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The genetics and archaeogenetics of the ethnic groups of South Asia aim at uncovering these groups' genetic history.

Their geographic position makes Indian populations important for the study of the early dispersal of human populations on the Eurasian continent. It has been found that the node of the phylogenetic tree of mtDNA, ancestral to more than 90 per cent of the present-day typically European maternal lineages 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.

The Indian Genome Variation Consortium observed high levels of genetic divergence between groups of populations that cluster largely on the basis of ethnicity and language. However studies based on mtDNA variation have reported genetic unity of Indian populations. Recent research based on molecular studies and archaeological record have confirmed this and suggest an autochthonous differentiation of the genetic structure of the populations in South Asia.

The major maternal lineages represented by mtDNA Haplogroups in India are M, R and U, whose coalescence times have been dated back to 50,000 BP. The major paternal lineages represented by Y chromosomes are haplogroups L, H and variations of R . Early studies on paternal lineages based on Y chromosomal markers had taken haplogroup R1a1, which is widespread in central and western Asia, the Middle East and large parts of Europe, as well as in the caste populations in India, as an indication of the Indo Aryan migration into India from Central Asia. But later studies revealed that R1a1 is widespread in the South Indian Dravidian speaking tribal populations also, which has led credence to the proposition that both caste and tribal populations of India derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene.

mtDNA

The largest Indian mtDNA haplogroups are M, R and U Most seem to be native to South Asia and show a wide distribution within the subcontinent.

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 Europe and East Asia descended from only four mtDNA lines that originated in South Asia 50,000-10,000 years ago.

Macrohaplogroup M

The macrohaplogroup M which is considered as a cluster of the proto-Asian maternal lineages, harbours more than 60% of Indian MtDNA

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 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.

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 is also inconsistent with the notion of 'Caucasoidness' of Indians.

Most important South Asian haplorgoups within M

Macrohaplogroup R

The macrohaplogroup R (a very large and old subdivision of macrohaplogroup N) is also widely represented and accounts for the other 40%. A very old an most important subdivision of it is haplogroup U that, while also present in West Eurasia, has several subclades specific of South Asia.

Most important South Asian haplogroups within R:

Haplogroup U

Haplogroup U is sub group 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 Indians. Indian U lineages differ substantially from those in Europe and their coalescence to a common ancestor also dates back to about 50,000 years.

Y chromosome

The major Y chromosome DNA haplogroup in the sub continent are L, H and variations of R like R1 and R2.

Haplogroup L

India

Haplogroup L is currently present in the Indian population at an overall frequency of ca. 7-15% . The presence of haplogroup L is quite rare among tribal groups (ca. 5,6-7%) (Cordaux et al. 2004, Sengupta et al. 2006, Thamseem et al. 2006)

Earlier studies (e.g. Wells et al. 2001) report a very high frequency (approaching 50%) of Haplogroup L in South India appear to have been due to extrapolation from data obtained from a sample of 84 Kallars, a Tamil-speaking warrior caste of Tamil Nadu, among whom 40 (approx. 48%) displayed the M20 mutation that defines Haplogroup L.

Pakistan

Haplogroup L3 (M357) is found frequently among Burusho (approx. 12%) and Pashtuns (approx. 7%), with a moderate distribution among the general Pakistani population (approx. 2%). Its highest frequency and diversity 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 Kalash in northwest Pakistan.

Haplogroup H

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Haplogroup R2

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R1a1

In South Asia, high levels of R1a1a(M17) have been observed in some high-caste populations. M17 is also found in relatively high frequencies in several South Indian Dravidian-speaking tribes including the Chenchu and Valmikis of Andhra Pradesh and the Kallar of Tamil Nadu suggesting that it is widespread in tribal southern Indians. To the south of India, it has also been found in >10% of Sinhalese in Sri Lanka. Studies arguing for South Asia as the probable origin of M17 are consistent with the latest surveys of its wide distribution across Europe and Asia.

Haplogroup J2

The J2 haplogroup is almost absent from tribals, but occurs among some Austro-Asiatic tribals (11%). The frequency of J2 is higher in South Indian castes (19%) than in North Indian castes (11%) or Pakistan (12%) .

Autosomal markers

Kivisild et al. 2003 emphasize that the combined results from mtDNA, Y-chromosome and autosomal markers suggest that "Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene"

South Asia and Central Asia

A recent study (Sengupta 2006) found that the “influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000–15,000 years, which attests to the antiquity of regional differentiation.” and it concluded: “Our reappraisal indicates that pre-Holocene and Holocene-era—not Indo-European—expansions have shaped the distinctive South Asian Y-chromosome landscape.”

