genetics and archaeogenetics of the ethnic groups of South Asia 

The study of the genetics and archaeogenetics of the ethnic groups of South Asia aims at uncovering these groups’ genetic history. The geographic position of India makes Indian populations important for the study of the early dispersal of all human populations on the Eurasian continent. R Studies based on mtDNA variation have reported genetic unity across various Indian sub–populations.[1][2][3][4] Conclusions of studies based on Y Chromosome variation and Autosomal DNA variation have been varied, although many researchers argue that most of the ancestral nodes of the phylogenetic tree of all the mtDNA types originated in the subcontinent. Recent genome studies appear to show that most South Asians are descendants of two major ancestral components, one restricted to South Asia and the other component shared with Central Asia, West Asia and Europe.[5][6]
It has been found that the ancestral node of the phylogenetic tree of all the mtDNA types typically found in Central Asia, the West Asia and Europe are also to be found in South Asia at relatively high frequencies. The inferred divergence of this common ancestral node is estimated to have occurred slightly less than 50,000 years ago.[7] In India the major maternal lineages, or mitochondrial DNA Haplogroups, are M, R and U, whose coalescence times have been approximated to 50,000 BP.[7]
The major paternal lineages represented by Y chromosomes are haplogroups R1a1, R2, H, L and J2.[8] Many researchers have argued that Y-DNA Haplogroup R1a1 (M17) is of autochthonous Indian origin.[9][10] However, proposals for a Central Asian origin for R1a1 are also quite common.[11][12]
Contents

Overview Edit
All the mtDNA and Y-chromosome lineages outside Africa descend from three founder lineages:
M, N and R haplogroups for mtDNA and

C, D and F haplogroups for the Y-chromosome.

All these six founder haplogroups can be found in the present day populations of South Asia. Moreover, the mtDNA haplogroup M and the Y-chromosome haplogroups C and D are restricted to the area east of South Asia. All the West Eurasian populations derive from the N and R haplogroups of mtDNA and the F haplogroup of the Y-chromosome.[13]
Endicott et al. state that these facts are consistent with the hypothesis of a single exodus from East Africa 65,000 years ago via a southern coastal route, with the West Eurasian lineages separating from the South Asian lineages somewhere between East/Northeast Africa and South Asia.[14]
mtDNA Edit
See also: Recent single origin hypothesis
Hypothesized map of human migration into the Indian subcontinent based on mitochondrial DNA and possible dispersal routes.

The most frequent mtDNA haplogroups in the Indian subcontinent are M, R and U (where U is a descendant of R).[8]
Arguing for the longer term “rival Y-Chromosome model”,[9] Stephen Oppenheimer believes that it is highly suggestive that India is the origin of the Eurasian mtDNA haplogroups which he calls the “Eurasian Eves”. According to Oppenheimer it is highly probable that nearly all human maternal lineages in Central Asia, the Middle East and Europe descended from only four mtDNA lines that originated in South Asia 50,000-100,000 years ago.[15]
Macrohaplogroup M Edit

The macrohaplogroup M which is considered as a cluster of the proto-Asian maternal lineages,[7] represents more than 60% of Indian MtDNA.[16]
The M macrohaplotype in India includes many subgroups that differ profoundly from other sublineages in East Asia especially Mongoloid populations.[7] The deep roots of M phylogeny clearly ascertain the relic of Indian lineages as compared to other M sub lineages (in East Asia and elsewhere) suggesting ‘in-situ’ origin of these sub-haplogroups in South Asia, most likely in India. These deep rooting lineages are not language specific and spread over all the language groups in India.[16]
Virtually all modern Central Asian MtDNA M lineages seem to belong to the Eastern Eurasian (Mongolian) rather than the Indian subtypes of haplogroup M, which indicates that no large-scale migration from the present Turkic-speaking populations of Central Asia occurred to India. The absence of haplogroup M in Europeans, compared to its equally high frequency among Indians, eastern Asians and in some Central Asian populations contrasts with the Western Eurasian leanings of South Asian paternal lineages.[7]
Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans.[17]
Haplogroup Important Sub clades Populations

M2 M2a, M2b Throughout the continent except in Northwest

Peaking in Bangladesh, Andhra Pradesh, coastal Tamil Nadu and Sri Lanka

M3 M3a All the subcontinent except the Northeast

20% in Rajasthan and Madhya Pradesh, being also very dense in Maharashtra, Uttar Pradesh, Haryana, Gujarat, Karnataka

M4 M4a Peaks in Pakistan, Kashmir and Andhra Pradesh

M6 M6a,M6b Kashmir and near the coasts of the Bay of Bengal, Sri Lanka

M18 Throughout the subcontinent

Peaking at Rajasthan and Andhra Pradesh

M25 Widespread in most of India (but rare outside it)

western Maharashtra and Kerala, Punjab

Macrohaplogroup R Edit

The spatial distribution of M, R and U mtDNA haplogroups and their sub-haplogroups in South Asia. .

