Haplogroup H (Y-DNA)

Haplogroup H (Y-DNA)

Possible time of origin	25,000–45,000 years BP
Possible place of origin	South Asia
Ancestor	GHIJK
Defining mutations	L901/M2939
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 (M52) – 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^[1]^[2] 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.

Structure

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");^[3] – 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.^[1]
H3: Z5857 – South Asians

Distribution

H-L901/M2939 is believed to have arisen in South Asia between 30,000 and 40,000 years ago.^[4] 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).

However, in South Asia, haplogroup H is by no means restricted to specific populations. For example, H is possessed by about 28.8% of Indo-Aryan castes.^[5]^[5] and in tribals about 25–35%.^[6]^[7]

South Asia

Haplogroup H-M69 is fairly common among populations of India, Sri Lanka, Pakistan and Nepal, with lower frequency in Afghanistan.^[8] The highest frequencies of H-M69 are in India, especially in southern India at (32.9%).^[5]^[9] and H-M52 among Kalash (20.5%) in Pakistan.^[10]^[11]

Haplogroup H-M69 has been found in:

South India – 27.2% (110/405) of a sample of unspecified ethnic composition.^[12]^[13] Another study has found haplogroup H-M69 in 26.4% (192/728) of an ethnically diverse pool of samples from various regions of India.^[5]
Sri Lanka – in 25.3% (23/91) of a sample of unspecified ethnic composition^[12]^[13] and in 10.3% (4/39) of a sample of Sinhalese.^[11]
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.^[14]
Pakistan – in 4.1% Burusho, 20.5% Kalash, 4.2% Pashtun, and 6.3% in other Pakistanis.^[5]^[10] 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.^[15]^[15]
Afghanistan – in 6.1% Pashtun.^[8]

Romani people

Haplogroup H-M82 is a major lineage cluster in the Balkan Romani group, accounting for approximately 60% of the total.^[16] 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.^[17]

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,^[18] 6% (1/17) H-M52 in a sample of Turks,^[18] 5% (1/20) H-M69 in a sample of Syrians,^[19] 4% (2/45) H-M52 in a sample of Uzbeks from Samarkand,^[18] 4% (2/53) H-M52 in a sample of Iranians from Samarkand,^[18] 3% (2/70) H-M52 in a sample of Uzbeks from Khorezm,^[18] 3% (1/38) H-M82 in a sample of Balkarians,^[20] 2.6% (3/117) H-M82 in a sample from southern Iran,^[21] 2% (1/41) H-M52 in a sample of Uyghurs from Kazakhstan,^[18] 1% (1/92 H-M82)^[20] to 2% (1/50 H-M69)^[19] of Ukrainians, 2% (1/56) H-M52 in a sample of Uzbeks from Bukhara,^[18] 2% (1/57) H-M82 in a sample of Macedonian Greeks,^[20] 2% (1/63) H-M52 in a sample of Uzbeks from the Fergana Valley,^[18] 0.9% (1/113) H-M82 in a sample of Serbians,^[16] 0.6% (3/523) H-M370 in a sample of Turks,^[22] and 0.5% (1/201) H-M52 in a sample of Somali immigrants in Denmark.^[23]

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),^[24] approximately 2% of males from Oman,^[25] 1.9% (3/157) of males from Saudi Arabia (including 2/157 = 1.3% H-M69(xM52) and 1/157 = 0.6% H-M82),^[26] and 1.4% (1/72 H-M82) of males from Qatar.^[24]

The subclade H-APT has been found in 1.3% (1/77) of a sample of Greeks.^[10]

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),^[27] Balinese (19/551 = 3.45% H-M69),^[13] Tibetans (3/156 = 1.9% H-M69(xM52, APT)),^[14] Bamars from Myanmar (1/59 = 1.7% H-M82, with the relevant individual having been sampled in Bago Region),^[28] Chams from Binh Thuan, Vietnam (1/59 = 1.7% H-M69),^[27] and Mongolians (1/149 = 0.7% H-M69).^[12] The subclade H-M39/M138 has been observed in the vicinity of Cambodia, including one instance in a sample of six Cambodians^[5] and one instance in a sample of 18 individuals from Cambodia and Laos.^[15]

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.^[1] 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.

Subclades

Tree

This phylogenetic tree of haplogroup subclades is based on the ISOGG Y-DNA Haplogroup H and its Subclades tree – 2016.^[29]

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-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-P96 (H2) (P96, M282; formerly known as Haplogroup F3 and H-M282.^[30])
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-Z13871 (H3b)
  - H-Z5859 (H3b1)

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.^[31]

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

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
	L	T ^{[χ 6]}		NO ^{[χ 7]}	K2b ^{[χ 8]}	K2c	K2d	K2e ^{[χ 9]}
	N	O		K2b1 ^{[χ 10]}	P
	K2b1a^{[χ 11]}	K2b1b	K2b1c	M		P1	P2
	K2b1a1	K2b1a2	K2b1a3	S ^{[χ 12]}		Q	R
Y-DNA by populations Famous Y-DNA haplotypes
↑ 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. PMID 24166809. ↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.) ↑ Haplogroup A0-T is also known as A0'1'2'3'4. ↑ Haplogroup A1 is also known as A1'2'3'4. ↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1. ↑ Between 2002 and 2008, Haplogroup T (M184) was known as "Haplogroup K2" – that name has since been re-assigned to K-M526, the sibling of Haplogroup LT. ↑ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a"). ↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS. ↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a, also known as Haplogroup NO). ↑ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure. ↑ Haplogroup K2b1a has also been known as Haplogroup S-P405. ↑ Haplogroup S (S-M230), also known as K2b1a4, was previously known as Haplogroup K5.

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↑ 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. PMC 3509117. PMID 23209554.

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