molecular anthropology study of indians

7/31/2019 Molecular Anthropology Study of Indians

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Kamla-Raj 2008 Int J Hum Genet, 8(1-2): 1-20 (2008)

Trends in Molecular Anthropological Studies in India

Vikal Tripathy1, A. Nirmala2 and B. Mohan Reddy1

1. Molecular Anthropology group, Biological Anthropology Unit, Indian Statistical Institute,Hyderabad 500 007, Andhra Pradesh, India,

2. School of Human Genome Research and Genetic Disorders, Mahathma Gandhi NationalInstitute of Research and Social Action (MGNIRSA), Hyderabad 500 029,

Andhra Pradesh, India

KEYWORDS Population structure; molecular anthropology; mtDNA; Y-chromosome; autosomal DNA; India

ABSTRACT Indian population is characterized by wide diversity and unique population structure shaped bydifferentwaves of migration and the practice of caste endogamy. Anthropologists have been studying the peopling of India andthe relationships between different populations using traditional genetic markers. With the advent of moleculargenetic techniques the focus has turned to using the DNA polymorphisms for resolving different anthropologicalquestions and to test the different hypotheses in vogue. In this paper we make an attempt to critically review the

trends in molecular anthropological studies till date and bring out salient features of the findings. An attempt has beenmade to evaluate the merit of the molecular studies in the perspective of unique population structure of India.

INTRODUCTION

Anthropology is defined as a study of manin time and space. In simple words the subjectmatter of Anthropology deals with Humanvariation and evolution, humans not as individualsbut ethic groups or populations as a units ofstudy. Although this subject is broadly dividedinto Cultural/Social and Biological/PhysicalAnthropology, anthropologists ideally, study man

holistically, taking into account both the biologicaland socio-cultural aspects of man. The subjecthad its beginning in the studies of smallmarginalized tribal communities but today anyhuman population comes under its ambit.

Biological anthropology started of asdescriptive science of physical variation of humansof both present and past (fossils). One major aimof studying this variation was to study humanevolution apart from the inherent desire ofknowing the other. In the beginning, anthro-pometric and anthroposcopic techniques weredeveloped and thoroughly used by anthro-pologist to study human variation, to describehumans through out the world and to classify them

into different races. Although dermatoglyphicswere also used along with anthropometry indescribing ethnic and/or population variation, itwas rarely used in the racial classification. Thediscovery of genetically determined blood cellpolymorphism in the beginning of twentiethcentury and later on protein polymorphismprovided anthropologist with new tools to studyhuman variation. Anthropometry, dermato-glyphics and serological markers were used

extensively in the twentieth century for studyingthe evolutionary relationships between differentpopulations both at the regional and global levels.The problem with anthropometric variables hadbeen the environmental noise as they areinfluenced by many confounding variablesbesides being genetically multifactorial. Theclassical genetic markers, which were mostlyserological, were used extensively to investigatepopulation relationships across the world, bothat micro and macro levels. The role of differentevolutionary forces like drift, selection, mutation,migration and gene flow in shaping the geneticmake up of populations has also beeninvestigated on the basis of classical geneticmarkers. Cavalli-Sforza et al. (1994) attempted asynthesis of the classical genetic marker dataavailable on populations from different parts ofthe world. One drawback of the classical markersin the study of evolutionary history andpopulation relationships has been that onecannot be sure under what selective pressures

Corresponding Authors Address: Professor B. MohanReddy, Ph.D. Molecular Anthropology Group, BiologicalAnthropology Unit, Indian Statistical InstituteStreet No. 8, Habsiguda, Hyderabad 500 007,Andhra Pradesh, IndiaTelephone: 040-27171906;Extn: 27;

E-mail: [email protected] (OR) [email protected]


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VIKAL TRIPATHY, A. NIRMALA AND B. MOHAN REDDY2

the genetic markers have been under differentenvironmental stresses. More over, few of theclassical genetic markers taken as one trait couldhave been a group of different polymorphism atthe DNA level (for example, G6PD deficiency;Tripathy and Reddy 2007).

The advent of PCR techniques in the 1980salong with the use of restriction enzymes and laterthe use of sequencing methods for identifyingpolymorphisms at the DNA level providedanthropologist with new and more powerfultechniques and markers for testing differentanthropological hypotheses. The study of Cannet al. (1987), which gave support to the Out ofAfrica theory of human evolution, revolutionizedthe field of molecular anthropology and within a

decade anthropologists/population geneticistsstarted using DNA sequence data for under-standing human evolution and for characterizinghuman populations based on Haplotype andHaplogroup frequencies.

We present here a review of the MolecularAnthropological studies carried out on Indianpopulations in the background of the uniquepopulation structure of India. Although the scopeof molecular anthropology can extend topopulation based approaches in molecularepidemiology and adaptation such studies arevery few and far apart or are lacking on Indianpopulations. Therefore, the focus of this reviewpertains basically to the molecular genetic studieson population structure and peopling of India.

THE UNIQUE INDIAN POPULATIONSTRUCTURE

Indian subcontinent is known for its enormousdiversity, cultural as well as biological. Thisdiversity owes itself to the innumerable waves ofmigration from different parts of the world atdifferent points of time. These migrants broughtwith them not only languages and cultures butalso genes. As a result, the present day Indianpopulation is a conglomeration of diverse ethnicelements, language families and cultures. In India,

one finds almost all the ethnic constituents thatcan be found anywhere in the world as there arepopulations with physical features of Australoids,Caucasoids, Mongoloids, and Negroids. Indianpopulations speak innumerable languages that canbe broadly grouped into Austro-Asiatic,Dravidian, Indo-European and Tibeto-Burmanlinguistic families. However, the most unique

feature of Indian population structure is thedivision of its population, within each linguisticarea, into strictly defined hierarchical endo-gamous castes, tribes and religious communitieswhose marriage, hence genetic boundaries werestrictly impermeable. While languages formbarriers between any two linguistic regions evenbetween the same castes, within a linguistic region,each caste/tribe/religious group is furthersubdivided into subcastes/subtribes/subgroups,depending on the size, nature of distribution etc.,besides the possibility of forming geographic/breeding isolates when a caste/subcaste or tribeis large and distributed in a wide geographic area.Because of the pattern of substructuring Indianpopulation contains a large number of

endogamous groups with isolated gene poolswhich have evolved for over 3000 years. The totalnumber of endogamous groups is estimated to bearound 40000 comprising about 37000 castes andsubcastes and 3000 tribal, religious and otherhistorical migrants populations (Gadgil andMalhotra 1983; Malhotra 1984). On the other hand,Anthropological Survey of India (Singh 1993)identified 4635 communities which are, strictlyspeaking, not endogamous units. The culturalpatterns governing marriage vary between theDravidian and Indo-European kinship system(Table 1) which is expected to result in high degreeof inbreeding and much smaller effectivepopulation sizes of the populations in the southas compared to those in the northern parts of India.Overall, the Indian populations show extremevariation in size, nature of sub-structuring etc,hence in the rate of their microevolution.