The neolithic spread of farmers to Europe from Levant/Middle East has also been linked to 12f2 (haplogroup J) and the markers M35 (haplogroup E1b1b) and M201 (haplogroup G). But while M35 (E1b1b) is present in Europe, Anatolia, South Caucasus and Iran. Indians generally do not have the Alu insertion in their Y chromosomes. The lack of YAP+ chromosomes (haplogroup E) in India suggests that M35 appeared in the Middle East only after a migration from Iran to South Asia had taken place, but earlier than the later migration of Near and Middle Eastern farmers to Europe .

According to Sahoo (2006), “The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family.”

Several recent studies of the distribution of alleles on the Y chromosome, microsatellite DNA, and mitochondrial DNA in India have cast strong doubt for a biological Dravidian "race" distinct from non-Dravidians in the Indian subcontinent. The only distinct ethnic groups present in South Asia, according to genetic analysis, are the Balochi, Brahui, Burusho, Hazara, Kalash, Pathan and Sindhi peoples, the vast majority of whom are found in today's Pakistan. A 2009 study of 132 individuals using 560,000 SNPs concluded that modern Indians are a 40.000 years old hybrid population of two divergent populations.

Notes

1. ^ Toomas Kivisild, Surinder S. Papiha, Siiri Rootsi, Jüri Parik, Katrin Kaldma, Maere Reidla, Sirle Laos, Mait Metspalu, Gerli Pielberg, Maa rja Adojaan, Ene Metspalu, Sarabjit S. Mastana, Yiming Wang, Mukaddes Golge, Halil Demirtas, Eckart Schnakenberg, Gian Franco de Stefano, Tarekegn Geberhiwot, Mireille Claustres & Richard Villems, An Indian Ancestry: a Key for Understanding Human Diversity in Europe and Beyond, 2000, McDonald Institute Monographs
2. Genetic landscape of the people of India: a canvas for disease gene exploration, Indian Genome Variation Consortium, 2008
3. Trends in Molecular Anthropological Studies in India, Vikal Tripathy, A. Nirmala and B. Mohan Reddy, 2008
4. Metspalu M, Kivisild T. et al, Peopling of South Asia: investigating the caste-tribe continuum in India, Bioessays Jan 2007
5. ^ Y Haplogroups of the World, 2005, McDonald
6. Passarino G, Semino O, Magri C, Al-Zahery N, Benuzzi G, Quintana-Murci L, Andellnovic S, Bullc-Jakus F, Liu A, Arslan A, Santachiara-Benerecetti AS (2001) The 49a,f haplotype 11 is a new marker of the EU19 lineage that traces migrations from northern regions of the Black Sea. Hum Immunol 62:922–932
7. T Kivisild et al, The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations, Am. J. Hum. Genet. 72:313–332, 2003
8. Stephen Oppenheimer, The Real Eve: Modern Man's Journey Out of Africa‎,2004
9. ^ Kumarasamy Thangaraj, Gyaneshwer Chaubey, Vijay Kumar Singh, Ayyasamy Vanniarajan, Ismail Thanseem, Alla G Reddy and Lalji Singh, In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India , 2006
10. ^ Nait Metspalu et al., Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genetics, 2004.
11. (Kivisild et al. 1999a)
12. (Kivisild et al. 1999b)
14. (Basu et al. 2003, Cordaux et al. 2004, Sengupta et al. 2006, Thamseem et al. 2006)
15. ^ Firasat S, Khaliq S, Mohyuddin A; et al. (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. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
16. Kivisild et al. (2003) harvcoltxt error: no target: CITEREFKivisild_et_al.2003 (help)
17. *Sengupta; et al. (2005), "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., vol. 78, no. 2, pp. 202–21, doi:10.1086/499411, PMID 16400607 {{citation}}: Explicit use of et al. in: |author= (help).
18. Sahoo; et al. (2006), "A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios", Proceedings of the National Academy of Sciences, 103 (4): 843–848, doi:10.1073/pnas.0507714103 {{citation}}: Explicit use of et al. in: |last= (help)
19. Underhill; et al. (2009), "Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a", European Journal of Human Genetics, doi:doi:10.1038/ejhg.2009.194 {{citation}}: Check |doi= value (help); Explicit use of et al. in: |author= (help)
20. (Sengupta 2006)
21. Kivisild 2003b (Kivisild et al. 2003b
22. (Kivisild 2003a)
23. Sahoo, Sanghamitra (2006-01-24). "A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios". Proceedings of National Academy of Sciences of United States of America. 103 (4): 843–848. doi:10.1073/pnas.0507714103. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
24. Sengupta, S. (2006-02-01). "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). The American Society of Human Genetics: 201–221. Retrieved 2007-12-03. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
25. Sharma, S. (2005). "Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups". J Hum Genet. 50 (10): 497–506. doi:10.1007/s10038-005-0284-2. Retrieved 2007-12-03. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
26. Human Genome Diversity Project
27. Reich, David (24 September 2009). "Reconstructing Indian population history". Nature. 461: 489–494. doi:10.1038/nature08365. Retrieved 2009-10-02. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
28. http://timesofindia.indiatimes.com/news/india/Aryan-Dravidian-divide-a-myth-Study/articleshow/5053274.cms

