Genetics and archaeogenetics 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 South Asia makes its biodiversity important for the study of the early dispersal of anatomically modern humans across Asia.
Studies based on mtDNA variation have reported genetic unity across various South Asian sub–populations. 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 South Asia. Recent genome studies appear to show that most South Asians are descendants of two major ancestral components, one restricted to South Asia (Ancestral South Indian) and the other component (Ancestral North Indian) more closely related to those in Central Asia, West Asia and Europe.
It has been found that the ancestral node of the phylogenetic tree of all the mtDNA types (mitochondrial DNA haplogroups) 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. In India, the major maternal lineages are various M subclades, followed by R and U sublineages. These mitochondrial haplogroups' coalescence times have been approximated to date to 50,000 BP.
The major paternal lineages represented by Y chromosomes are haplogroups R1a1, R2, H, L and J2. Many researchers have argued that Y-DNA Haplogroup R1a1 (M17) is of autochthonous South Asian origin. However, proposals for a Central Asian origin for R1a1 are also quite common.
All the mtDNA and Y-chromosome lineages outside Africa descend from three founder lineages:
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.
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.
Arguing for the longer term "rival Y-Chromosome model", 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.
The M macrohaplotype in India includes many subgroups that differ profoundly from other sublineages in East Asia especially Mongoloid populations. The deep roots of M phylogeny clearly ascertain the relic of South Asian 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.
Virtually all modern Central Asian MtDNA M lineages seem to belong to the Eastern Eurasian (Mongolian) rather than the South Asian 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 South Asians, East Asians and in some Central Asian populations contrasts with the Western Eurasian leanings of South Asian paternal lineages.
Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans.
|Haplogroup||Important Sub clades||Populations|
|M2||M2a, M2b||Throughout the continent with low presence in Northwest |
Peaking in Bangladesh, Andhra Pradesh, coastal Tamil Nadu and Sri Lanka
|M3||M3a||Concentrated into northwestern India |
Highest amongst the Parsees of Mumbai
|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 South Asia|
Peaking at Rajasthan and Andhra Pradesh
|M25||Moderately frequent in Kerala and Maharashtra but rather infrequent elsewhere in India|
The macrohaplogroup R (a very large and old subdivision of macrohaplogroup N) is also widely represented and accounts for the other 40% of South Asian 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:
|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 northwestern states. |
Peaks in Gujarat, Punjab and Kashmir, frequency is low elsewhere.
Haplogroup U is a sub-haplogroup of macrohaplogroup R. 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 South Asians. South Asian U lineages differ substantially from those in Europe and their coalescence to a common ancestor also dates back to about 50,000 years.
|U2*||(a parahaplogroup) is sparsely distributed specially in the northern half of the South Asia.
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 Gujarat, Punjab and Pakistan. The possible homeland of this haplogroup spans Gujarat (highest frequency, 12%) and Iran because from there its frequency declines steeply both to the east and to the west.|
|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 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 the Maldives. All three branches of Haplogroup H (Y-DNA) are found in South Asia.
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. 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 South Asia. Some individuals in South Asia have also been shown to belong to the much rarer subclade H3 (Z5857). Haplogroup H is by no means restricted to specific populations. For example, H is possessed by about 28.8% of Indo-Aryan castes. and in tribals about 25–35%.
Haplogroup J2 reflects presence from neolithic period in South Asia. The frequency of J2 is higher in South Indian castes (19%) than in North Indian castes (11%) or Pakistan (12%). Haplogroup J2 frequency is higher among south Indian middle castes at 21%, followed by upper castes at 18.6%, and lower castes 14%. Among caste groups, the highest frequency of J2-M172 was observed among Tamil Vellalar's of South India, at 38.7%. 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%). J2 is also present in the South Indian hill tribe Toda at 38.46%, in the Andh tribe of Telangana at 35.19% and in the Kol tribe of Uttar Pradesh at a frequency of 33.34%. Haplogroup J-P209 was found to be more common in India's Shia Muslims, of which 28.7% belong to haplogroup J, with 13.7% in J-M410, 10.6% in J-M267 and 4.4% in J2b (Eaaswarkhanth 2009).
In Pakistan, the highest frequencies of J2-M172 were observed among the Parsis at 38.89%, the Dravidian speaking Brahuis at 28.18% and the Makrani Balochs at 24%. It also occurs at 18.18% in Makrani Siddis and at 3% in Karnataka Siddis.
