Genetics and archaeogenetics of South Asia

The

Most important South Asian haplogroups within R:^[47]

Haplogroup U

The major South Asian Y-chromosome DNA haplogroups are

Probable site of introduction; South Asia or West Asia^[49] or Southern Central Asia.^[50] It seems to represent the main Y-Chromosome haplogroup of the paleolithic inhabitants of South Asia and Europe respectively. Some individuals in South Asia have also been shown to belong to the much rarer subclade H3 (Z5857).^[51] Haplogroup H is by no means restricted to specific populations. For example, H is possessed by about 28.8% of Indo-Aryan castes.^[37][52] and in tribals about 25–35%.^[39][52]

Haplogroup J2

Haplogroup J2 has been present in South Asia mostly as J2a-M410 and J2b-M102, since neolithic times (9500 YBP).

J2-M172 is found at an overall frequency of 10.3% among the Sinhalese people of Sri Lanka.^[42] In Maldives, 20.6% of Maldivian population were found to be haplogroup J2 positive.^[60]

Haplogroup L

According to Dr.

The clade is present in moderate distribution among the general Pakistani population (14% approx).[58]^[63]

Sri Lanka

In one study, 16% of the Sinhalese were found to be Haplogroup L-M20 positive.^[71] In another study 18% were found to belong to L1.^[42]

Haplogroup R1a1

In South Asia, R1a1 has been observed often with high frequency in a number of demographic groups,^[38][37][72] as well as with highest STR diversity which lead some to see it as the locus of origin.^[56][42][73]

While R1a originated c. 22,000^[56] to 25,000^[74] years ago, its subclade M417 (R1a1a1) diversified c. 5,800 years ago.^[74] The distribution of M417-subclades R1-Z282 (including R1-Z280)^[75] in Central and Eastern Europe and R1-Z93 in Asia^[74][75] suggests that R1a1a diversified within the Eurasian Steppes or the Middle East and Caucasus region.^[75] The place of origin of these subclades plays a role in the debate about the origins of Indo-Europeans.

India

In

23% of the Sinhalese people out of a sample of 87 subjects were found to be R1a1a (R-SRY1532) positive according to a 2003 research,^[71] while another research in the same year found 12.8% of 38 samples belonged to this specific haplogroup.^[42]

Maldives

In the

People in Terai region, Nepal show R1a1a at 69%.^[76]

Haplogroup R2

In South Asia, the frequency of

38% of the Sinhalese of Sri Lanka were found to be R2 positive according to a 2003 research.^[42]

Maldives

12% of the Maldivians are found to have R2.^[60]

Nepal

In Nepal, R2 percentages range from 2% to 26% within different groups under various studies.

Haplogroup O1 (O-F265) and O2 (O-M122), the primary branches of

Most of the studies based on mtDNA variation have reported genetic unity of South Asian 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 78,000 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 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."^[1] Basu et al. (2003) also emphasises underlying unity of female lineages in India.^[69]

Y Chromosome variation

Conclusions based on Y Chromosome variation have been more varied than those based on mtDNA variation. While Kivisild et al.^[42] 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 modern west Eurasians proportionate to upper-caste rank and places upper-caste populations of southern Indian states closer to East Europeans.^[91]

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.^[69] Whereas, Kumar et al. (2007) analysed 25 South Asian Austro-Asiatic tribes and found a strong paternal genetic link among the sub-linguistic groups of the South Asian Austro-Asiatic populations.^[79] Mukherjee et al. (2001) places Pakistanis and North Indians between west Asian and Central Asian populations,^[92] whereas Cordaux et al. (2004) argues that the Indian caste populations are closer to Central Asian populations.^[52] Sahoo et al. (2006) and Sengupta et al. (2006) suggest that Indian caste populations have not been subject to any recent admixtures.^[37][38] Sanghamitra Sahoo concludes his study with:^[38]

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.