Theories on the Peopling of India

With the wide acceptance of Out of Africahypothesis, India is considered a major corridorof human evolution and expansion. Of thevarious groups which inhabit India the Austro-Asiatic speaking tribal groups are considered thefirst inhabitants of Indian subcontinent (Kumarand Reddy 2003, Thapar 1966, Risley 1915,

Rapson 1955, Pattanayak 1998). Some like Buxton(1925) and Sarkar (1958) has supported Dravidiansas the original immigrants.

The Skeletal and Archaeological evidencesfrom India points towards an early habitation ofhumans on the Indian subcontinent and stonetool evidences have been found from early StoneAge. However, which species of genus Homo had


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TRENDS IN MOLECULAR ANTHROPOLOGY 3

used these tools is not clear. Skeletal evidence ofearliest Anatomical Modern Humans (AMH)remains is dated at around 8000 ybp (Malhotra1978). The skeletal evidence points towardspresence of both Australoid and Caucasoidelements at all the periods. The Mongoloid featuresare missing from the skeletal remains.

Conclusions from the Earlier Studies Basedon Traditional Variables

A number of studies have reported genefrequencies of one or more traditional geneticmarkers on many Indian populations. Genefrequencies for different markers from differentstudies on Indian populations have been compiledand presented by Bhasin et al. (1992). They alsoattempted to find some patterns in average genefrequencies of groups of populations defined bygeography, language, ethnicity and occupation(Bhasin et al. 1994; Bhasin and Walter, 2001). Afew studies have attempted studying differentpopulations of India using the genetic and

anthropometric markers at regional and local level.Studies at the local level have examined the degreeof biological similarity between endogamousgroups living in a very restricted area or betweensubdivisions of a single caste/tribal population(Reid 1984). Indian population structure asrevealed from the studies based on anthropometric,serological and other classical markers assummarized by Malhotra and Vasulu (1993) ispresented below:1. There is wide range of gene frequency in all

genetic systems and a great deal of variation,sometimes, even in the same geographicalregion

2. With exception to Africa, India harbors moregenetic diversity than the other comparableglobal regions.

3. Tribals are genetically and morphologicallydifferent from non-tribal populations. Thesouthern Indian tribal populations aredifferent from the central and north easterntribal populations

4. Geographically contiguous populations aregenetically more similar than those withlinguistic affiliation.

5. The amount of genetic diversity in IndianPopulations is comparable to that existingin the major races of the man (Majumder andMukherjee 1993)

The classical genetic markers have also been

used to study the relationships between differentcastes as well as between caste and tribal groups.The general conclusions which emerged fromthese studies are:1. Large genetic diversity between castes

belonging to two different Varnas.2. Geographically contiguous castes are

genetically and morphologically closer,irrespective of caste or social hierarchy

3. Genetic diversity among castes is 1-3%,whereas between castes and tribes it is about5%.

4. Geographic clines are observed in some traits,viz. ABO, Sickle cell, HbE, G6PD, whichindicates role of selection as well.

5. Processes of drift, founder effect, gene flowand the fission and fusion are responsible forthe micro-evolutionary differentiations inIndian populations.

6. Average heterozygosity, more or less, is ofsame magnitude in tribal or caste populations.

7. Genetic differentiation between castes andtribes, measured by the ratio of genetic dis-tance to the mean of the average hetero-zygosity is of the same order (0.006) ascompared to that among the human races(Roychoudhury 1984).

Molecular Anthropology Studies

With this background of pre-molecular geneticstudies and inferences on Indian populationstructure, we review the Molecular Anthropologystudies on the Indian populations focusing ongenetic variation and peopling of India. We payspecific attention to reviewing studies that triedto test different anthropological/sociological

Table 1: Difference in marriage patterns in Dravidian and Indo-European kinship system

Dravi dia n Indo Eur ope an

1. Consanguineous marriages highly preferred 1. Sapinda rule prohibits consanguineous marriages2. Village endogamy preferred 2. Village exogamy is the norm3. No restriction of marriage with neighboring villages 2. Marriages with neighboring villages not favored4. Limited marital network; restricted choice of mates 3. Much wider marital network and greater choice

of mates


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hypotheses concerning population structure andpeopling of India, routes of migration of modernHumans through India, the genetic basis of thecaste system, and relationships among differentcaste and tribal populations.

The molecular anthropology studies can bedivided into three categories based on the typeof markers used:(i) Mitochondrial DNA (mtDNA) Variation:

Maternally inherited, highly polymorphic.Inferences provide clues to maternallineages.

(ii) Y Chromosome Variation: Uniparentaltransmission along the male lines, smalleffective population size and absence ofrecombination (except pseudo-autosomal

region). Suitable for tracing male initiatedmigrations.

(iii) Autosomal DNA Variation

mtDNA VARIATION IN INDIA

Studies Based on Hypervariable Region I & IISequences in mtDNA

One of the first studies reporting use ofmtDNA variation among Indian populations wasthat of Mountain et al. (1995). mtDNA sequencesobtained from three culturally divergent Indianendogamous caste groups from coastal southwestern India indicated that the Indian populationsrepresented a major expansion possibly origina-ting in Southern Asia. The date of expansionestimated at some time point after modern humaninitially left Africa. Bamshad et al. (1996) reportedmtDNA variation in four caste populations, viz.Brahmin (9), Yadava (10), Kapu (7) and Relli (10) ofAndhra Pradesh and compared them with African,European and East Asian populations. mtDNAdiversity in Indian Caste populations was foundto be intermediate between African and othercontinental populations. mtDNA variation in theIndian caste populations was more than that ofEuropeans and East Asains. Higher diversityamong Indian populations next only to Africans

had earlier been observed for classical geneticmarkers as well. In a study of 250 individuals from12 Telegu-speaking caste populations fromnortheastern Andhra Pradesh, southern India,Bamshad et al. (1998) showed that differences insocial rank between castes correspond tomitochondrial DNA (mtDNA) distances betweencastes, suggesting genetic stratification corres-

ponding to social stratification and this theyinterpreted as due to the system of hypergamywherein women of lower caste hierarchy is allowedto marry men of higher castes.

