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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.<ref>Genetic landscape of the people of India: a canvas for disease gene exploration, Indian Genome Variation Consortium, 2008</ref> Studies based on mtDNA variation have also reported genetic similarities amongst the various Indian sub-populations.<ref>Trends in Molecular Anthropological Studies in India, Vikal Tripathy, A. Nirmala and B. Mohan Reddy, 2008</ref> Recent research based on molecular studies and the archaeological record have also suggested an autochthonous differentiation of the genetic structure of the populations in South Asia.<ref name="ReferenceA">Metspalu M, Kivisild T. et al, Peopling of South Asia: investigating the caste-tribe continuum in India, Bioessays Jan 2007</ref>
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.<ref>Genetic landscape of the people of India: a canvas for disease gene exploration, Indian Genome Variation Consortium, 2008</ref> Studies based on mtDNA variation have also reported genetic similarities amongst the various Indian sub-populations.<ref>Trends in Molecular Anthropological Studies in India, Vikal Tripathy, A. Nirmala and B. Mohan Reddy, 2008</ref> Recent research based on molecular studies and the archaeological record have also suggested an autochthonous differentiation of the genetic structure of the populations in South Asia.<ref name="ReferenceA">Metspalu M, Kivisild T. et al, Peopling of South Asia: investigating the caste-tribe continuum in India, Bioessays Jan 2007</ref>


It has been found that the ancestral node of the phylogenetic tree of all the [[mtDNA]] types typically found in [[Central Asia]], the [[Middle East]] 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.<ref name=Kivisild2000a>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 [http://evolutsioon.ut.ee/publications/Kivisild2000.pdf]</ref> In India the major maternal lineages, or [[mitochondrial DNA Haplogroup]]s, are [[Haplogroup M (mt-DNA)|M]], [[Haplogroup R (mt-DNA)|R]] and [[Haplogroup U (mt-DNA)|U]], whose coalescence times have been approximated to 50,000 BP.<ref name=Kivisild2000a/> The major paternal lineages represented by [[Y chromosome]]s are haplogroups [[Haplogroup R1a (Y-DNA)|R1a]], [[Haplogroup R2a (Y-DNA)|R2]], [[Haplogroup H (Y-DNA)|H]], [[Haplogroup L (Y-DNA)|L]] and [[Haplogroup J2 (Y-DNA)|J2]].<ref name=mcDonald>[http://www.scs.uiuc.edu/~mcdonald/WorldHaplogroupsMaps.pdf Y Haplogroups of the World, 2005, McDonald]</ref> Some researchers have argued that Y-DNA Haplogroup R1a1a (M17) is of autochthonous Indian origin. However, the latest research sheds doubt on this claim, postulating an Eastern European origin for R1a1. Stepanov et al. (2011) writes:"The age of the cluster admittedly brought to Hindustan from Central Asia / Southern Siberia is 3,9 +/- 1,3 ky. Probably, the primary center of the generation of diversity and expansion of R1a1a was the territory of the Eastern European Steppe. With the spread of of R1a1 carriers, secondary centers of genetic diversity and population expansions were formed in the Southern Siberia and Hindustan." <ref>http://www.ichg2011.org/cgi-bin/ichg11s?abst=Phylogeography%20of%20R1a1%20Y-chromosomal%20haplogroup%20and%20genetic%20history%20of%20Indo-Europeans.&sort=ptimes&sbutton=Detail&absno=20168&sid=874567</ref>
It has been found that the ancestral node of the phylogenetic tree of all the [[mtDNA]] types typically found in [[Central Asia]], the [[Middle East]] 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.<ref name=Kivisild2000a>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 [http://evolutsioon.ut.ee/publications/Kivisild2000.pdf]</ref> In India the major maternal lineages, or [[mitochondrial DNA Haplogroup]]s, are [[Haplogroup M (mt-DNA)|M]], [[Haplogroup R (mt-DNA)|R]] and [[Haplogroup U (mt-DNA)|U]], whose coalescence times have been approximated to 50,000 BP.<ref name=Kivisild2000a/> The major paternal lineages represented by [[Y chromosome]]s are haplogroups [[Haplogroup R1a (Y-DNA)|R1a]], [[Haplogroup R2a (Y-DNA)|R2]], [[Haplogroup H (Y-DNA)|H]], [[Haplogroup L (Y-DNA)|L]] and [[Haplogroup J2 (Y-DNA)|J2]].<ref name=mcDonald>[http://www.scs.uiuc.edu/~mcdonald/WorldHaplogroupsMaps.pdf Y Haplogroups of the World, 2005, McDonald]</ref> Early studies on paternal lineages based on Y chromosomal markers had taken haplogroup R1a1, which is widespread in central Asia, southern Siberia (especially among Altaians) and eastern part of Europe (especially Slavic populations), as well as in the caste populations in India, as an early indication of the Indo-European migration into India from Central Asia.<ref name="Passarino G 2001">{{cite journal | author = Passarino G, Semino O, Magri C, Al-Zahery N, Benuzzi G, Quintana-Murci L, Andellnovic S, Bullc-Jakus F, Liu A ''et al.'' | year = 2001 | title = The 49a,f haplotype 11 is a new marker of the EU19 lineage that traces migrations from northern regions of the Black Sea | url = | journal = Hum Immunol | volume = 62 | issue = 9| pages = 922–932 | doi = 10.1016/S0198-8859(01)00291-9 | pmid = 11543894 }}</ref> But later studies have found South Asia to have the highest level of diversity of [[Y-STR]] haplotype variation within [[R1a1a]]. A survey study as of December 2009, including a collation of retested Y-DNA from previous studies, makes a South Asian R1a1a origin the strongest proposal amongst the various possibilities.<ref>{{Cite journal|author=Underhill et al.|last2=Myres|year=2009|pages=479–84|first2=Natalie M|last3=Rootsi|first3=Siiri|last4=Metspalu|first4=Mait|last5=Zhivotovsky|first5=Lev A|last6=King|issue=4|pmid=19888303|first6=Roy J|last7=Lin|first7=Alice A|last8=Chow|first8=Cheryl-Emiliane T|last9=Semino|first9=Ornella|title=Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a|volume=18|journal=European Journal of Human Genetics|doi=10.1038/ejhg.2009.194|ref=harv|postscript=<!-- Bot inserted parameter. Either remove it; or change its value to "." for the cite to end in a ".", as necessary. -->{{inconsistent citations}}|pmc=2987245}}</ref>




