia et al. 2009|
|Europe||Slovenians||75||0||Battaglia et al. 2009|
|Europe||Northeastern Italians||67||0||Battaglia et al. 2009|
|Europe||Hungarians||53||0||Battaglia et al. 2009|
|Europe||Czechs||75||0||Battaglia et al. 2009|
|Europe||Poles||99||0||Battaglia et al. 2009|
|Europe||Ukrainians||92||1.1||Battaglia et al. 2009|
|Europe||Herzegovinians (Mostar, Široki Brijeg)||141||0||Peričić et al. 2005|
|Europe||Serbians (Belgrade)||113||0.9||Peričić et al. 2005|
|Evolutionary tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]|
|A00||A0-T [χ 3]|
|I||J||LT [χ 5]||K2|
|L||T||NO [χ 6]||K2b [χ 7]||K2c||K2d||K2e [χ 8]|
|N||O||K2b1 [χ 9]||P|
|M||S [χ 10]||Q||R|
- Günther, T; Valdiosera, C; Malmström, H; Ureña, I; Rodriguez-Varela, R; Sverrisdóttir, Óddny Osk; Daskalaki, E. A.; Skoglund, P; Naidoo, T; Svensson, E. M.; Bermúdez De Castro, J. M.; Carbonell, E; Dunn, M; Storå, J; Iriarte, E; Arsuaga, J. L.; Carretero, J. M.; Götherström, A; Jakobsson, M (2015). "Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques". Proceedings of the National Academy of Sciences 112 (38): 11917–22. doi:10.1073/pnas.1509851112. PMC 4586848. PMID 26351665.
- "Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities". PLOS Biology. 2010-11-09. Retrieved 2013-11-19.
- Magoon, G. R.; Banks, R. H.; Rottensteiner, C.; Schrack, B. E.; Tilroe, V. O.; Robb, T.; Grierson, A. J. (2013). "Generation of high-resolution a priori Y-chromosome phylogenies using next-generation sequencing data". doi:10.1101/000802.
- Y-DNA Haplogroup H and its Subclades – 2015. isogg.org
- Sengupta S, Zhivotovsky LA, King R, et al. (February 2006). "Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists". Am. J. Hum. Genet. 78 (2): 202–21. doi:10.1086/499411. PMC 1380230. PMID 16400607.
- Cordaux R, et al. (2004). "Independent Origins of Indian Caste and Tribal Paternal Lineages". Current Biology 14 (3): 231–5. doi:10.1016/j.cub.2004.01.024. PMID 14761656.
- Thanseem I, Thangaraj K, Chaubey G, et al. (2006). "Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA". BMC Genet. 7: 42. doi:10.1186/1471-2156-7-42. PMC 1569435. PMID 16893451.
- Marc, Haber; Platt, DE; Ashrafian Bonab, M; Youhanna, SC; Soria-Hernanz, DF; et al. (2012). "Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events". PLoS ONE 7 (3): e34288. doi:10.1371/journal.pone.0034288. PMC 3314501. PMID 22470552.
- Sahoo, S. (2006). "A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios" (PDF). Proceedings of the National Academy of Sciences 103 (4): 843–8. Bibcode:2006PNAS..103..843S. doi:10.1073/pnas.0507714103. PMC 1347984. PMID 16415161.
- Firasat S, Khaliq S, Mohyuddin A, et al. (January 2007). "Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan". Eur. J. Hum. Genet. 15 (1): 121–6. doi:10.1038/sj.ejhg.5201726. PMC 2588664. PMID 17047675.
- Kivisild T, Rootsi S, Metspalu M, et al. (February 2003). "The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations". American Journal of Human Genetics 72 (313–332): 313–32. doi:10.1086/346068. PMC 379225. PMID 12536373.
- Hammer MF, Karafet TM, Park H, et al. (2006). "Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes". J. Hum. Genet. 51 (1): 47–58. doi:10.1007/s10038-005-0322-0. PMID 16328082.
- Tatiana M. Karafet, J. S. Lansing, Alan J. Redd et al., "Balinese Y-Chromosome Perspective on the Peopling of Indonesia: Genetic Contributions from Pre-Neolithic Hunter-Gatherers, Austronesian Farmers, and Indian Traders," Human Biology, February 2005, v. 77, no. 1, pp. 93–114.
- Gayden T, Cadenas AM, Regueiro M, et al. (May 2007). "The Himalayas as a directional barrier to gene flow". Am. J. Hum. Genet. 80 (5): 884–94. doi:10.1086/516757. PMC 1852741. PMID 17436243.
- Underhill, P. A.; Shen, P; Lin, A. A.; Jin, L; Passarino, G; Yang, W. H.; Kauffman, E; Bonné-Tamir, B; Bertranpetit, J; Francalacci, P; Ibrahim, M; Jenkins, T; Kidd, J. R.; Mehdi, S. Q.; Seielstad, M. T.; Wells, R. S.; Piazza, A; Davis, R. W.; Feldman, M. W.; Cavalli-Sforza, L. L.; Oefner, P. J. (2000). "Y chromosome sequence variation and the history of human populations". Nature Genetics 26 (3): 358–61. doi:10.1038/81685. PMID 11062480.