RFLP Based Bi-allelic Marker Studies

Passarino et al. (1996a) used mtDNA haplo-types for studying variation in 70 individuals fromPunjab and 96 from UP (Uttar Pradesh) andAP (Andhra Pradesh) and concluded that Indo-European migration affected the populationstructure mainly in the north and in the center ofthe Indian sub-continent, not in the south. Using6 restriction enzymes, Barnabas et al. (1996)studied mtDNA variation of 100 Indians

belonging to 14 different languages and foundthat the Indian population is closer to Caucasiansand has an admixture with Asian. These datafurther suggested that the North Indian popu-lations appears to have a recent admixture of theCaucasian mtDNA, which is absent in the South,thus supporting the recent peopling of the Indo-European language speaking people in India. Onthe other hand, Passarino et al. (1996b) found 50%of the Indians (in a sample of 133 Hindus and 30tribals) to represent the two mtDNA haplotypesthatwere considered to be the ancient East Asianmarkers and not found among the Caucasians ofthe Mediterranean basin and concluded that theIndo-European speakers were genetically differentfrom the pre-existing Indian population. Theyfurther speculated that the Indians behave astypical Caucasoid for other genes (other thenmtDNA) because the relative contribution of theIndo-European speaker to final Indian geneticmake-up was mostly a paternal one.

Studies Based on 9 BP Deletion between COIIand tRNAlys

mtDNA haplogroup B, is defined by a 9bpdeletion in the intergenic region V of mtDNA,which is frequent in SE Asian populations,reaching almost fixation in some Polynesian

populations. The 9bp motif is present betweencytochrome oxidase II (COII) and tRNA lysine(tRNAlys) genes. Most individuals have twotandem copies of this 9bp motive. This 9bpdeletion was earlier considered as a marker ofAsian populations, subsequently found in mostother population in varying frequencies.

Majumder (2001) reported absence of 9bp


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deletion in Indian populations as reflected froma study of some 30 population from differentregions. On the other hand, Watkins et al. (1999),Clark et al. (2000), Prasad et al. (2001), Thangarajet al. (2005) and Kumar et al. (2006a) reportedthat the 9bp deletion is present in some casteand tribal populations with varying frequencies.Watkins et al. (1999) studied 9bp deletion inmtDNA in 646 Indians from 12 caste and 14 tribalsfrom south India and suggested that 9bp deletionhas arisen independently in some Indian tribalpopulations. Other 9bp deletion haplotypes areof Asian and African origin. Different affinitiesfor 9bp deletion among caste and tribalpopulations thus suggested different origins forthese populations. Clark et al. (2000) analyzed

9bp deletion in mtDNA of 898 individuals from16 tribal populations of Northeast and SouthernIndia. The frequency of 9bp deletion was foundto be very low, just 0.8% in northeast and 1.5% inNilgiri hills in South India. The 9bp deletion wasreported only in 6 individuals and the sequencesof these 6 formed 3 clusters in phylogeneticanalysis, one cluster from northeast showingsimilarity to Southeast Asian mtDNA types andthe other two from south India were unique toIndia and showed no similarity with AfricanmtDNA types.

Thangaraj et al. (2005) analyzed 3239individuals from 58 endogamous populations ofIndia. They found that the frequency of the 9bpdeletion/insertion does not vary significantlyacross different ethnic and linguistic populations.A total of 20 independent origins of the 9bpdeletion and insertion were reported and theseevents were not found to be population specific.The frequency of 9bp deletion was found to behighest among the Austro-Asiatic speakingNicobarese (45.8%). In contrast to Nicobarese, themainland Austro-Asiatic populations showed noincidence of 9bp deletion, pointing towards anindependent origin of Nicobarese and themainland Austro-Asiatic populations.

Kumar et al. (2006a) analyzed 1,686 samplesfrom 31 tribal populations of India for the

mitochondrial DNA 9-bp deletion/insertionpolymorphism. The results suggest multipleorigins/migrations of Austro-Asiatic groups intothe Indian Subcontinent and also distinct originfor Austro-Asiatic linguistic groups. Austro-Asiatic populations of India have come in multiplewaves of migration, and the ancestors of presentday Mundari groups might have been the first to

arrive in India through the western Indiancorridor, subsequently migrating to SoutheastAsia.

Haplogroup Based Studies

The study of Kivisild et al. (1999) for the firsttime contradicted the commonly acceptedhypothesis of massive Indo-Aryan invasionsome 3500 to 4000 years ago and thus recentmassive admixture of Caucasoids with Indianpopulations. The genetic link for the commonmtDNA haplogroup U, which roughly accountsfor a fifth of mtDNA lineages of both thesepopulations, was found to be very deep anddated to late Pleistocene. The coalescence time

(~50,000yr) of the Indian-specific subset of thewest Eurasian haplotype (U2i) suggests that thewest Eurasian admixture may have been mucholder than the proposed Dravidian and Indo-European incursions based on languagephylogeny. Estimate for this split for haplotypeU2i is close to the estimated time for the peoplingof Asia and the first expansion of anatomicallymodern humans in Eurasia and perhaps predatestheir spread to Europe. Only a small fraction ofthe Caucasoid-specific mtDNA lineages foundin Indian populations can be ascribed to arelatively recent admixture. Thus these resultsquestioned the commonly held hypothesis ofmassive Indo-Aryan invasion to India some 4,000years ago. Most subsequent studies yieldedresults confirmatory to the findings of Kivislid etal. (1999).

Roychoudhury et al. (2000) studied mtDNAvariation among 23 ethnic populations of Indiafrom diverse cultural, linguistic and geographicbackgrounds. They found extensive sharing ofone or two haplotypes across population groupswithin India, irrespective of the geography,linguistic affinity or social proximity. Most of themtDNA diversity observed in Indian populationswas found between individuals within popu-lation. No significant structure of haplotypediversity by socio-religious affiliation, geography

or linguistic affiliation was found, suggesting afundamental unity of mtDNA lineages in India,in spite of the extensive cultural and linguisticdiversity.