==mtDNA==
==mtDNA==
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{{Main|Haplogroup R1a1 (Y-DNA)}}
{{Main|Haplogroup R1a1 (Y-DNA)}}
In South Asia R1a1 has been observed often with high frequency in a number of demographic groups.<ref name="Sengupta et al. 2005">{{Harvcoltxt|Sengupta et al.|2005}}</ref><ref name="Sahoo et al. 2006">{{Harvcoltxt|Sahoo et al.|2006}}</ref>
In South Asia R1a1 has been observed often with high frequency in a number of demographic groups.<ref name="Sengupta et al. 2005">{{Harvcoltxt|Sengupta et al.|2005}}</ref><ref name="Sahoo et al. 2006">{{Harvcoltxt|Sahoo et al.|2006}}</ref>
Its parent clade Haplogroup R1a is believed to have its origins on the Eurasian Steppe and reached India via a series of Indo-European migrations.<ref name="Stepanov et al. 2011">{{Harvcoltxt|Stepanov et al.|2011}}</ref>
Its parent clade Haplogroup R1a is belived to have its origins in the Indus Valley or the Eurasian Steppe<ref>http://www.isogg.org/tree/ISOGG_HapgrpR.html</ref>whereas its successor clade R1a1* both have the highest frequency and time depth in South Asia making it the likely locus of origin<ref>http://www.nature.com/ejhg/journal/v18/n4/full/ejhg2009194a.html</ref>
<ref>http://www.nature.com/jhg/journal/v54/n1/full/jhg20082a.html</ref>
<ref>http://www.nature.com/ejhg/journal/v17/n10/full/ejhg20096a.html</ref>.
====India====
====India====
In India, high percentage of this haplogroup is observed in [[Bengali Brahmins|West Bengal Brahmins]] (72%) <ref name="Sengupta et al. 2005"/> to the east, [[Konkanastha| Konkanastha Brahmins]] (48%) <ref name="Sengupta et al. 2005"/> to the west, [[Khatri]]s (67%)<ref name="Underhill et al. 2009">{{Harvcoltxt|Underhill et al.|2009}}</ref> in north and Iyenger Brahmins (31%)<ref name="Sengupta et al. 2005"/> of south. It has also been found in several [[South Indian]] [[Dravidian]]-speaking [[Adivasi|Tribals]] including the [[Chenchu]] (26%)<ref name=kivisild2003/> and Valmikis of [[Andhra Pradesh]] as well as the [[Kallar]] of [[Tamil Nadu]] suggesting that M17 is widespread in these Southern Indians tribes.<ref name=kivisild2003>{{Harvcoltxt|Kivisild et al.|2003}}</ref>
In India, high percentage of this haplogroup is observed in [[Bengali Brahmins|West Bengal Brahmins]] (72%) <ref name="Sengupta et al. 2005"/> to the east, [[Konkanastha| Konkanastha Brahmins]] (48%) <ref name="Sengupta et al. 2005"/> to the west, [[Khatri]]s (67%)<ref name="Underhill et al. 2009">{{Harvcoltxt|Underhill et al.|2009}}</ref> in north and Iyenger Brahmins (31%)<ref name="Sengupta et al. 2005"/> of south. It has also been found in several [[South Indian]] [[Dravidian]]-speaking [[Adivasi|Tribals]] including the [[Chenchu]] (26%)<ref name=kivisild2003/> and Valmikis of [[Andhra Pradesh]] as well as the [[Kallar]] of [[Tamil Nadu]] suggesting that M17 is widespread in these Southern Indians tribes.<ref name=kivisild2003>{{Harvcoltxt|Kivisild et al.|2003}}</ref>
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==Autosomal markers==
==Autosomal markers==
Kivisild et al. 2003 emphasize that the combined results from mtDNA, [[Y-chromosome]] and [[autosomal marker]]s 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]]" <ref>Kivisild 2003b ([http://evolutsioon.ut.ee/publications/Kivisild2003b.pdf Kivisild et al. 2003b]</ref>
Basu et al. (2003) emphasize that the combined results from mtDNA, [[Y-chromosome]] and [[autosomal marker]]s suggest that "(1) there is an underlying unity of female lineages in India, indicating that the initial number of female settlers may have been small; (2) the tribal and the caste populations are highly differentiated; (3) the Austro-Asiatic tribals are the earliest settlers in India, providing support to one anthropological hypothesis while refuting some others; (4) a major wave of humans entered India through the northeast; (5) the Tibeto-Burman tribals share considerable genetic commonalities with the Austro-Asiatic tribals, supporting the hypothesis that they may have shared a common habitat in southern China, but the two groups of tribals can be differentiated on the basis of Y-chromosomal haplotypes; (6) the Dravidian tribals were possibly widespread throughout India before the arrival of the Indo-European-speaking nomads, but retreated to southern India to avoid dominance; (7) formation of populations by fission that resulted in founder and drift effects have left their imprints on the genetic structures of contemporary populations; (8) the upper castes show closer genetic affinities with Central Asian populations, although those of southern India are more distant than those of northern India; (9) historical gene flow into India has contributed to a considerable obliteration of genetic histories of contemporary populations so that there is at present no clear congruence of genetic and geographical or sociocultural affinities." <ref>http://genome.cshlp.org/content/13/10/2277.full</ref>