Closest-neighbor analysis done by Mondal et al. in 2017 concluded that Indian Y-lineages are close to southern European populations and the time of divergence between the two predated Steppe migration:^[78]

These results suggest that the European-related ancestry in Indian populations might be much older and more complex than anticipated, and might originate from the first wave of agriculturists or even earlier

— Mondal et al. 2017

Autosomal DNA variation

AASI-ANI-ASI

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 indigenous

According to Gallego Romero et al. (2011), their research on lactose tolerance in India suggests that "the west Eurasian genetic contribution identified by Reich et al. (2009) principally reflects gene flow from Iran and the Middle East".[93] Gallego Romero notes that Indians who are lactose-tolerant show a genetic pattern regarding this tolerance which is "characteristic of the common European mutation".^[94] According to Romero, this suggests that "the most common lactose tolerance mutation made a two-way migration out of the Middle East less than 10,000 years ago. While the mutation spread across Europe, another explorer must have brought the mutation eastward to India – likely traveling along the coast of the Persian Gulf where other pockets of the same mutation have been found."^[94]

Moorjani et al. 2013 state that the ASI, though not closely related to any living group, are "related (distantly) to indigenous Andaman Islanders." Moorjani et al. however suggest possible gene flow into the Andamanese from a population related to the ASI, causing the modeled relationship. The study concluded that "almost all groups speaking Indo-European or Dravidian languages lie along a gradient of varying relatedness to West-Eurasians in PCA (referred to as "Indian cline")".^[95]

A 2013 study by Chaubey using the single-nucleotide polymorphism (SNP), shows that the genome of Andamanese people (Onge) is closer to those of other Oceanic Negrito groups than to that of South Asians.^[96]

According to Basu et al. 2016, further analysis revealed 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 East Asian ancestral components in mainland India that are major for the Austro-Asiatic-speaking tribals and the Tibeto-Burman speakers, which they denoted as AAA (for "Ancestral Austro-Asiatic") and ATB (for "Ancestral Tibeto-Burman") respectively. The study also infers that the populations of the Andaman Islands archipelago form a distinct ancestry, which "was found to be coancestral to Oceanic populations" but more distant from South Asians.^[30]

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 deurbanisation of the

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.

Chaubey et al. 2015 detected a distinctive East Asian ancestral component, mainly restricted to specific populations in the foothills of Himalaya and northeastern part of India. Highest frequency of the component is observed among the Tibeto-Burmese speaking groups of northeast India and was also detected in Andamanese populations at 32%, with substantial presence also among Austroasiatic speakers. It is found to be largely absent in Indo-European and Dravidian speakers, except in some specific ethnic groups living in the Himalayan foothills and central-south India.^[11] The researchers however suggested that the East Asian ancestry (represented by the Han) measured in the studied Andamanese groups may actually reflect the capture of the affinity of the Andamanese with Melanesians and Malaysian Negritos (rather than true East Asian admixture),^[11] as a previous study by Chaubey et al. suggested "a deep common ancestry" between Andamanese, Melanesians and other Negrito groups,^[11] and an affinity between Southeast Asian Negritos and Melanesians (as well as the Andamanese) with East Asians.^[96]

Lazaridis et al. (2016) notes "The demographic impact of steppe related populations on South Asia was substantial, as the

David Reich in his 2018 book Who We Are and How We Got Here states that the 2016 analyses found the ASI to have significant amounts of an ancestry component deriving from Iranian farmers (about 25% of their ancestry), with the remaining 75% of their ancestry deriving from native South Asian hunter-gatherers. He adds that ASI were unlikely the local hunter-gatherers of South Asia as previously established, but a population responsible for spreading agriculture throughout South Asia. In the case of the ANI, the Iranian farmer ancestry is 50%, with the rest being from steppe groups related to the Yamnaya.^[41]