Roychoudhury et al. (2001) sampled tribalpopulations belonging to all the three languagegroups Austro-Asiatic speakers: Santal (n=21),Munda (n=7), Lodha (n=32); Dravidian speakers:


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Muria (n=49), Kota (n=45), Kurumba (n=54), Irula(n=50); Tibeto-Burman speakers: Tipperah (n=51).MtDNA RSP haplotypes showed extensivehaplotype sharing among all tribal populations.However, there is very little sharing of mtDNAHVS-1 sequences across populations, and noneacross language groups. Analyses of haplogroupand HVS-1 sequence data provided evidence insupport of the hypothesis that the Austro-Asiaticspeakers are the most ancient inhabitants of India.Subsequently, this group analyzed data for mtDNARSPs and HVS1 sequences of 44 populations(Basu et al. 2003) and found a significant sharingboth in the number of sequences and in proportionof individuals sharing these sequences andsuggested uniformity of female lineages across

India. They also found that Austro-Asiatic tribalspossess highest frequency of the ancient EastAsian mtDNA haplogroup M and exhibit highestHVS1 nucleotide diversity, and used this evidenceto reiterate support to the hypothesis that Austro-Asiatic speakers may be the earliest inhabitantsof India. However, this conclusion was based onjust 3 of the 30 Austro-Asiatic tribes inhabitingthe Indian subcontinent. Given that the analysesof mtDNA was at the level of macro haplogroup,M, which is ubiquitous to Asia and other regionsand due to inadequate representation of popu-lations of different linguistic groups (particularlyof Austro-Asiatics) with only a few samples theseconclusions are at the best tentative and shouldawait further evidence with formidable samplesand better representation of the different linguisticgroups.

Two tribal groups from southern India - theChenchus and Koyas - were analyzed by Kivislidet al. (2003) for variation in mitochondrial DNA(mtDNA), the Y chromosome, and one autosomallocus and were compared with six caste groupsfrom different parts of India, as well as with westernand central Asians. Variation in the mtDNA, Y-Chromosome and autosomes suggested thatIndian caste and tribal populations are derivedlargely from the same genetic heritage ofPleistocene southern and western Asians and

have received limited gene flow from externalregions since the Holocene. The phylogeographyof the primal mtDNA and Y-chromosome founderssuggests that these southern Asian Pleistocenecoastal settlers from Africa would have providedthe inocula for the subsequent differentiation ofthe distinctive eastern and western Eurasian genepools.

Bamshad et al. (2001) analysed mtDNA (HVS1) and 14 RSPs, Y-Chromosome (5 STR and 20SNPs) and autosomal (1 LINE-I and 39 Alu inserts)variation in ~265 males from 8 different Teluguspeaking caste populations of AP in South India.Comparisons were made with ~400 individualsfrom tribal and Hindi speaking populations. Formaternally inherited mtDNA, each caste was foundto be more similar to Asians. However, 20%30%of Indian mtDNA haplotypes belong to WestEurasian haplogroups, and the frequency of thesehaplogroups is proportional to caste rank, hencethe affinity of different populations to Europeansis proportionate to caste rank. Upper castes havegreater genetic affinity to Europeans than toAsians and the upper castes are also significantly

more similar to Europeans than are the lowercastes. Indian castes are more likely to be of proto-Asian origin with west Eurasian admixtureresulting in rank related sex-specific differencesin the genetic affinities of castes to Asians andEuropeans. They conclude that Indo-Europeanlanguages may not reflect a common origin ofEuropeans and most Indians, but ratherunderscores the transfer of languages mediatedby contact between west Eurasians and nativeproto-Indians.

Cordaux et al. (2003) analyzed 370 bp of thefirst hypervariable region of the mitochondrialDNA (mtDNA) control region in 752 individualsfrom 17 tribal and four non-tribal groups from theIndian subcontinent. Southern Indian tribesshowed reduced diversity and large geneticdistances. By contrast, northern groups exhibitedmore diversity. Phylogenetic analyses revealed thatsouthern and northern groups (except north-eastern ones) have related mtDNA sequencesalbeit at different frequencies. Within India,northeastern tribes are quite distinct from othergroups. The Indian mtDNA gene pool appears tobe more closely related to the east Eurasian genepool than the west Eurasian one. Overall, analysesof molecular variance suggested that caste andtribal groups are genetically similar with respectto mtDNA variation.

Baig et al. (2004) analyzed mtDNA variationamong seven communities belonging to tribes andcastes of different hierarchy from westernMaharastra to test the hypothesis of tribal originof some caste groups. Nucleotide diversity, genediversity and average mismatches were found toof the same magnitude. The mtDNA haplogroupsshowed that both caste and tribal populations


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share similar branches of the trees and the maternallineages have their roots in early late Pleistocene.Thanseem et al. (2006) also did not find significantdifference between Indian caste and tribalpopulations for mtDNA; still higher frequency ofwest Eurasian specific haplogroups were foundin the higher castes especially from north westernpart of India.

Quintana-Murci (2004) studied the mtDNAvariation in the southwestern and Central Asianregions, the area which has witnessed numerouswaves of migration in the history of humankind.The 910 mitochondrial DNAs (mtDNAs) heanalyzed represented 23 populations of Iranianplateau, Indus Valley and Central Asia. Indus Valleypopulation comprised of populations from

Pakistan and a group of Gujaratis from India. Boththe geographical distribution of lineages andspatial analysis of molecular variance showed thatpopulations located west of the Indus Valley mainlyharbor mtDNAs of western Eurasian origin,whereas those inhabiting the Indo-Gangetic regionand Central Asia present substantial proportionsof lineages that can be allocated to three differentgenetic components of western Eurasian, easternEurasian, and south Asian origin.

Metspalu et al. (2004) analyzed 796 Indiansand 436 Iranians for mtDNA variation andcompared with previous studies from India andalso from Europe, China and Thailand. Thenorthern states (caste populations) showed higherfrequencies of western Eurasian haplogroups. Thewest Eurasian haplogroups can be broadly dividedinto two groups, one showing admixture withinthe last 10000 years and the other (one third)showing much deeper time depths (40000 years).Tibeto-Burman speaking tribal populations ofeastern and northern India exhibits the highestfrequencies of East Eurasians specific mtDNAhaplogroups. They concluded that deep auto-chthonous history of these haplogroups in theregion remains to be the most parsimoniousexplanation. They propose that the initial mtDNApool established upon the peopling of South Asiahas not been replaced but has rather been

reshaped in situ by major events of gene flowboth from the west and the east during more recentchapters of the demographic history of the region

Sahoo and Kashyap (2006) reported variationin mtDNA hypervariable sequence (HVS) I and II,eight Y-chromosome short tandem repeats (Y-STRs), and lineage-defining mutations diagnosticfor Indian- and Eurasian-specific haplogroups

among seven caste and tribal populations ofOrissa. The mitochondrial data show hierarchicalassociation with the Indo-European speakers ofEastern Europe.