==South Asia and Central Asia==
==South Asia and Central Asia==
{{See|Ancient India and Central Asia}}
{{See|Ancient India and Central Asia}}
A study (Sengupta 2006) insisted 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.”


It should be noted that these "ages" and "variations" were acquired by the highly-criticised "Zhivotovsky method".
According to Agrawal et al. (2005): "The other important fact about Indian culture and the society is that India has experienced various migrational events, invasions and massive gene flow from Central Asia, South China and Southeast Asia, in particular, migration of the Indo-Aryan speakers (Indo-Europeans) from the steppes of Central Asia, who settled in the Indus Valley (northwestern India) ~ 4000 yrs BP. Migration of the Indo-Aryan speakers led to the southward retreat of Dravidians in India."<ref>http://www.ias.ac.in/currsci/jun252005/1977.pdf</ref>


The [[neolithic]] spread of farmers to regions as far away as Europe 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 Iran, South Caucasus, Anatolia and Europe. 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.<ref>(Kivisild 2003a)</ref>
After observing that "the Indo-European (Aryan) language was introduced into India from the Iranian plateau approximately 4000–3000 ybp, where this language was probably brought by pastoral nomads from the Central Asian steppes (Renfrew 1989)" and that "the Y lineages of Indian castes are more closely related to Central Asians than to Indian tribal populations", Zhao et. al. (2008) conclude that "a substantial part of today's North Indian paternal gene pool was contributed by Central Asian lineages who are Indo-European speakers, suggesting that extant Indian caste groups are primarily the descendants of Indo-European migrants."<ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755252/</ref>
However, in a recent study underhill et al.(2009) did not find any substantial paternal geneflow to the indian subcontinent since the mid-holocene<ref>http://www.nature.com/ejhg/journal/v18/n4/full/ejhg2009194a.html</ref>.


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.”
According to the The Indian Genome Variation Consortium (2005), the population of the subcontinent can be divided into four morphological types: Caucasoids, Mongoloids, Australoids and Negritos, however these groups tend to overlap because of the admixture brought by previous waves of migration<ref name="IGVC2005">{{Citation | title=The Indian Genome Variation database (IGVdb): a project overview | authors=The Indian Genome Variation Consortium | publisher=Human Genetics | date=: 28 February 2005 | accessdate=26 May 2005 | url=http://www.imtech.res.in/raghava/reprints/IGVdb.pdf | quote=''... The "Caucasoid" and "Mongoloid" populations are mainly concentrated in the north and northeastern parts of the country. The "Australoids" are mostly confined to the central, western and southern India, while the "Negritos" are restricted only to the Andaman Islands ...''}}</ref>. Genetic differences among Indians appears to be along caste lines, rather than along ethnic lines, although genetic differences do exist between northern and southern India.<ref>http://genome.cshlp.org/content/13/10/2277.short</ref>

Several recent studies of the distribution of alleles on the Y chromosome,<ref name="sahoo">{{cite journal
| last = Sahoo
| first =Sanghamitra
| authorlink =
| coauthors = Anamika Singh, G. Himabindu, Jheelam Banerjee, T. Sitalaximi, Sonali Gaikwad, R. Trivedi, Phillip Endicott, Toomas Kivisild, Mait Metspalu, Richard Villems and V. K. Kashyap
| title =A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios
| journal =Proceedings of National Academy of Sciences of United States of America
| volume =103
| issue =4
| pages =843–848
| publisher =
| location =
| date =2006-01-24
| url =http://www.pnas.org/cgi/content/full/103/4/843
| doi =10.1073/pnas.0507714103
| id =
| accessdate =
| pmid = 16415161
| pmc = 1347984
| ref = harv
| bibcode=2006PNAS..103..843S}}</ref> microsatellite DNA,<ref name="sengupta">{{cite journal
| last = Sengupta
| first = S.
| authorlink =
| coauthors = et al.
| title =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
| journal =Am J Hum Genet.
| volume =78
| issue =2
| pages =201–221
| publisher =The American Society of Human Genetics
| location =
| date =2006-02-01
| url =http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16400607
| doi =10.1086/499411
| id =
| accessdate =2007-12-03
| ref = harv
| pmid=16400607
| pmc = 1380230}}</ref> and mitochondrial DNA <ref name="sharma">
{{cite journal
| last =Sharma
| first = S.
| authorlink =
| coauthors =Saha A, Rai E, Bhat A, Bamezai R.
| title =Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups
| journal = J Hum Genet.
| volume =50
| issue =10
| pages =497–506
| publisher =
| location =
| year =2005
| doi =10.1007/s10038-005-0284-2
| id =
| accessdate = 2007-12-03
| pmid =16205836
| ref =harv}}</ref> in India have cast strong doubt for a biological Dravidian "race" distinct from non-Dravidians in the Indian subcontinent.