According to Dr. Spencer Wells, L-M20 originated in the Pamir Knot region in Tajikistan and migrated into Pakistan and India ca. 30,000 years ago. However, most other studies have proposed a West Asian origin for L-M20 and associated its expansion in the Indus valley (~7,000 YBP) to neolithic farmers. There are three subbranches of haplogroup L: L1-M76 (L1a1), L2-M317 (L1b) and L3-M357 (L1a2), found at varying levels in South Asia.
Haplogroup L shows time of neolithic expansion. The clade is present in the Indian population at an overall frequency of ca.7–15%. 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%). The presence of haplogroup L is quite rare among tribal groups (ca. 5,6–7%), however a moderate, 14.6% has been observed among the Chenchus.
In Pakistan, L1-M76 and L3-M357 subclades of L-M20 reaches overall frequencies of 5.1% and 6.8%, respectively. Haplogroup L3 (M357) is found frequently among Burusho (approx. 12%) and Pashtuns (approx. 7%). 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.
In South Asia, R1a1 has been observed often with high frequency in a number of demographic groups, as well as with highest STR diversity which lead some to see it as the locus of origin.
While R1a originated ca. 22,000 to 25,000 years ago, its subclade M417 (R1a1a1) diversified ca. 5,800 years ago. The distribution of M417-subclades R1-Z282 (including R1-Z280) in Central- and Eastern Europe and R1-Z93 in Asia suggests that R1a1a diversified within the Eurasian Steppes or the Middle East and Caucasus region. The place of origin of these subclades plays a role in the debate about the origins of Indo-Europeans.
In India, high percentage of this haplogroup is observed in West Bengal Brahmins (72%) to the east, Gujarat Lohanas (60%) to the west, Khatris (67%) in north, Iyengar Brahmins (31%) in the south. It has also been found in several South Indian Dravidian-speaking tribals including the Kotas (41%) of Tamil Nadu Chenchu (26%) 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. Besides these, studies show high percentages in regionally diverse groups such as Manipuris (50%)  to the extreme North East and in among Punjabis (47%) to the extreme North West.
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 South Asia. It is also reported in Caucasus and Central Asia at lower frequency.
Among regional groups, it is found among West Bengalis (23%), New Delhi Hindus (20%), Punjabis (5%) and Gujaratis (3%). Among tribal groups, Karmalis of West Bengal showed highest at 100% followed by Lodhas (43%) to the east, while Bhil of Gujarat in the west were at 18%, Tharus of north showed it at 17%, Chenchu and Pallan of south were at 20% and 14% respectively. Among caste groups, high percentages are shown by Jaunpur Kshatriyas (87%), Kamma Chaudhary (73%), Bihar Yadav (50%), Khandayat (46%)and Kallar (44%).
It is also significantly high in many Brahmin groups including Punjabi Brahmins (25%), Bengali Brahmins (22%), Konkanastha Brahmins (20%), Chaturvedis (32%), Bhargavas (32%), Kashmiri Pandits (14%) and Lingayat Brahmins (30%).
North Indian Muslims have a frequency of 19% (Sunni) and 13% (Shia), while Dawoodi Bohra Muslim in the western state of Gujarat have a frequency of 16% and Mappila Muslims of South India have a frequency of 5%.
The R2 haplogroup is found in 14% of the Burusho people. Among the Hunza people it is found at 18% while the Parsis show it at 20%. It is also found in the northeastern part of Afghanistan.
Reconstructing South Asian population historyEdit
The Indian Genome Variation Consortium (2008), divides the population of South Asia into four ethnolinguistic groups: Indo-European, Dravidian, Tibeto-Burman and Austro-Asiatic. 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.:04
Most of the studies based on mtDNA variation have reported genetic unity of South Asian populations across language, caste and tribal groups. It is likely that haplogroup M was brought to Asia from East Africa along the southern route by earliest migration wave 78,000 years ago.
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 South Asians. Despite the variations found within India, these populations stem from a limited number of founder lineages. These lineages were most likely introduced to South Asia during the Middle Palaeolithic, before the peopling of Europe 48,000 years ago and perhaps the Old World in general." Basu et al. (2003) also emphasizes underlying unity of female lineages in India.
Y Chromosome variationEdit
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 South Asia, Bamshad et al. (2001) suggests an affinity between South Asian male lineages and west Eurasians proportionate to upper caste rank and places upper caste populations of southern Indian states closer to East Europeans.