Sun et al. (2006) performed complete genomesequencing of 56 mtDNA which covered all therecognized M lineages. They found that M Macro-haplogroup is ubiquitous in South Asia and coversmore than half of Indian mtDNA. Only previousattempt at complete sequencing of mtDNA for Mhaplogroup was that of Rajkumar et al. (2005). Sunet al. (2006) points to errors typical of large mtDNAsequencing in their data. They found that the basalvariation in macrohaplogroup M in India clearlyoutnumbers that of macrohaplogroup M in EastAsia. The mtDNA phylogeny of M haplogroup

is in good agreement with the proposed scenariothat the initial dispersal of modern humans intoEurasia ~ 60K years ago was rather rapid alongthe Asian Coast line. Using 11 whole mtDNAand 2231 partial coding sequence of Indian Mlineage selected from 8670 HVS1 sequencesacross India, Thangaraj et al. (2006) defined onenovel haplogroup M41 and revised the classi-fication of haplogroups M3, M18 and M31. Otherhaplogroups were also further classified intosubhaplogroups. Phylogenetic tree was contruc-ted including the data of Sun et al. (2006). Mostof the new M lineages were found to be deeprooted and more likely arose in situ in Indian-subcontinent. The autochthonous lineagesemerge directly from the root of the macro-haplogroup M. The deep rooting lineages arenot language specific and are spread over all thelanguage groups in India.

Palanichamy et al. (2004) did completesequencing of 75 individuals belonging tomacrohaplogroup N, to study the phylogeneticrelationship of Indian and Western EurasianmtDNA. They found that Indian N macro-haplogroup consists of some lineages which areas deep rooted as the western Eurasian mtDNAlineages. Also, some typical European haplo-groups like H, V, K, U5, J and T provide an entrytime into India which is less than 11.5 Kya. They

conclude that these results along with theevidence for M macrohaplogroup suggest three-founder-mtDNA lineages migrating into the sub-continent at different time periods.

Studies which focus on Northeasternpopulations largely conclude that they differ frommainland populations and show affinity to SouthEast Asian populations. In a study of biallelic


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and five short tandemrepeat Y-chromosomemarkers and mtDNA hypervariable region 1sequence variation in 192 northeast IndiansCordaux et al. (2004a) found that northeast IndianmtDNAs consistently show strikingly highhomogeneity among groups and strong affinitiesto East Asian groups. They detected virtually nomtDNA admixture between northeast and otherIndian groups. Northeast Indian groups are alsocharacterized by a greatly reduced Y-chromo-some diversity, which contrasts with extensivemtDNA diversity. Based on both the mtDNA andY-Choromosome results they conclude that thereis a strong evidence for a genetic discontinuitybetween northeast Indian groups and otherIndian groups, hence the northeast Indian

passageway acted as a geographic barrier ratherthan as a corridor for human migrations betweenthe Indian subcontinent and East/SoutheastAsia. Given the representation of populations inthis study the above conclusions are to be takenwith a pinch of salt. In this context, it is importantto note that the northeast Indian studies hitherto neglect certain important tribal populationslike Khasis who speak Khasi-Khmuic, an Austro-Asiatic language in the midst of predominantlyIndo-European speakers. In a recent study Reddyet al.. (2007) found mtDNA evidence on relicgenetic link between Indian and Northeast Indianpopulations, contrary to Cardoux et al. (2004a)inference, besides a strong Y-chromosomalconnection between the Mundari tribes fromCentral India, Khasi and Monkhmer Nicobarese(the three linguistic subfamilies) as well as withtheir linguistic counterparts from the southeastAsian region (Kumar et al. 2007).

There have been a few studies focusing onthe affinities of Indian Muslim populations thelargest religious minority of India, as well.Terreros et al. (2007) studied the mtDNAvariation in the two Muslim sects from thenorthern Indian province of Uttar Pradesh, theSunni and Shia. A comparison of this data tothat from Middle Eastern, Central Asian, NorthEast African, and other Indian groups revealed

that, at the mtDNA haplogroup level, both ofthese Indian-Sunni and Shia populations aremore similar to each other and to the other Indiangroups than to those from the other regions.These two Muslim sects exhibit a conspicuousabsence of West Asian mtDNA haplogroupssuggesting that their maternal lineages are ofIndian origin.

Y-CHROMOSOME VARIATION IN INDIA

The paternally inherited Y-Chromosomeprovides insights into the origin, history andmigratory pathways of the male lineages andhelps reconstruct the evolutionary history of thepopulations. In fact one of the first papersdescribing Y-Chromosome variation comparedrelative Y-Chromosome and mtDNA distancesamong the hierarchically stratified castes in AP(Bamshad et al. 1998). In contrast to mtDNA, Y-Chromosome distances showed no correlationwith social rank. This was interpreted as due tolack of male gene flow between castes of differentsocial rank. Bamshad et al. (1998) concluded thatthe genetic stratification of the Hindu caste

system is driven by the social mobility of womenin a patrilocal society and social laws of hyper-gyny played a role in it. Subsequently, based ona few STR markers, Bhattacharya et al. (1999)found that different ethnic groups of Indiarepresented in this study primarily by certainIndo-European and Austroasiatic linguisticgroups harbor disjoint sets of haplotypes. Also,there was a significant haplotype variation bet-ween castes and tribes. The authors interpretedthis as due to lack of male gene flow across ethnicgroups of India. Nevertheless, it may be pertinentto note that the populations included in this studywere geographically, linguistically and ethnicallyso disperse that they had no possibility forexchange of genes either historically or currently.Based on Y-Chromosome data, Sahoo andKashyap (2006) reported that Y-Chromosomedata suggest that genetic distances of thepopulations are not correlated with their positionin the Caste hierarchy, which was in contrast totheir mtDNA data. Though the genetic distancesbased on Y were not correlated with social rankthe higher caste groups were closer to the Indo-European speakers of Eastern Europe. Basu etal. (2003) observed significant differences in thefrequency of Y-Chromosome haplogroups, incontrast to those of mtDNA, between the tribaland caste groups. Also the frequencies of Central

Asian haplogroups are higher in the caste thanthe tribal populations. In a study of Y-Chromo-some variation among 4 caste populations, 3 tribalpopulations and Siddis from Andhra Pradesh,Ramana et al. (2001) found that Y-Chromosomehaplotypes are unique to castes and tribes, sothat they could be distinguished on the basis ofhaplotypes. But there were certain haplotypes


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which were present in all the caste and tribalgroups studied. Ramana et al. (2001) concludedthis as evidence of male gene flow across castesand tribes in the region. This conclusion is incontrast to what has been proposed by Bamshadet al. (1998) and Bhatacharya et al. (1999).