==Ancestral South Indians==
==Ancestral South Indians==
⚫
'''Ancestral South Indians''' is a term used in the study of [[genetics and archaeogenetics of South Asia]].<ref name="reich2009jsd">{{Citation | title=Reconstructing Indian population history | author=David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes Price, Lalji Singh | date=Vol 461, 24 September 2009 | isbn= | journal=Nature |url=http://genepath.med.harvard.edu/~reich/2009_Nature_Reich_India.pdf | quote=''... two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other ...''}}</ref><ref name="hrv2009sda">{{Citation | title=Genetics Weaves Tapestry of Indian Heritage | author=Richard F. Nyrop | date=Oct 2, 2009 | isbn= | journal=Focus: News from Harvard Medical, Dental and Public Health Schools | url=http://focus.hms.harvard.edu/2009/100209/indian_genetics.shtml | quote=''... nearly all Indians alive today carry various mixtures of genomic contribution from the two ancient populations. One group the authors call “Ancestral North Indians” is genetically most similar to western Eurasians (including Europeans) and accounts for 40 to 80 percent of the ancestry found in the Indian genomes. The rest comes from the “Ancestral South Indians,” a distinct population not closely related to populations anywhere else in the world. ... The only exception to the mixed ancestries of all Indians came from the Andaman Islanders, who have exclusive descent from the Ancestral South Indian lineage ...''}}</ref> They are believed to have been genetically unique and not closely related to any other human populations in the world.<ref name="hrv2009sda" />.
'''Ancestral South Indians''' is a term used to describe the aboriginal population of southern India. They are believed to have been genetically unique and not closely related to any other human populations in the world, although some evidence exists which suggests that they share a number of mitochondrial lineages with Australian aborigines.<ref>http://www.biomedcentral.com/1471-2148/9/173</ref>
⚫
==ANI ASI admixture time==


⚫
The modern indian population is a result of admixture between these two ancient groups, though the exact admixture time is still unknown. Recent research has suggested a major admixture taking place between 3500 to 1200 years ago.<ref>http://www.ichg2011.org/cgi-bin/ichg11s?author=Moorjani%20P&sort=ptimes&sbutton=Detail&absno=20758&sid=15004</ref>.
⚫
==Indo-Aryan migration and ANI-ASI admixture time==
{{see|Indo-Aryan migration}}

The modern Indian population is a result of admixture between these two ancient groups, which correspond to Indo-European-speaking groups (ANI) on the one hand and Dravidian-speaking groups (ASI) on the other. According to Reich et al. (2009): "It is tempting to assume that the population ancestral to ANI and CEU spoke 'Proto-Indo-European', which has been reconstructed as
⚫
ancestral to both Sanskrit and European languages, although we cannot be certain without a date for ANI–ASI mixture." <ref>http://genepath.med.harvard.edu/~reich/2009_Nature_Reich_India.pdf</ref> Recent research indicates a massive admixture event between ANI-ASI populations 3500 to 1200 years ago.<ref>http://www.ichg2011.org/cgi-bin/ichg11s?author=Moorjani%20P&sort=ptimes&sbutton=Detail&absno=20758&sid=15004</ref>