The macrohaplogroup R (a very large and old subdivision of macrohaplogroup N) is also widely represented and accounts for the other 40% of Indian MtDNA. A very old and most important subdivision of it is haplogroup U that, while also present in West Eurasia, has several subclades specific to South Asia.
Most important South Asian haplogroups within R:[17]
Haplogroup Populations

R2 Distributed widely across the sub continent

R5 widely distributed by most of India.

Peaks in coastal SW India

R6 widespread at low rates across India.

Peaks among Tamils and Kashmiris

W Found in Pakistan, Kashmir, Gujarat, Maharashtra and Punjab.

It is rare further east and not to be found in the rest of India.

Haplogroup U Edit

Haplogroup U is a sub-haplogroup of macrohaplogroup R.[17] The distribution of haplogroup U is a mirror image of that for haplogroup M: the former has not been described so far among eastern Asians but is frequent in European populations as well as among Indians.[18] Indian U lineages differ substantially from those in Europe and their coalescence to a common ancestor also dates back to about 50,000 years.[1]
Haplogroup Populations

U2* (a parahaplogroup) is sparsely distributed specially in the northern half of the subcontinent.

It is also found in SW Arabia.
U2a shows relatively high density in Pakistan and NW India but also in Karnataka, where it reaches its higher density.

U2b has highest concentration in Uttar Pradesh but is also found in many other places, specially in Kerala and Sri Lanka.

It is also found in Oman.
U2c is specially important in Bangladesh and West Bengal.

U2l is maybe the most important numerically among U subclades in South Asia, reaching specially high concentrations (over 10%) in Uttar Pradesh, Sri Lanka, Sindh and parts of Karnataka. It also has some importance in Oman. mtDNA haplogroup U2i is dubbed “Western Eurasian” in Bamshad et al. study but “Eastern Eurasian (mostly India specific)” in Kivisild et al. study.

U7 this haplogroup has a significant presence in Gujrat, Punjab and Pakistan. The possible homeland of this haplogroup spans Indian Gujarat(highest frequency, 12%) and Iran because from there its frequency declines steeply both to the east and to the west.

Y chromosome Edit

The diversion of Haplogroup F and its descendants.

For more details on individual groups by Y-DNA, see Y-DNA haplogroups in South Asian populations.

The major Y chromosome DNA haplogroups in the subcontinent are Haplogroup F’s descendant haplogroups R (mostly R1a1, R2 and R2a), L, H and J (mostly J2).[8]
The South Asian Y-chromosomal gene pool is characterized by five major lineages: R1a, R2, H, L and J2. Their geographical origins are listed as follows, according to the latest scholarship:
Major South Asian Y-chromosomal lineages: H J2 L R1a R2

Basu et al. (2003) no comment no comment no comment Central Asia no comment

Kivisild et al. (2003) India Western Asia India Southern and Western Asia South-Central Asia

Cordaux et al. (2004) India West or Central Asia Middle Eastern Central Asia South-Central Asia

Sengupta et al. (2006) India The Middle East and Central Asia South India North India North India

Thanseem et al. (2006) India The Levant The Middle East Southern and Central Asia Southern and Central Asia

Sahoo et al. (2006) South Asia The Near East South Asia South or West Asia South Asia

Mirabal et al. (2009) no comment no comment no comment Northwestern India or Central Asia no comment

Zhao et al. (2009) India The Middle East The Middle East Central Asia or West Eurasia Central Asia or West Eurasia

Sharma et al. (2009) no comment no comment no comment South Asia no comment

Thangaraj et al. (2010) South Asia The Near East The Near East South Asia South Asia

Haplogroup L Edit

Main article: Haplogroup L (Y-DNA)

India Edit

Haplogroup L shows time of neolithic expansion.[19] The clade is present in the Indian population at an overall frequency of ca.7-15%.[9][11][20][21] There are three subbranches of Haplogroup L and all three are found mostly in South Asia. Haplogroup L has higher frequency among south Indian castes (ca. 17-19%) and reaches up to 68% in some castes in Karnataka but is somewhat rarer in north Indian castes (ca. 5-6%) and reaches up to 38% in some castes in Gujarat.[9][22] They make a case for an indigenous origin of L-M76 in South Asia as the spatial distributions of both L-M76 HG frequency and associated microsatellite variance show a pattern of spread emanating from southern India.[9] The presence of haplogroup L is quite rare among tribal groups (ca. 5,6-7%)[9][11][21]
Pakistan Edit