Studies focusing on relative affinity of Indiancaste and tribal gene pools with that of Asiansand Europeans have also reported contras-ting results for mtDNA and Y-Chromosomes.Mukherjee et al. (2001) in a study of 18 Y-Chromosomal polymorphic markers in 4 ethnicpopulations of Northern India reported higherfrequencies of haplogroups HG-3 and HG-9, whichare known to have arisen in central Asian region.NJ tree based on Y-Chromosome frequencies

showed that North Indians are genetically placedbetween west Asian and central Asian popu-lations.

In Contrast to mtDNA variation, Y-Chromo-some variation in each of eight castes fromAndhra was found to be more similar to EastEuropeans than to Asians (Bamshad et al. 2001).The affinity of Indian castes to Europeans wasobserved to be proportionate to caste rank. Basedon mtDNA variation Bamshad et al. (2001)concluded that Indian castes are likely to be ofproto-Asian in origin and the Y-Chromosomevariation indicates west Eurasian admixturewhich is proportionate to the caste rank.

Some studies reported similar results for bothmtDNA and Y-Chromosome variation. Kivisild etal. (2003) found that the major Indian Y-Chromosome haplogroups H, L and R2 occur inboth the castes and tribal populations and arerarely found outside the subcontinent.Haplogroup R1a which was earlier associated withIndo-Aryan invasion was found in high frequencyin Punjab as well as in the Chenchu tribe in SouthIndia, thus the results of both mtDNA and Y-Chromosome variation suggest a common geneticheritage of Indian castes and tribes.

Thanseem et al. (2006) analyzed three tribalpopulations from Andhra Pradesh and comparedresults with other populations. They found that

in contrast to mtDNA, Y-Chromsome variation inIndia is distinct among caste and tribalpopulations. The lower castes showed closeraffinity to tribal populations than to upper castesand the frequencies of deep rooted Y-haplo-groups were higher in the lower castes and tribescompared to upper castes prompting them to infertribal origin of the lower castes.

Sahoo et al. (2006) typed 38 single-nucleotidepolymorphic markers in 936 Y chromosomes,representing 32 tribal and 45 caste groups fromall four major linguistic groups of India,. Variationin the major Y-chromosomal haplogroups in Indiasuggests that the recent external contribution toDravidian and Hindi-speaking caste groups hasbeen low and rule out recent major influx fromnorth and west of India.

Sengupta et al. (2006) analyzed 69 Y-chromosome SNPs and 10 microsatellite markersfrom a large set of geographically, socially,linguistically and ethnically diverse groups ofSouth Asia and found that the influence of CentralAsia on the pre-existing gene pool was minor.The ages estimated for the accumulated micro-

satellite variation in the majority of Indianhaplogroups exceeded 10,00015,000 years thusruling out the pronounced recent genetic inputfrom Central Asia. Their results also support thedeep antiquity of Indian Populations.

Basu et al. (2003) reported that Austro-Asiatictribal groups possess high frequencies of Y-chromosomal haplogroup K* which is found inhigher frequencies in Chinese and SoutheastAsians populations. They concluded that Austro-Asiatic tribal populations entered India first fromthe Northwest corridor and much later some ofthem through Northeastern corridor. On the otherhand, Kumar et al. (2007) analyzed a battery ofrelevant Y-Chromosome SNPs and 20 STRs among25 Indian Austro-Asiatic tribes, including thetransitional ones, and compared with 214 relevantpopulations from Asia and Oceania to trace theorigin and historic expansion of Austro-Asiaticgroups of India. Strong paternal genetic link wasfound not only among the sub-linguistic groups ofthe Indian Austro-Asiatic populations but also withthose of South East Asia. Maternal link based onmtDNA was not that apparent, however. Resultsalso indicate that the haplogroup O-M95 hadoriginated in the ancestors of Indian Austro-Asiaticpopulations ~65,000 yrs BP and was further carriedto Southeast Asia via the Northeast Indian corridor(Fig. 1). The conclusions of Kumar et al. (2007) and

Basu et al. (2003) are different from that of Cordauxet al. (2004a) who had proposed that Northeast Indiaacted as a barrier. Nevertheless, Kumar et al. (2007)and Basu et al. (2003) differ in the direction ofmigration for Austro-Asiatic populations throughthe Northeast corridor.

Cordoux et al. (2004b) analyzed Y-Chromo-some data from 155 individuals from 9 tribal groups


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and one caste population and compared withpublished data. The total dataset consisted of 931individuals from 15 tribal and 12 caste groups.They found that seven most frequent haplogroupsaccount for 80-90% of both caste and tribalsamples, suggesting extensive overlapping ofcaste and tribal chromosomes. However, thecastes and tribes differed in the frequency of themajor haplogroups. Haplogroup O-M95 showedhigher frequency in tribal than in caste groups.Caste groups were homogenous and were moreclosely related to Central Asian groups than toIndian tribal groups. From these results theyconcluded that caste and tribal populations ofIndia have Independent origin. The sharing of mosthaplogroups was explained by admixture. They

provide a very recent estimate for the time (3500years) for migration of Indo-European speakersfrom central Asia from whom the Indian castepopulations are supposed to have been derived.

Kumar et al. (2006b) tested the hypothesisthat Y-Chromosome variants tend to be morelocalized geographically than those of mtDNAvariants because of the widespread phenomenonof patrilocality (Seielstad et al. 1998). Thishypothesis is based on the model of isolation bydistance and it got some support from studies inThailand (Oota et al. 2001). Kumar et al. (2006b)tested the universality of this hypothesis byanalyzing Y-chromosome and mtDNA data inthree different sets of Indian populations thatfollow endogamy rules to varying degrees. Theresults showed that the Indian patrilocal and thematrilocal groups do not conform to the sex-specific variation as observed among the tribesof Thailand. The patterns of genetic variabilityin India are not consistent with the abovehypothesis as the population structure is uniquebased on the endogamy rules, hence adhere tothe island model.

Redd et al. (2002) showed additional DNAevidence in support of Huxleys hypothesis ofan Indian-Australian connection using SNPs andSTRs on the non-recombining portion of the Ychromosome (NRY). Phylogenetic analyses of

STR variation associated with a major AustralianSNP lineage indicated tight clustering withsouthern Indian/Sri Lankan Y chromosomes.Estimates of the divergence for these Indian andAustralian chromosomes overlap with importantchanges in the archaeological and linguisticrecords in Australia. These results provide strongevidence for an influx of Y chromosomes from

the Indian subcontinent to Australia that mayhave occurred during the Holocene.