==Ancestral North Indians==
==Ancestral North Indians==



⚫
The term '''Ancestral North Indians''' is used in the study of [[genetics and archaeogenetics of South Asia]].<ref name="reich2009jsd">{{Citation | title=Reconstructing Indian population history | author=David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes Price, Lalji Singh | date=Vol 461, 24 September 2009 | isbn= | journal=Nature |url=http://genepath.med.harvard.edu/~reich/2009_Nature_Reich_India.pdf | quote=''... two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other ...''}}</ref><ref name="hrv2009sda">{{Citation | title=Genetics Weaves Tapestry of Indian Heritage | author=Richard F. Nyrop |date=Oct 2, 2009 | isbn= | journal=Focus: News from Harvard Medical, Dental and Public Health Schools | url=http://focus.hms.harvard.edu/2009/100209/indian_genetics.shtml |quote=''... nearly all Indians alive today carry various mixtures of genomic contribution from the two ancient populations. One group the authors call “Ancestral North Indians” is genetically most similar to western Eurasians (including Europeans) and accounts for 40 to 80 percent of the ancestry found in the Indian genomes. The rest comes from the “Ancestral South Indians,” a distinct population not closely related to populations anywhere else in the world. ... The only exception to the mixed ancestries of all Indians came from the Andaman Islanders, who have exclusive descent from the Ancestral South Indian lineage ...''}}</ref> They are believed to have been closely related to people from the Middle East and Europe, and the percentage of ancestry traceable to them in a given modern Indian ethnic group varies from 40% to 80% depending on region and caste.<ref name="hrv2009sda" /> Recent work involving the reconstruction of an Ancestral North Indian chromosome indicates that the ANI population may have been more closely related to people from central and northern Europe than to people from the Caucasus <ref name="egap2011bga">{{Citation | title=Reconstructing the Ancestral North Indian (ANI) Genome | author = David W |url=http://bga101.blogspot.com/ | date=Tuesday, March 22, 2011 | quote="Back in 2009, Reich et al. theorized that the current South Asian gene pool was basically made up of two founding genetic components; Ancestral North Indian (ANI), and Ancestral South Indian (ASI). The distilled ANI, they noted, was more similar to the genomes of modern Northwest Europeans than those of the Adygei from the Caucasus. This is obviously out of whack with geography, but it does make sense based on what I've seen in my experiments on the Pakistani samples from the HGDP. Many of them, especially the Pathans, carry numerous segments, or haploblocks, that basically look North European. This gave me an idea to try and reconstruct the ANI genome based on such fragments. The first chromosome of my composite sample, which I call the "ANI composite" is available for download here....I used information from my earlier experiments with ADMIXMAP, HAPMIX and RHH Counter to locate and delineate North European-like segments in phased Pakistani HGDP samples. I phased the data myself with BEAGLE, in a pool of South Asian and Middle Eastern samples, so as not to bias the results of phasing and imputation towards Northern Europe. In order to keep the alleles in phase when loaded into PLINK, I duplicated the haplotypes, basically producing completely homozygous individuals out of each one. Then I created an "ANI composite" dummy with 100% no calls, and loaded the haplotypes into this sample with a Python script. The first to "load" were the Pathan haplotypes, followed by the Burusho. I chose individuals from these two groups to make up the backbone of the putative ANI genome because they always seem to come out most "North European" in my ADMIXTURE and MDS runs compared to other South Asians. ..."}}</ref>.
'''Ancestral North Indians''' were present in the indian subcontinent from 40,000-45,000 ybp<ref>http://www.nature.com/nature/journal/v461/n7263/full/nature08365.html</ref>.The term is also used in the study of [[genetics and archaeogenetics of South Asia]].<ref name="reich2009jsd">{{Citation | title=Reconstructing Indian population history | author=David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes Price, Lalji Singh | date=Vol 461, 24 September 2009 | isbn= | journal=Nature |url=http://genepath.med.harvard.edu/~reich/2009_Nature_Reich_India.pdf | quote=''... two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other ...''}}</ref><ref name="hrv2009sda">{{Citation | title=Genetics Weaves Tapestry of Indian Heritage | author=Richard F. Nyrop |date=Oct 2, 2009 | isbn= | journal=Focus: News from Harvard Medical, Dental and Public Health Schools | url=http://focus.hms.harvard.edu/2009/100209/indian_genetics.shtml |quote=''... nearly all Indians alive today carry various mixtures of genomic contribution from the two ancient populations. One group the authors call “Ancestral North Indians” is genetically most similar to western Eurasians (including Europeans) and accounts for 40 to 80 percent of the ancestry found in the Indian genomes. The rest comes from the “Ancestral South Indians,” a distinct population not closely related to populations anywhere else in the world. ... The only exception to the mixed ancestries of all Indians came from the Andaman Islanders, who have exclusive descent from the Ancestral South Indian lineage ...''}}</ref> They are believed to have been closely related to people from the Middle East and Europe, and the percentage of ancestry traceable to them in a given modern Indian ethnic group varies from 40% to 80% depending on region and caste.<ref name="hrv2009sda" /> Recent work involving the reconstruction of an Ancestral North Indian chromosome indicates that the ANI population may have been more closely related to people from central and northern Europe than to people from the Caucasus <ref name="egap2011bga">{{Citation | title=Reconstructing the Ancestral North Indian (ANI) Genome | author = David W |url=http://bga101.blogspot.com/ | date=Tuesday, March 22, 2011 | quote="Back in 2009, Reich et al. theorized that the current South Asian gene pool was basically made up of two founding genetic components; Ancestral North Indian (ANI), and Ancestral South Indian (ASI). The distilled ANI, they noted, was more similar to the genomes of modern Northwest Europeans than those of the Adygei from the Caucasus. This is obviously out of whack with geography, but it does make sense based on what I've seen in my experiments on the Pakistani samples from the HGDP. Many of them, especially the Pathans, carry numerous segments, or haploblocks, that basically look North European. This gave me an idea to try and reconstruct the ANI genome based on such fragments. The first chromosome of my composite sample, which I call the "ANI composite" is available for download here....I used information from my earlier experiments with ADMIXMAP, HAPMIX and RHH Counter to locate and delineate North European-like segments in phased Pakistani HGDP samples. I phased the data myself with BEAGLE, in a pool of South Asian and Middle Eastern samples, so as not to bias the results of phasing and imputation towards Northern Europe. In order to keep the alleles in phase when loaded into PLINK, I duplicated the haplotypes, basically producing completely homozygous individuals out of each one. Then I created an "ANI composite" dummy with 100% no calls, and loaded the haplotypes into this sample with a Python script. The first to "load" were the Pathan haplotypes, followed by the Burusho. I chose individuals from these two groups to make up the backbone of the putative ANI genome because they always seem to come out most "North European" in my ADMIXTURE and MDS runs compared to other South Asians. ..."}}</ref>. Such findings are consistent with the research of Reich et al.
Evidences are also there to say indo-europeans moving out of indian subcontinent in prehistoric times as they probably had a pan indian presence with Y-dna R1a1a*(M-173 and M-420) is found to be native in india while most of the eurasian indo-european sites shows the presence of relatively new R1a1a7 (M-458) <ref name= "new indology">[http://new-indology.blogspot.com/ ]</ref>. However, genetic evidence has no bearing on the languages that these early groups might have spoken.


==See also==
==See also==

Revision as of 04:08, 30 September 2011

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.