Haplogroup L3 (M357) is found frequently among Burusho (approx. 12%[23]) and Pashtuns (approx. 7%[23]), Its highest frequency can be found in south western Balochistan province along the Makran coast (28%) to Indus River delta. L3a (PK3) is found in approximately 23% of Nuristani in northwest Pakistan,[23]
The clade is present in moderate distribution among the general Pakistani population (approx. 11.6%[23]).
Haplogroup H Edit

Main article: Haplogroup H (Y-DNA)

Haplogroup H (Y-DNA) is found at a high frequency in South Asia. H is rarely found outside of the South Asia but is common among the Romanis, particularly the H-M82 subgroup. Haplogroup H is frequently found among populations of India, Sri Lanka, Nepal, Pakistan and Maldives. All three branches of Haplogroup H (Y-DNA) are found in Indian-subcontinent.
It is a branch of Haplogroup F and descends from GHIJK family. Haplogroup H is believed to have arisen in South Asia between 30,000 and 40,000 years ago.[24] 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).[24] Haplogroup H is by no means restricted to specific populations. For example, H is possessed by about 28.8% of Indo-Aryan castes.[9][21] and in tribals about 25-35%.[11][21]
Haplogroup R2 Edit

Main articles: Haplogroup R2 (Y-DNA) and Haplogroup R2a (Y-DNA)

In South Asia, the frequency of R2 and R2a lineage is around 10-15% in India and Sri Lanka and 7-8% in Pakistan. At least 90% of R-M124 individuals are located in the Indian sub-continent.[25] It is also reported in Caucasus and Central Asia at lower frequency.
India Edit

It is found among people of West Bengal at 23%, Hindus from New Delhi at 20% and Baniya from Bihar at 36%. Among tribal groups, Lodhas of West Bengal show it at 43% while Bhil of Gujarat at 18%. Chenchu and Pallan of South India at 20% and 14% respectively. Tharu of North India shows it at 17%.[4]
It is also significantly high in many Brahmin groups including Punjabi Brahmins (25%), Bengali Brahmins (22%), Bengali Kayasthas (21%), Konkanastha Brahmins (20%), Chaturvedis (32%), Bhargavas (32%), Kashmiri Pandits (14%) and Lingayat Brahmins (30%).[4]
North Indian Muslims have a frequency of 11%(Sunni) and 9%(Shia), while Dawoodi Bohra Muslim in the western state of Gujarat have a frequency of 16% and Mappla Muslims of South India have a frequency of 5%.[26] This lineage also forms 5% of Punjabi males.
Pakistan Edit

The R2 haplogroup is found in 14% of the Burusho people.[23] Among the Hunza it is found at 18% while the Parsis show it at 20%. It is also found in the northeastern part of Afghanistan.[citation needed]
Sri Lanka Edit

24.1% of the Sinhalese of Sri Lanka are found to have R2 as subclades of Haplogroup P (92R7) according to the research of Dr. Toomas Kivisild published in “The Genetics of Language and Farming Spread in India”. Sample size used was 87 subjects.[27]
Maldives Edit

13% of the Maldivian people of Maldives are found to have R2.[28]
Nepal Edit

In Nepal, R2 percentages range from 2% to 26% within different groups under various studies. Newars show a significantly high frequency of 26% while people of Kathmandu show it at 10%.
Haplogroup R1a1 Edit

Main article: Haplogroup R1a1a

In South Asia R1a1 has been observed often with high frequency in a number of demographic groups,[10][29][30] which lead some to see it as the locus of origin.[31][32]
According to Pamjav et al. (2012), “Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages [which] implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe.”[33] Underhill et al. (2014/2015) concluded that R1a1a1, the most frequent subclade of R1a, split into R1a-Z282 (Europe) and R1a-Z93 (Asia) at circa 5,800 before present[34] in the vicinity of Iran and Eastern Turkey. According to Underhill et al. (2014/2015), “[t]his suggests the possibility that R1a lineages accompanied demic expansions initiated during the Copper, Bronze, and Iron Ages.”[35] They further note that the diversification of Z93 and the “early urbanization within the Indus Valley also occurred at this time and the geographic distribution of R1a-M780 (Figure 3d) may reflect this.”[35] Poznik et al. (2016) note that ‘striking expansions’ occurred within R1a-Z93 at ~4,500-4,000 years ago, which “predates by a few centuries the collapse of the Indus Valley Civilisation.”[36] Mascarenhas et al. (2015) note that the expansion of Z93 from Transcaucasia into South Asia is compatible with “the archeological records of eastward expansion of West Asian populations in the 4th millennium BCE culminating in the socalled Kura-Araxes migrations in the post-Uruk IV period.”[37]
India Edit