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. Whereas, Kumar et al. (2007) analyzed 25 South Asian Austro-Asiatic tribes and found strong paternal genetic link among the sub-linguistic groups of the South Asian Austro-Asiatic populations. Mukherjee et al. (2001) places Pakistanis and North Indians between west Asian and Central Asian populations, whereas Cordaux et al. (2004) argues that the Indian caste populations are closer to Central Asian populations. Sahoo et al. (2006) and Sengupata et al. (2006) suggest that Indian caste populations have not been subject to any recent admixtures. Sanghamitra Sahoo concludes his study with:
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 South Asia 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 variationEdit
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 South Asian 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." While the ANI is genetically close to Middle Easterners, Central Asians and Europeans, the ASI is not closely related to groups outside of the subcontinent. As no "ASI" ancient DNA is available, the Onge, a possibly distantly related population native to the Andaman Islands is used as an (imperfect) proxy. But they concluded that the Onge may in fact be very different from the ASI and suggest a possible gene flow from India to the Andamanese populations.
Such a pattern would be expected if there was ancient gene flow into the Andaman Islanders from a group more closely related to the ASI ancestry of some present-day Indian groups than others.
Another study (2013) using the single-nucleotide polymorphism (SNP), also shows that the genome of Andamanese people (Onge) is closest to those of other Oceanic Negrito groups and distinct from South Asians. This suggests that there is no relation between Andaman islanders and ancient South Asians.
Further analysis reveals that the genomic structure of mainland Indian populations is best explained by contributions from four ancestral components. In addition to the ANI and ASI, Basu et. al (2016) identified two ancestral components in mainland India that are major for the Austro-Asiatic-speaking tribals and the Tibeto-Burman speakers, which we respectively denote as AAA (for “Ancestral Austro-Asiatic”) and ATB (for “Ancestral Tibeto-Burman”). The study also infers that the populations of the Andaman Islands archipelago form a distinct ancestry, which is "coancestral to Oceanic populations." 
The cline of admixture between the ANI and ASI lineages is dated to the period of c. 4.2–1.9 kya by Moorjani et al. (2013), corresponding to the Indian Bronze Age, and associated by the authors with the process of deurbanization of the Indus Valley Civilization and the population shift to the Gangetic system in the incipient Indian Iron Age. 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". 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:
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.
Lazaridis et al. (2016) notes "The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian Dalit population with minimal Ancestral North Indian (ANI) along the 'Indian Cline' of such ancestry is inferred to have ~ 18 % steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~ 50 % steppe-related ancestry." Lazaridis et al.'s 2016 study estimated (6.5–50.2 %) steppe related admixture in South Asians. Lazaridis et al. further notes that "A useful direction of future research is a more comprehensive sampling of ancient DNA from steppe populations, as well as populations of central Asia (east of Iran and south of the steppe), which may reveal more proximate sources of the ANI than the ones considered here, and of South Asia to determine the trajectory of population change in the area directly.
Narasimhan et al. (2018) conclude that ANI and ASI were formed in the 2nd millennium BCE. They were preceded by a mixture of AASI (ancient ancestral south Indians, that is, hunter-gatherers), and Iranian agriculturalists who arrived in India at ca. 4700–3000 BCE, and "must have reached the Indus Valley by the 4th millennium BCE". According to Narasimhan et al., this population, which probably was native to the Indus Valley Civilisation, "contributed in large proportions to both the ANI and ASI", which took shape during the 2nd millennium BCE. ANI formed out of a mixture of "Indus_Periphery-related groups" and migrants from the steppe, while ASI was formed out of "Indus_Periphery-related groups" who moved south and mixed with hunter-gatherers.
Pathak et al. 2018 concluded that the Indo-European speakers of Gangetic Plains and Dravidian speakers have significant Yamnaya Early-Middle Bronze Age (Steppe_EMBA) ancestry but no Middle-Late Bronze Age Steppe (Steppe_MLBA) ancestry. On the other hand, the "North-Western Indian and Pakistani" populations (PNWI) showed significant Steppe_MLBA ancestry along with Yamnaya (Steppe_EMBA) ancestry. The study also noted that ancient South Asian samples had significantly higher Steppe_MLBA than Steppe_EMBA (or Yamnaya). The study also suggested that the Rors could be used as a proxy for the ANI.
Genetic distance between caste groups and tribesEdit
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. 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.
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."
A 2011 study published in the American Journal of Human Genetics 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.
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