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.[1] Studies based on mtDNA variation have also reported genetic similarities amongst the various Indian sub-populations.[2] Recent research based on molecular studies and the archaeological record have also suggested an autochthonous differentiation of the genetic structure of the populations in South Asia.[3]

It has been found that the ancestral node of the phylogenetic tree of all the mtDNA types typically found in Central Asia, the Middle East 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.[4] 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.[4] The major paternal lineages represented by Y chromosomes are haplogroups R1a, R2, H, L and J2.[5] Early studies on paternal lineages based on Y chromosomal markers had taken haplogroup R1a1, which is widespread in central Asia, southern Siberia (especially among Altaians) and eastern part of Europe (especially Slavic populations), as well as in the caste populations in India, as an early indication of the Indo-European migration into India from Central Asia.[6] But later studies have found South Asia to have the highest level of diversity of Y-STR haplotype variation within R1a1a. A survey study as of December 2009, including a collation of retested Y-DNA from previous studies, makes a South Asian R1a1a origin the strongest proposal amongst the various possibilities.[7]

mtDNA

Hypothesized map of human migration based on mitochondrial DNA and possible dispersal routes of Eurasian mtDNA macro-haplogroups from South Asia.
See also: Recent single origin hypothesis

The largest Indian mtDNA haplogroups are M, R and U [5]

Arguing for the longer term "rival Y-Chromosome model",[8] 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.[9]

Macrohaplogroup M

The macrohaplogroup M which is considered as a cluster of the proto-Asian maternal lineages,[4] represents more than 60% of Indian MtDNA.[10]

The M macrohaplotype in India includes many subgroups that differ profoundly from other sublineages in East Asia especially Mongoloid populations.[4] 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.[10]

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.[4]

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans.[11]

Haplogroup Important Sub clades Populations
M2 M2a, M2b All through out 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 Rajastan and Madhya Pradesh, being also very dense in Maharastra, Uttar Pradesh, Haryana, Gujarat, Karnataka
M4 M4a Peaks in Pakistan and Kashmir
M6 M6a,M6b Kashmir and near the coasts of the Bay of Bengal, Srilanka
M18 All through out the subcontinent
Peaking at Rajastan and Andhra Pradesh
M25 Widespread in most of India (but rare outside it)
western Maharastra and Kerala, Punjab

Macrohaplogroup R

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[11]:

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 and Punjab.
It is rare further east and not to be found in India.

Haplogroup U

Haplogroup U is sub group of Macrohaplogroup R.[11] 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.[12] Indian U lineages differ substantially from those in Europe and their coalescence to a common ancestor also dates back to about 50,000 years.[13]

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

The diversion of Haplogroup F and its descendants.

Further information: Y-DNA haplogroups in South Asian populations and individual groups by Y-DNA

The major Y chromosome DNA haplogroups in the subcontinent are F's descendant haplogroups R(mostly R1a and R2), L, H and J(mostly J2).[14]

Haplogroup L

Main article: Haplogroup L (Y-DNA)

India

Haplogroup L is currently present in the Indian population at an overall frequency of ca. 7-15%.[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 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%[16]) and Pashtuns (approx. 7%[16]), with a moderate distribution among the general Pakistani population (approx. 2%[16]). 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.[16]

Haplogroup H

Main article: Haplogroup H (Y-DNA)

This haplogroup is found at a high frequency in South Asia. It is generally rare outside of the South Asia but is common among the Romani people, particularly the H-M82 subgroup. Haplogroup H is frequently found among populations of India, Sri Lanka, Nepal, and Pakistan.

It is a branch of Haplogroup F, and is believed to have arisen in India between 20,000 and 30,000 years ago. Its probable site of introduction is India since it is concentrated there. It seems to represent the main Y-haplogroup of the indigenous paleolithic inhabitants of India, because it is the most frequent Y-haplogroup of tribal populations (25-35%). Its presence in upper castes is quite rare (ca. 10%).[17] [18] [19]

Haplogroup R2

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

In South Asia, the frequency of R2 lineage is around 10-15% in India and Sri Lanka and 7-8% in Pakistan.

India

In India, R2 percentage is around 15% among Indo-European speaking groups while Dravidian speakers show it at 8%. Among social groups, very high percentages are shown by Indo-European speaking Karmali from West Bengal at 100%, Jaunpur Kshatriya from Uttar Pradesh at 87% and Kamma Chaudhary from Andhra Pradesh at 73%.

Other than these, significantly high percentages are shown by the people of West Bengal at 23%, Hindus from New Delhi at 20% and Baniya from Bihar at 36%. 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%).

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%.

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%.[20] This lineage also forms 5% of Punjabi males.

Pakistan

The R2 haplogroup is found in 14% of the Burusho people.[21] Among the Hunza it is found at 18% while the Parsis show it at 20%.

Sri Lanka

39% of the Sinhalese of Sri Lanka are found to have R2.

Nepal

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

Main article: Haplogroup R1a1 (Y-DNA)

In South Asia R1a1 has been observed often with high frequency in a number of demographic groups.[22][23] Its parent clade Haplogroup R1a is belived to have its origins in the Indus Valley or the Eurasian Steppe[24]whereas its successor clade R1a1* both have the highest frequency and time depth in South Asia making it the likely locus of origin[25] [26] [27].