See also

• Ethnic groups of South Asia
• Archaeogenetics

References

• Indian Genome Variation Consortium (2008). "Genetic landscape of the people of India: a canvas for disease gene exploration". Journal of Genetics. 87 (1): 3–20. doi:10.1007/s12041-008-0002-x.
• Jorde et al.
• Bamshad, M., T. Kivisild; et al. (2001). "Genetic evidence on the origins of Indian caste populations". Virus Research. 75 (2): 95–106. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
• Basu; et al. (2003). "Ethnic India: a genomic view, with special reference to peopling and structure". Genome Research. 13: 2277–2290. doi:10.1101/gr.1413403. PMID 14525929. {{cite journal}}: Explicit use of et al. in: |author= (help)
• Cann, R. (2001). "Genetic clues to dispersal in human populations: retracing the past from the present". Science. 291: 1742–1748. doi:10.1126/science.1058948. PMID 11249820.
• Cordaux, R., R. Aunguer, G. Bentley, I. Nasidze, S.M. Sirajuddin, and M. Stoneking (3 February 2004). "Independent origins of Indian caste and tribal paternal lineages". Current Biology. 14: 231–235.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Hemphill & Christensen: “The Oxus Civilization as a Link between East and West: A Non-Metric Analysis of Bronze Age Bactrain Biological Affinities”, paper read at the South Asia Conference, 3-5 November 1994, Madison, Wisconsin; p. 13.
• Hemphill, B.E. ; Lukacs, J.R.; and Kennedy, K.A.R. (1991). "Biological adaptions and affinities of the Bronze Age Harappans". Harappa Excavations 1986-1990. (ed. R.Meadow): 137–182.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• Kennedy, Kenneth 1984. “A Reassessment of the Theories of Racial Origins of the People of the Indus Valley Civilization from Recent Anthropological Data.” In Studies in the Archaeology and Palaeoanthropology of South Asia (99-107).
• --- 1995. “Have Aryans been identified in the prehistoric skeletal record from South Asia?”, in George Erdosy, ed.: The Indo-Aryans of Ancient South Asia, p. 49-54.
• Kivisild, Toomas et al. 1999a. "Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages" Curr Biol 9:1331–1334
• ---1999b. "The Place of the Indian mtDNA Variants in the Global Network of Maternal Lineages and the Peopling of the Old World"
• ---2000a. "An Indian Ancestry: a Key for Understanding Human Diversity in Europe and Beyond"
• ---2000b. "The origins of southern and western Eurasian populations: an mtDNA study"
• ---2003a. "The Genetics of Language and Farming Spread in India" In: Bellwood P, Renfrew C (eds) Examining the farming/language dispersal hypothesis. McDonald Institute for Archaeological Research, Cambridge, United Kingdom, pp 215–222
• ---2003b. "The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations" Am J Hum Genet 72: 313–332 ,
• Metspalu, M. et al. 2004. Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans and
• Oppenheimer, Stephen; (2003) "The Real Eve: Modern Man's Journey out of Africa" New York: Carroll and Graf Publishers ,
• Sahoo, S.; Kivisild, T. et al. (2006) A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios.
• Sengupta, S.; Cavalli-Sforza, L. Luca et al. (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.
• Underhill, P. Inferring Human History: Clues from Y-Chromosome Haplotype
• Wells, S.; (2003) 'The Journey of Man: A Genetic Odyssey', Princeton University Press, January.
• Excavating Y-chromosome haplotype strata in Anatolia
• Introduction to haplogroups and haplotypes
• High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from Central Asia and West Asia into India
• The human Y chromosome: an evolutionary marker comes of age
• Minimal Sharing of Y-Chromosome STR Haplotypes Among Five Endogamous Population Groups from Western and Southwestern India
• Negligible Male Gene Flow Across Ethnic Boundaries in India, Revealed by Analysis of Y-Chromosomal DNA Polymorphisms
• Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area
• Y-Chromosomal DNA Variation in Pakistan
• Phylogeography of Y-Chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow in Europe
• Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations (Gives variances for R1a1)

External links

• New paper on Indian Y-chromosome variation Dienekes Anthropology Blog
• Indian Genome Variation Database Institute of Genomics and Integrative Biology
• Indian Genome Variation Consortium (2008). "Genetic landscape of the people of India: a canvas for disease gene exploration". Journal of Genetics. 87 (1): 3–20. doi:10.1007/s12041-008-0002-x.

• Human Y-DNA haplogroups
• Human genetics
• Modern human genetic history
• South Asia