Gutala et al. (2006) typed eight microsatelliteloci and 16 binary markers from the Y chromosomein 246 Muslims from Andhra Pradesh, andcompared them to published data on 4,204 malesfrom East Asia, Central Asia, India, Sri Lanka,Pakistan, Iran, the Middle East, Turkey, Egypt andMorocco. They found that the Muslim populationsin general are genetically closer to their non-Muslimneighbors than to other Muslims in India. Theyconclude that the Muslim expansion in India waspredominantly a cultural change and was notaccompanied by significant gene flow. Theconclusions are similar to what was observed formtDNA among the Muslims of Uttar Pradesh

(Terreros et al. 2007). Basu et al. (2003) have alsofound the Muslims of Uttar Pradesh to clusterwith Indo-European Upper-Caste groups for Y-Chromosome and autosomal markers.

AUTOSOMAL VARIATION IN INDIA

As against mtDNA and Y-Chromosome whichshow a simple pattern of inheritance, theautosomal DNA has not been a favorite in thestudies of peopling of India, especially those whichfocused on the migration of humans. Still quite afew studies have used autosomal markers inunderstanding the genetic affinities of Indianpopulations. A lot of data have also been generat-ed on many autosomal (and Y as well) STR/microsatellite markers by Central Forensic ScienceLaboratory, Kolkata and others. Many publishedarticles from this institution and others havefocused on forensic utility of specific markers instudied populations.

Majumder et al. (1999) analyzed DNA samplesform 396 individuals belonging to 14 ethnicpopulations of India for 8 human specificpolymorphic insertion/deletion loci and observedthat geographically closer populations showedgreater affinity than populations with socio-cultural similarity. In contrast, Roychoudhury etal. (2001) observed genomic affinity to show good

association with linguistic affinity for autosomalloci. Viswanathan et al. (2004), on the other hand,found that genetic distances based on 24 auto-somal markers were not correlated with geographicdistances for 5 Dravidian speaking tribalpopulations from Nilgiri hills area of Tamil Nadu.They also found that the Indian populations wereclosely related to each other, regardless of the fact


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that some tribal populations showed Negritophenotypic characteristics. Basu et al. (2003)observed that the clustering (based on mtDNA,Y-Chromosome and autosomal markers) ofpopulations was not strictly consistent with theirsocial, geographical or linguistic affiliations, exceptthat the Tibeto-Burman speakers of Northeast forma separate cluster. Population structure analysisalso showed that Indo-European speakers andDravidian speakers are the most similar forAutosomal data, though these two groups aregeographically wide apart.

Autosomal STRs and Population Structure atMicro and Macrolevels

Ashma and Kashyap (2003) demonstratedsocial hierarchical relationship among four castegroups from Bihar, for 15 microsatellite markers.

Kashyap et al. (2004a) reported that the clusteringpattern corresponds with the spatial and ethnicaffiliation of the eight population groups fromWest Bengal and Manipur for 22 autosomal loci.Based on twelve microsatellite markers, Kritikaet al. (2006) found that genetic affinity wascorrelated with geographical distance for 14Tibeto-Burman populations.

Bamshad et al. (2001) using 40 autosomalmarkers found highly significant hierarchicalstratification of the caste populations of AndhraPradesh. However, Reddy et al. (2005) typed 9AmpF/STR Profiler Plus loci on 948 individualsfrom 27 populations (both caste and tribal) fromSouthern Andhra Pradesh and the inferences weresomewhat contradictory. They found allelefrequency distributions are fairly uniform acrossthe populations of southern Andhra Pradesh. Thecaste groups showed the largest genetic distanceswith tribes when compared to the mutual distancesamong them, suggesting genetic isolation of thetribes and castes. There is also a meek trend ofincrease in genetic distances with the increasinghierarchy of populations and this they inferred asprobably due to unauthorized male gene flowrather than hypergamy of females. Further, theyreported lack of any pattern in the population

clustering based on ethnohistoric or geographicalaffiliations. But when compared with other Indianand continental populations, the studied Andhrapopulations form a single and compact cluster (Fig.2). Thus, at an all India level, irrespective of thesocial hierarchy these populations from a singlegeographical area are genetically homogenousto each other. Langstieh et al. (2004) analyzed 9

Fig. 1. Map showing the distribution of Austro-Asiatic populations and the origin of haplogroupO-M95 among the Mundari and the route of its migration.(Source: Kumar et al. 2007)


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Fig. 2. Cladogram depicting the relationship of the populations of Andhra Pradesh to other Indian andcontinental populations(Source: Reddy et al. 2005)

AmpFLSTR loci for 932 Chromosomes from 9populations out of which 7 were subpopulationsof Austro-Asiatic Mon-Khmer speaking Khasi,one neighboring Tibeto-Burman speaking Garoand an intermediate population, Lyngngam. Thedifferent analyses revealed lack of cleardifferentiation and clustering pattern in these

populations. The reduced microsatellite diversityis interpreted by the authors as partly due tomatriliny/matrilocality practiced by these popu-lations. When these populations are comparedwith other Indian, Southeast Asian, and othercontinental populations, the Mehalaya popu-lations form a compact cluster separated from other


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populations, suggesting genetic identity of thesepopulations. Overall, the observation of Reddy etal. (2005) that geographically closer populationsare genetically closer is true for different linguisticpopulations of Meghalaya as well. However, thesepopulations show greater proximity to the otherMongoloid populations from the Southeast/EastAsian countries. Similar findings were apparentin case of Northeast Indian populations in generalvis--vis the other Indian and East /SoutheastAsian populations (Dutta et al. 2002). In anotherstudy from Andhra Pradesh, Reddy et al. (2001a)used 13 STR loci in seven populations of asubstructured Golla caste from Chittoor district ofAP. Genetic distance measures revealed clustersof popu-lations that are consistent with the known

ethnohistorical and geographical backgrounds ofthe groups. Similar results were obtained by Reddyet al. (2001b) based on only 3 of the above 13 STRloci among the Gollas. Thus, the patterns observedat a local level, within a sub-structured castepopulation, were not apparent when many tribaland caste populations from heterogeneousgeographic background were studied.

Kivisild et al. (2003) found that frequency ofautosomal haplogroups MX1 and Ch21distinguished the Koyas and Chenchus, two tribesfrom South India, along with other Indian castepopulations, from the European and Eastern Asianpopulations. This result corroborates with theirmtDNA and Y-Chromosome based conclusionsuggesting common ancient genetic heritage forIndian caste and tribal populations.