India

In India, high percentage of this haplogroup is observed in West Bengal Brahmins (72%) [22] to the east, Konkanastha Brahmins (48%) [22] to the west, Khatris (67%)[28] in north and Iyenger Brahmins (31%)[22] of south. It has also been found in several South Indian Dravidian-speaking Tribals including the Chenchu (26%)[29] and Valmikis of Andhra Pradesh as well as the Kallar of Tamil Nadu suggesting that M17 is widespread in these Southern Indians tribes.[29]

Besides these, studies show high percentages in geographically distant groups in India such as Manipuris (50%)[28] in the extreme North East and in Punjab (47%)[29] to the extreme North West.

Pakistan

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.[28]

Sri Lanka

In Sri Lanka, 13% of the Sinhalese people were found to be R1a1a(M17) positive.[29]

Nepal

People in Terai Region, Nepal show R1a1a at 69%.[30]

Haplogroup J2

Main article: Haplogroup J2 (Y-DNA)

Haplogroup J2 is likely to reflect neolithic expansion from the Middle East to the subcontinent[31]. J2 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%).[32] J2 appears at 20% among the Yadavas of South India while among the Lodhas of West Bengal it is 32%.

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" [33]

South Asia and Central Asia

Further information: Ancient India and Central Asia

A study (Sengupta 2006) insisted 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.”

It should be noted that these "ages" and "variations" were acquired by the highly-criticised "Zhivotovsky method".

The neolithic spread of farmers to regions as far away as Europe 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 Iran, South Caucasus, Anatolia and Europe. 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.[34]

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,[35] microsatellite DNA,[36] and mitochondrial DNA [37] in India have cast strong doubt for a biological Dravidian "race" distinct from non-Dravidians in the Indian subcontinent.

Ancestral South Indians

Ancestral South Indians is a term used in the study of genetics and archaeogenetics of South Asia.[38][39] They are believed to have been genetically unique and not closely related to any other human populations in the world.[39].

ANI ASI admixture time

The modern indian population is a result of admixture between these two ancient groups, though the exact admixture time is still unknown. Recent research has suggested a major admixture taking place between 3500 to 1200 years ago.[40].

Ancestral North Indians

Ancestral North Indians were present in the indian subcontinent from 40,000-45,000 ybp[41].The term is also used in the study of genetics and archaeogenetics of South Asia.[38][39] They are believed to have been closely related to people from the Middle East and Europe, and the percentage of ancestry traceable to them in a given modern Indian ethnic group varies from 40% to 80% depending on region and caste.[39] Recent work involving the reconstruction of an Ancestral North Indian chromosome indicates that the ANI population may have been more closely related to people from central and northern Europe than to people from the Caucasus [42]. Such findings are consistent with the research of Reich et al. Evidences are also there to say indo-europeans moving out of indian subcontinent in prehistoric times as they probably had a pan indian presence with Y-dna R1a1a*(M-173 and M-420) is found to be native in india while most of the eurasian indo-european sites shows the presence of relatively new R1a1a7 (M-458) [43]. However, genetic evidence has no bearing on the languages that these early groups might have spoken.