In India, high percentage of this haplogroup is observed in West Bengal Brahmins (72%) [29] to the east, Konkanastha Brahmins (48%) [29] to the west, Khatris (67%)[30] in north and Iyengar Brahmins (31%) of south.[29] It has also been found in several South Indian Dravidian-speaking Tribals including the Chenchu (26%)[27] and Valmikis of Andhra Pradesh as well as the Yadav and Kallar of Tamil Nadu suggesting that M17 is widespread in these Southern Indians tribes.[27] and 47% in Punjab.[27][30]
Pakistan Edit

In Pakistan it is found at 71% among the Mohanna of Sindh Province to the south and 46% among the Baltis of Gilgit-Baltistan to the north.[30]
Sri Lanka Edit

23% of the Sinhalese people were found to be R1a1a (R-SRY1532) positive according to the research of Dr. Toomas Kivisild published in “The Genetics of Language and Farming Spread in India”. Sample size used was 87 subjects.[27]
Maldives Edit

In Maldives, 24% of the Maldivian people were found to be R1a1a (M17) positive.[28]
Nepal Edit

People in Terai Region, Nepal show R1a1a at 69%.[38]
Haplogroup J2 Edit

Main article: Haplogroup J2 (Y-DNA)

Haplogroup J2 reflects presence from neolithic period in the subcontinent.[19] The frequency of J2 is higher in South Indian castes (19%) than in North Indian castes (11%) or Pakistan (12%).[9] Haplogroup J2 frequency is higher among south Indian middle castes at 21%, followed by upper castes at 18.6%, and lower castes 14%.[9] J2 is present in tribals too and has a frequency of 11% in Austro-Asiatic tribals. Among the Austro-Asiatic tribals, the predominant J2 occurs in the Lodha(35%).[9] J2 is also present in the South Indian hill tribe Toda at a frequency of 38.46%[39] and in the Kol tribe of Uttar Pradesh at a frequency of 33.34%.[40] It is also found at 3%, among the Siddi’s.[41] In Maldives, 22% of Maldivian population were found to be haplogroup J2 positive.[42]
Reconstructing Indian population history Edit
The Indian Genome Variation Consortium (2008), divides the population of the subcontinent into four linguistic groups— Indo-European, Dravidian, Tibeto-Burman and Austro-Asiatic.[43][44][45][46][47] The molecular anthropology studies use three different type of markers: Mitochondrial DNA (mtDNA) variation which is maternally inherited and highly polymorphic, Y Chromosome variation which involves uniparental transmission along the male lines, and Autosomal DNA variation.[4]:04
mtDNA variation Edit

Most of the studies based on mtDNA variation have reported genetic unity of Indian populations across language, caste and tribal groups.[1][2][3] It is likely that haplogroup M was brought to Asia from East Africa along the southern route by earliest migration wave 60,000 years ago.[1]
According to Kivisild et al. (1999), “Minor overlaps with lineages described in other Eurasian populations clearly demonstrate that recent immigrations have had very little impact on the innate structure of the maternal gene pool of Indians. Despite the variations found within India, these populations stem from a limited number of founder lineages. These lineages were most likely introduced to the Indian subcontinent during the Middle Palaeolithic, before the peopling of Europe and perhaps the Old World in general.”[1] Basu et al. (2003) also emphasizes underlying unity of female lineages in India.[20]
Y Chromosome variation Edit