- Pericić M, Lauc LB, Klarić IM, et al. (October 2005). "High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations". Mol. Biol. Evol. 22 (10): 1964–75. doi:10.1093/molbev/msi185. PMID 15944443.
- Ferri, Gianmarco (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. PMID 20238122.
- Wells RS, Yuldasheva N, Ruzibakiev R, et al. (August 2001). "The Eurasian heartland: a continental perspective on Y-chromosome diversity". Proc. Natl. Acad. Sci. U.S.A. 98 (18): 10244–9. Bibcode:2001PNAS...9810244W. doi:10.1073/pnas.171305098. PMC 56946. PMID 11526236.
- Semino O, Passarino G, Oefner PJ, et al. (November 2000). "The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective". Science 290 (5494): 1155–9. Bibcode:2000Sci...290.1155S. doi:10.1126/science.290.5494.1155. PMID 11073453.
- Battaglia, V; Fornarino, S; Al-Zahery, N; Olivieri, A; Pala, M; Myres, N. M.; King, R. J.; Rootsi, S; Marjanovic, D; Primorac, D; Hadziselimovic, R; Vidovic, S; Drobnic, K; Durmishi, N; Torroni, A; Santachiara-Benerecetti, A. S.; Underhill, P. A.; Semino, O (2009). "Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe". European Journal of Human Genetics 17 (6): 820–30. doi:10.1038/ejhg.2008.249. PMC 2947100. PMID 19107149.
- Regueiro M, Cadenas AM, Gayden T, Underhill PA, Herrera RJ (2006). "Iran: tricontinental nexus for Y-chromosome driven migration". Hum. Hered. 61 (3): 132–43. doi:10.1159/000093774. PMID 16770078.
- Cinnioglu, Cengiz; King, Roy; Kivisild, Toomas; Kalfoglu, Ersi; Atasoy, Sevil; Cavalleri, Gianpiero L.; Lillie, Anita S.; Roseman, Charles C.; Lin, Alice A.; Prince, Kristina; Oefner, Peter J.; Shen, Peidong; Semino, Ornella; Cavalli-Sforza, L. Luca; Underhill, Peter A. (2004). "Excavating Y-chromosome haplotype strata in Anatolia". Human Genetics 114 (2): 127. doi:10.1007/s00439-003-1031-4. PMID 14586639.
- Sanchez JJ, Hallenberg C, Børsting C, Hernandez A, Morling N (2005). "High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males". European Journal of Human Genetics 13 (7): 856–866. doi:10.1038/sj.ejhg.5201390. PMID 15756297.
- Cadenas AM, Zhivotovsky LA, Cavalli-Sforza LL, Underhill PA, Herrera RJ (March 2008). "Y-chromosome diversity characterizes the Gulf of Oman". Eur. J. Hum. Genet. 16 (3): 374–86. doi:10.1038/sj.ejhg.5201934. PMID 17928816.
- Luis JR, Rowold DJ, Regueiro M, et al. (March 2004). "The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations". Am. J. Hum. Genet. 74 (3): 532–44. doi:10.1086/382286. PMC 1182266. PMID 14973781.
- Abu-Amero KK, Hellani A, Gonzalez AM, Larruga JM, Cabrera VM, Underhill PA (2009). "Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions". BMC Genetics 10: 59. doi:10.1186/1471-2156-10-59. PMC 2759955. PMID 19772609.
- He J-D, Peng M-S; Quang, HH; Dang, KP; Trieu, AV; et al. (2012). "Patrilineal Perspective on the Austronesian Diffusion in Mainland Southeast Asia". PLoS ONE 7 (5): e36437. doi:10.1371/journal.pone.0036437. PMC 3346718. PMID 22586471.
- Peng, Min-Sheng; He, Jun-Dong; Fan, Long; Liu, Jie; Adeola, Adeniyi C; Wu, Shi-Fang; Murphy, Robert W; Yao, Yong-Gang; Zhang, Ya-Ping (2013). "Retrieving Y chromosomal haplogroup trees using GWAS data". European Journal of Human Genetics 22 (8): 1046. doi:10.1038/ejhg.2013.272. PMID 24281365.
- International Society of Genetic Genealogy (25 May 2016). "Y-DNA Haplogroup Tree 2016 Version: 11.144".
- van Oven M, Van Geystelen A, Kayser M, et al. (2013). "Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome.". Hum. Mutat. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.
- Rai, Niraj; Chaubey, Gyaneshwer; Tamang, Rakesh; Pathak, Ajai Kumar; Singh, Vipin Kumar; Karmin, Monika; Singh, Manvendra; Rani, Deepa Selvi; Anugula, Sharath; Yadav, Brijesh Kumar; Singh, Ashish; Srinivasagan, Ramkumar; Yadav, Anita; Kashyap, Manju; Narvariya, Sapna; Reddy, Alla G.; Van Driem, George; Underhill, Peter A.; Villems, Richard; Kivisild, Toomas; Singh, Lalji; Thangaraj, Kumarasamy (2012). "The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations". PLoS ONE 7 (11): e48477. doi:10.1371/journal.pone.0048477. PMID 23209554.