See also

Notes

  1. ^ Genetic landscape of the people of India: a canvas for disease gene exploration, Indian Genome Variation Consortium, 2008
  2. ^ Trends in Molecular Anthropological Studies in India, Vikal Tripathy, A. Nirmala and B. Mohan Reddy, 2008
  3. ^ Metspalu M, Kivisild T. et al, Peopling of South Asia: investigating the caste-tribe continuum in India, Bioessays Jan 2007
  4. ^ a b c d e 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 [1]
  5. ^ a b 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; et al. (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 (9): 922–932. doi:10.1016/S0198-8859(01)00291-9. PMID 11543894. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
  7. ^ Underhill; Myres, Natalie M; Rootsi, Siiri; Metspalu, Mait; Zhivotovsky, Lev A; King, Roy J; Lin, Alice A; Chow, Cheryl-Emiliane T; Semino, Ornella; et al. (2009). "Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a". European Journal of Human Genetics. 18 (4): 479–84. doi:10.1038/ejhg.2009.194. PMC 2987245. PMID 19888303Template:Inconsistent citations {{cite journal}}: Explicit use of et al. in: |author= (help); Invalid |ref=harv (help)CS1 maint: postscript (link)
  8. ^ 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
  9. ^ Stephen Oppenheimer, The Real Eve: Modern Man's Journey Out of Africa‎,2004
  10. ^ a b 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 [2]
  11. ^ a b c 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.
  12. ^ (Kivisild et al. 1999a)
  13. ^ (Kivisild et al. 1999b)
  14. ^ http://www.scs.uiuc.edu/~mcdonald/WorldHaplogroupsMaps.pdf
  15. ^ (Basu et al. 2003, Cordaux et al. 2004, Sengupta et al. 2006, Thamseem et al. 2006)
  16. ^ a b c d 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); Invalid |ref=harv (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  17. ^ Cordaux R; et al. (2004). "Independent Origins of Indian Caste and Tribal Paternal Lineages". Current Biology. 14 (3): 231–5. doi:10.1016/j.cub.2004.01.024. PMID 14761656. {{cite journal}}: Explicit use of et al. in: |author= (help)
  18. ^ Sengupta S, Zhivotovsky LA, King R; 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". Am. J. Hum. Genet. 78 (2): 202–21. doi:10.1086/499411. PMC 1380230. PMID 16400607. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  19. ^ Thanseem I, Thangaraj K, Chaubey G; et al. (2006). "Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA". BMC Genet. 7: 42. doi:10.1186/1471-2156-7-42. PMC 1569435. PMID 16893451. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  20. ^ Muthukrishnan Eaaswarkhanth, Ikramul Haque, Zeinab Ravesh, Irene Gallego Romero, Poorlin Ramakodi Meganathan, Bhawna Dubey, Faizan Ahmed Khan, Gyaneshwer Chaubey, Toomas Kivisild, Chris Tyler-Smith, Lalji Singh and Kumarasamy Thangaraj (2010). "Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations". European journal of human genetics : EJHG. 18 (3): 354–63. doi:10.1038/ejhg.2009.168. PMC 2859343. PMID 19809480. {{cite journal}}: Invalid |ref=harv (help)CS1 maint: multiple names: authors list (link)
  21. ^ Firasat S, Khaliq S, Mohyuddin A, Papaioannou M, Tyler-Smith C, Underhill PA, Ayub Q. "Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan". {{cite journal}}: Cite journal requires |journal= (help); Invalid |ref=harv (help)CS1 maint: multiple names: authors list (link)
  22. ^ a b c d Sengupta et al. (2005)
  23. ^ Sahoo et al. (2006)
  24. ^ http://www.isogg.org/tree/ISOGG_HapgrpR.html
  25. ^ http://www.nature.com/ejhg/journal/v18/n4/full/ejhg2009194a.html
  26. ^ http://www.nature.com/jhg/journal/v54/n1/full/jhg20082a.html
  27. ^ http://www.nature.com/ejhg/journal/v17/n10/full/ejhg20096a.html
  28. ^ a b c Underhill et al. (2009)
  29. ^ a b c d Kivisild et al. (2003)
  30. ^ Fornarino et al. (2009)
  31. ^ http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015283
  32. ^ (Sengupta 2006)
  33. ^ Kivisild 2003b (Kivisild et al. 2003b
  34. ^ (Kivisild 2003a)
  35. ^ Sahoo, Sanghamitra (24 January 2006). "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. Bibcode:2006PNAS..103..843S. doi:10.1073/pnas.0507714103. PMC 1347984. PMID 16415161. {{cite journal}}: Invalid |ref=harv (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  36. ^ Sengupta, S. (1 February 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". Am J Hum Genet. 78 (2). The American Society of Human Genetics: 201–221. doi:10.1086/499411. PMC 1380230. PMID 16400607. Retrieved 3 December 2007. {{cite journal}}: Invalid |ref=harv (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  37. ^ 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. PMID 16205836. {{cite journal}}: |access-date= requires |url= (help); Invalid |ref=harv (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  38. ^ a b David Reich, Kumarasamy Thangaraj, Nick Patterson, Alkes Price, Lalji Singh (Vol 461, 24 September 2009), "Reconstructing Indian population history" (PDF), Nature, ... two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the 'Ancestral North Indians' (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the 'Ancestral South Indians' (ASI), is as distinct from ANI and East Asians as they are from each other ... {{citation}}: Check date values in: |date= (help)CS1 maint: multiple names: authors list (link)
  39. ^ a b c d Richard F. Nyrop (2 October 2009), "Genetics Weaves Tapestry of Indian Heritage", Focus: News from Harvard Medical, Dental and Public Health Schools, ... nearly all Indians alive today carry various mixtures of genomic contribution from the two ancient populations. One group the authors call "Ancestral North Indians" is genetically most similar to western Eurasians (including Europeans) and accounts for 40 to 80 percent of the ancestry found in the Indian genomes. The rest comes from the "Ancestral South Indians," a distinct population not closely related to populations anywhere else in the world. ... The only exception to the mixed ancestries of all Indians came from the Andaman Islanders, who have exclusive descent from the Ancestral South Indian lineage ... Cite error: The named reference "hrv2009sda" was defined multiple times with different content (see the help page).
  40. ^ http://www.ichg2011.org/cgi-bin/ichg11s?author=Moorjani%20P&sort=ptimes&sbutton=Detail&absno=20758&sid=15004
  41. ^ http://www.nature.com/nature/journal/v461/n7263/full/nature08365.html
  42. ^ David W (Tuesday, March 22, 2011), Reconstructing the Ancestral North Indian (ANI) Genome, Back in 2009, Reich et al. theorized that the current South Asian gene pool was basically made up of two founding genetic components; Ancestral North Indian (ANI), and Ancestral South Indian (ASI). The distilled ANI, they noted, was more similar to the genomes of modern Northwest Europeans than those of the Adygei from the Caucasus. This is obviously out of whack with geography, but it does make sense based on what I've seen in my experiments on the Pakistani samples from the HGDP. Many of them, especially the Pathans, carry numerous segments, or haploblocks, that basically look North European. This gave me an idea to try and reconstruct the ANI genome based on such fragments. The first chromosome of my composite sample, which I call the "ANI composite" is available for download here....I used information from my earlier experiments with ADMIXMAP, HAPMIX and RHH Counter to locate and delineate North European-like segments in phased Pakistani HGDP samples. I phased the data myself with BEAGLE, in a pool of South Asian and Middle Eastern samples, so as not to bias the results of phasing and imputation towards Northern Europe. In order to keep the alleles in phase when loaded into PLINK, I duplicated the haplotypes, basically producing completely homozygous individuals out of each one. Then I created an "ANI composite" dummy with 100% no calls, and loaded the haplotypes into this sample with a Python script. The first to "load" were the Pathan haplotypes, followed by the Burusho. I chose individuals from these two groups to make up the backbone of the putative ANI genome because they always seem to come out most "North European" in my ADMIXTURE and MDS runs compared to other South Asians. ... {{citation}}: Check date values in: |date= (help)
  43. ^ [3]

References

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