Narasimhan et al. (2018), similarly, conclude that ANI and ASI were formed in the 2nd millennium BCE.^[22]: 15 They were preceded by a mixture of AASI (ancient ancestral south Indian, i.e. hunter-gatherers sharing a distant root with the Andamanese, Australian Aboriginals, and East Asians); and Iranian agriculturalists who arrived in India c. 4700–3000 BCE, and "must have reached the Indus Valley by the 4th millennium BCE".^[22]: 15 According to Narasimhan et al., this mixed 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 further with local hunter-gatherers. The ancestry of the ASI population is suggested to have averaged about 73% from the AASI and 27% from Iranian-related farmers. Narasimhan et al. observe that samples from the Indus periphery group are always mixes of the same two proximal sources of AASI and Iranian agriculturalist-related ancestry; with "one of the Indus Periphery individuals having ~42% AASI ancestry and the other two individuals having ~14–18% AASI ancestry" (with the remainder of their ancestry being from the Iranian agriculturalist-related population).^[22]: 15 The authors propose that the AASI indigenous hunter-gatherers represent a divergent branch that split off around the same time that East Asian, Onge (Andamanese) and Australian Aboriginal ancestors separated from each other. It inferred, "essentially all the ancestry of present-day eastern and southern Asians (prior to West Eurasian-related admixture in southern Asians) derives from a single eastward spread, which gave rise in a short span of time to the lineages leading to AASI, East Asians, Onge, and Australians."^[22]: 15

A genetic study by Yelmen et al. (2019) argues that the native South Asian genetic component is rather distinct from the Andamanese, and that the Andamanese are thus an imperfect proxy. This component (when represented by the Andamanese Onge) was not detected in the northern Indian Gujarati, and thus it is suggested that the South Indian tribal Paniya people (a group of predominantly ASI ancestry) would serve as a better proxy than the Andamanese (Onge) for the "native South Asian" component in modern South Asians, as the Paniya are directly derived from the natives of South Asia (rather than distantly related to them as the Onge are). Their improved results, based on "local ancestry deconvolution and masking of 500 samples from 25 South Asian populations via coalescent simulations", suggest that the AASI diverged from the common ancestor of Andamanese and East Asians shortly after these have diverged from West Eurasians. They also found that there were "multiple waves of West Eurasian arrival, as opposed to a simpler one wave scenario".^[6]

Two genetic studies (Narasimhan et al. 2019 & Shinde et al. 2019) analysing remains from the Indus Valley civilisation (of parts of Bronze Age Northwest India and East Pakistan), found them to have a mixture of ancestry, both from native South Asian hunter-gatherers sharing a distant root with the Andamanese, and from a group related to Iranian farmers. The samples analyzed by Shinde derived about 50–98% of their genome from Iranian-related peoples and from 2–50% from native South Asian hunter-gatherers. The samples analyzed by Narasimhan et al. had 45–82% of Iranian farmer-related ancestry and 11–50% of South Asian hunter-gatherer origin. The analysed samples of both studies have little to none of the "

Viswanathan et al. (2004) in a study on genetic structure and affinities among tribal populations of southern India concludes,[100]

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^[27] 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.^[27]

Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians.

Narasimhan et al. 2019 found Austroasiatic-speaking Munda tribals could not be modeled simply as mixture of ASI, AASI, or ANI ancestry unlike other South Asians but required additional ancestry component from Southeast Asia. They were modeled as mixture of 64% AASI, and 36% East Asian-related ancestry, represented by the Nicobarese, thus the ancestry profile of the Mundas provides an independent line of ancestry from Southeast Asia around the 3rd millennium BCE.^[5] Lipson et al. 2018 found similar admixture results in regard to Munda tribals stating "we obtained a good fit with three ancestry components: one western Eurasian, one deep eastern Eurasian (interpreted as an indigenous South Asian lineage), and one from the Austroasiatic clade".^[101] Lipson et al. 2018 further found that the Austroasiatic source clad (proportion 35%) in Munda tribals was inferred to be closest to Mlabri.^[101] Singh et al. 2020 similarly found Austroasiatic speakers in South Asia fall out of the South Asian cline due to their Southeast Asian genetic affinity.^[102]

Origin of caste endogamy in India

Tournebize et al.^[103] analyze founder events spread across the world and write:

Our direct estimates of founder ages provide an independent line of evidence to understand the origin of endogamy in India. We inferred that these founder events occurred between ~120–3,500 years ago across 78 ethno-linguistic groups in India. Our dates are consistent with a previous smaller survey including 13 ethno-linguistic groups from India [18]. In a majority of the populations, the founder events occurred within the past 600–1,000 years, suggesting this period was integral to shaping endogamy in India.