Conclusions based on Y Chromosome variation have been more varied than those based on mtDNA variation. While Kivisild et al. (2003) proposes an ancient and shared genetic heritage of male lineages in India, Bamshad et al. (2001) suggests an affinity between Indian male lineages and west Eurasians proportionate to caste rank and places caste populations of southern Indian states closer to East Europeans.[48]
Basu et al. (2003) concludes that Austro–Asiatic tribal populations entered India first from the Northwest corridor and much later some of them through Northeastern corridor.[20] Whereas, Kumar et al. (2007) analyzed 25 Indian Austro-Asiatic tribes and found strong paternal genetic link among the sub-linguistic groups of the Indian Austro-Asiatic populations.[49] Mukherjee et al. (2001) places North Indians between west Asian and Central Asian populations,[50] whereas Cordaux et al. (2004) argues that the Indian caste populations are closer to Central Asian populations.[21] Sahoo et al. (2006) and Sengupata et al. (2006) suggest that Indian caste populations have not been subject to any recent admixtures.[9][10] Sanghamitra Sahoo concludes his study with:[10]
It is not necessary, based on the current evidence, to look beyond South Asia for the origins of the paternal heritage of the majority of Indians at the time of the onset of settled agriculture. The perennial concept of people, language, and agriculture arriving to India together through the northwest corridor does not hold up to close scrutiny. Recent claims for a linkage of haplogroups J2, L, R1a, and R2 with a contemporaneous origin for the majority of the Indian castes’ paternal lineages from outside the subcontinent are rejected, although our findings do support a local origin of haplogroups F* and H. Of the others, only J2 indicates an unambiguous recent external contribution, from West Asia rather than Central Asia. The current distributions of haplogroup frequencies are, with the exception of the lineages, predominantly driven by geographical, rather than cultural determinants. Ironically, it is in the northeast of India, among the TB groups that there is clear-cut evidence for large-scale demic diffusion traceable by genes, culture, and language, but apparently not by agriculture.
Autosomal DNA variation Edit

Results of studies based upon autosomal DNA variation have also been varied. In a major study (2009) using over 500,000 biallelic autosomal markers, Reich hypothesized that the modern Indian population was the result of admixture between two genetically divergent ancestral populations dating from the post-Holocene era. These two “reconstructed” ancient populations he termed “Ancestral South Indians” (ASI) and “Ancestral North Indians” (ANI). According to Reich: “ANI ancestry is significantly higher in Indo-European than Dravidian speakers, suggesting that the ancestral ASI may have spoken a Dravidian language before mixing with the ANI.”[51]
Further building on Reich et al.’s characterization of the South Asian population as historically based on admixture of ANI (Ancestral North Indian) and ASI (Ancestral South Indian) populations, a 2013 paper by Moorjani et al. states that a major mixture between populations in India occurred 1,900–4,200 years BP characterized by the deurbanization of the Indus civilization and population shift to the Gangetic system.[6]
Basu et al. (2003) suggests concludes that “Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads” and that “formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations”.[20] The geneticist PP Majumder (2010) has recently argued that the findings of Reich et al. (2009) are in remarkable concordance with previous research using mtDNA and Y-DNA:[52]
Central Asian populations are supposed to have been major contributors to the Indian gene pool, particularly to the northern Indian gene pool, and the migrants had supposedly moved into India through what is now Afghanistan and Pakistan. Using mitochondrial DNA variation data collated from various studies, we have shown that populations of Central Asia and Pakistan show the lowest coefficient of genetic differentiation with the north Indian populations, a higher differentiation with the south Indian populations, and the highest with the northeast Indian populations. Northern Indian populations are genetically closer to Central Asians than populations of other geographical regions of India… . Consistent with the above findings, a recent study using over 500,000 biallelic autosomal markers has found a north to south gradient of genetic proximity of Indian populations to western Eurasians. This feature is likely related to the proportions of ancestry derived from the western Eurasian gene pool, which, as this study has shown, is greater in populations inhabiting northern India than those inhabiting southern India.
Genetic distance between caste groups and tribes

Studies by Watkins et al. (2005) and Kivisild et al. (2003) based on autosomal markers conclude that Indian caste and tribal populations have a common ancestry.[53][54] Reddy et al. (2005) found fairly uniform allele frequency distributions across caste groups of southern Andhra Pradesh, but significantly larger genetic distance between caste groups and tribes indicating genetic isolation of the tribes and castes.[55]
Viswanathan et al. (2004) in a study on genetic structure and affinities among tribal populations of southern India concludes, “Genetic differentiation was high and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations. Otherwise, analyses of population relationships showed that all Indian and South Asian populations are still similar to one another, regardless of phenotypic characteristics, and do not show any particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence.”[56]
A 2011 study published in the American Journal of Human Genetics[5] indicates that Indian ancestral components are the result of a more complex demographic history than was previously thought. According to the researchers, South Asia harbours two major ancestral components, one of which is spread at comparable frequency and genetic diversity in populations of Central Asia, West Asia and Europe; the other component is more restricted to South Asia. However, if one were to rule out the possibility of a large-scale Indo-Aryan migration, these findings suggest that the genetic affinities of both Indian ancestral components are the result of multiple gene flows over the course of thousands of years.[5]

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