See also

• Archaeogenetics
• Ethnic groups of South Asia
• Peopling of India
• Y-DNA haplogroups in populations of South Asia
• Genetic studies on Gujarati people
• Genetic studies on Sinhalese
• Genetic history of Europe
• Genetic history of the Middle East
• Genetic history of Southeast Asia

Notes

References

Further reading

• Endicott P, Metspalu M, Kivisild T (2007). "Genetic evidence on modern human dispersals in South Asia: Y chromose and mitochondrial DNA perspectives". In Petraglia MD, Allchin B (eds.). The Evolution and History of Human Populations in South Asia. Springer. pp. 201–228.
  ISBN 978-1-4020-5561-4
  .
• Hemphill BE, Lukacs JR, Kennedy KA (1991). "Biological Adaptations and Affinities of Bronze Age Harappans". In Meadow RH (ed.). Harappa excavations 1986–1990: a multidisciplinary approach to third millennium urbanism. Prehistory Press. pp. 137–82.
  ISBN 978-0-9629110-1-9
  .
• Jobling MA (June 2001). "In the name of the father: surnames and genetics". Trends in Genetics. 17 (6): 353–7.
  PMID 11377798
  .
• Kennedy KA (1984). "A Reassessment of the Theories of Racial Origins of the People of the Indus Valley Civilization from Recent Anthropological Data". In Kennedy KA, Possehl GL (eds.). Studies in the Archaeology and Palaeoanthropology of South Asia. Atlantic Highlands, NJ
  : Humanities Press. pp. 99–107.
• Kennedy KA (1995). "Have Aryans been identified in the prehistoric skeletal record from South Asia?". In Erdosy G (ed.). The Indo-Aryans of Ancient South Asia. Walter de Gruyter. pp. 49–54.
  ISBN 978-3-11-014447-5
  .
• Kivisild T (2000b). The origins of southern and western Eurasian populations: an mtDNA study (PDF). Tartu University, Estonia. Archived from the original (PDF) on 3 March 2016. Retrieved 11 November 2005. (PhD)
• Mascarenhas DD, Raina A, Aston CE, Sanghera DK (2015). "Genetic and Cultural Reconstruction of the Migration of an Ancient Lineage". BioMed Research International. 2015: 651415.
  PMID 26491681
  .
• Underhill PA (2003). "Inferring human history: clues from Y-chromosome haplotypes". Cold Spring Harbor Symposia on Quantitative Biology. 68: 487–493.
  S2CID 15527457
  .
• Renfrew C, Boyle KV (2000a). Renfrew C, Boyle K (eds.). An Indian Ancestry: a Key for Understanding Human Diversity in Europe and Beyond (PDF). McDonald Institute for Archaeological Research.
  ISBN 978-1-902937-08-3. Archived from the original
  (PDF) on 19 February 2006. Retrieved 11 November 2005.
• Wells S (2003). The Journey of Man: A Genetic Odyssey. Princeton University Press.
  ISBN 9780691115320
  .

External links

Wikiquote has quotations related to Genetics and archaeogenetics of South Asia.

• Jobling MA. "Surnames, Genes and the History of Britain". The University of Leicester. Archived from the original on 4 March 2016. Retrieved 11 November 2005.
• Oppenheimer J. "Journey of Man: Peopling of the World". Bradshaw Foundation.
• "Indian Genome Variation Database". Institute of Genomics and Integrative Biology.
• "List of R2 frequency". R2dnainfo. Archived from the original on 30 September 2022. Retrieved 17 September 2022.
• "Ancestry of Maldivian People in Light of Population Genetics". Archived from the original on 4 July 2015.