Rajkumar and Kashyap (2004) describedpolymorphism at 15 autosomal STR in fourendogamous populations from Karnataka on theSouthwest coast of India and their results indicatedcommon ancestry for the four diverse populationsof Karnataka. Similar study (Sahoo and Kashyap2005) among seven populations belonging to twomajor ethnic groups and different linguistic familiesinhabiting the same geographical area suggestedgenetic homogeneity although still the contem-porary caste and tribal groups formed distinctclusters in both Principal Component plot and

Neighbor Joining tree. Congruent to this, Watkinset al. (2005) study of 45 unlinked autosomal STRloci portray relative closeness of Indian tribal andcaste populations between them than to other majorethnic groups from outside. The sharedphenotypic characteristics of some tribes withAfrican were not reflected in their geneticcomposition. South Indian populations showed

lower within population heterozygositiescompared to the Northeast Indian populations.

Gaikwad et al. (2006) reported Microsatellitediversity among four Proto-Australoid tribes fromwest-central India. The relationship of these tribeswith neighboring tribal and caste populations werestudied. Overall, the results suggested that theProto-Australoid tribal populations weregenetically differentiated from castes of similarmorphology, suggesting different evolutionarymechanisms and their intensities upon thesepopulations. On the other hand, Kashyap et al.(2004b, 2006) assessed the variation in micro-satellite markers among 3522 individuals belongingto 54 endogamous Indian populations represen-ting all major ethnic, linguistic and geographic

groups and observed that the distribution of themost frequent alleles were uniform acrosspopulations, revealing an underlying geneticsimilarity, as observed by Reddy et al. (2005) in anarray of hierarchical caste and tribal groups ofsouthern Andhra Pradesh. Autosomal micro-satellite markers detected no evidence of generalclustering of population groups based on ethnic,linguistic, geographic or socio-cultural affiliations.These conclusions are in agreement withconclusion of common genetic heritage of Indianpopulations based on mtDNA and Y-Chromosome(Kivisild et al. 2003; Roychoudhury et al. 2000;Basu et al. 2003 ).

Studies Focusing on Populations of Andamanand Nicobar Islands

The issue of the origin of Andaman Nicobartribes has always been intriguing to Anthro-pologists. These tribes have been proposed toprovide foot prints of migration of early wave ofmodern humans to Australia (Redd et al. 2002;Macaulay 2005). A few recent studies havefocused on the molecular genetic features ofpopulations from Andaman Nicobar islands.Analyzing mtDNA sequences and RFLPpolymorphisms, Y-Chromosome biallelic markerand microsatellites in the populations of Andaman

and Nicobar islands, Thangraj et al. (2003)observed low genetic variation among them. Thecloser genetic affinity of Andamanese to the Asiansthan to African populations suggests that theyare the descendants of the early Paleolithiccolonizers of South-East Asia. Thangaraj et al.(2005) reported low haplotype diversity amongthe 9bp samples in the Nicobarese, which


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suggests recent founder effect and origin in Chinavia Cambodia and Thailand. Complete mtDNAsequences of five Onge, five Great Andamanese,and five Nicobarese individuals analyzed byThangaraj et al. (2005) suggest that the two ancientmaternal lineages, M31 and M32, in the Onge andthe Great Andamanese have evolved in theAndaman Islands independently and not derivedfrom the South and/or Southeast Asianpopulations. These lineages have been suggestedas probably isolated since the initial colonizationof the northern coastal areas of the Indian Oceanby anatomically modern humans, in the trail oftheir out-of-Africa migration ~ 50- 70 kya. Incontrast, the Nicobarese show a close geneticrelation to the populations of Southeast Asia,

suggesting their recent arrival from the east duringthe past 18 thousand years. Concurrent to this,Thangraj et al. (2006), based on autosomal STRloci, concluded that the Andaman Negritopopulations do not show particular affinities eitherto the African or Indian populations whereas theNicobarese show close affinities with the SoutheastAsian populations, suggesting their recentcolonization of the Islands as reflected by themtDNA data. Prasad et al. (2001) analyzed mtDNAhypervariable region 1 sequence data from 33Nicobarese Islanders and compared their mtDNAhaplotypes to those of neighboring East Asians,mainland and island Southeast Asians, Indians,Australian aborigines, Pacific Islanders, andAfricans. They found that the unique NicobaresemtDNA haplotypes were most closely related toSoutheast Asian Mon-Khamer speakingCambodian populations. They concluded that theNicobarese population is the result of westwardexpansion of the Southeast Asian populations.

Trivedi et al. (2006) analyzed the mitochon-drial, Y-chromosomal and autosomal gene poolsof contemporary Shompen, which belongs to MonKhmer linguistic subfamily of the Austro-Asiatics.Overall, as was the case with other tribes of theseislands, this tribe shows low genetic diversity.Mitochondrial DNA sequence analyses revealedthe presence of two haplo-groups of R lineage:

B5a, and a newly defined clade, R12. Y-chromo-somal analyses suggest predominant occurrenceof a single lineage, O-M95, which was found mostpredominantly in Mundari Austro-Asiatic tribesand Nicobarese as well as among the other Austro-Asiatics found across Asia. With the differenttypes of genetic markers analysed, the Shompenexhibits varying levels of genetic relatedness to

the Nicobarese, and to the other Austro-Asiatic

speakers of mainland India and Southeast Asia.Based on the analyses of wide array of YChromosome SNP and STR markers among a largenumber of Austro-Asiatic tribes, representingentire micro-geographic and linguistic variationamong them, Kumar et al. (2007) suggested thatthe Austro-Asiatic tribes of Andaman Nicobarislands were probably the descendents of Mon-Khmer populations from Southeast Asia, who inturn traced their origin from the Mundari popu-lations of mainland India. However, the datasuggest their colonization of Andaman andNicobar Islands at a much later point of time.

Using relatively ancient DNA retrieved frommuseum specimens mitochondrial DNA sequences

of 11 Andaman Islanders were obtained by Endicottet al. (2003) and the mtDNA data suggest long-termisolation of the Andamanese, extensive populationsubstructure, and/or two temporally distinctsettlements. They conclude that the Negritofeatures of the Andaman Islanders are due toconvergence rather than to common ancestry withAfricans. Further they claim that their data supportthe Southern route hypothesis, though Courdauxand Stoneking (2003) differ with this conclusionand opine that the southern route hypothesisshould await adequate genetic support.

EMERGING PICTURE

Most of the studies based on mtDNA varia-tion have reported genetic unity of Indianpopulations. The basic clustering of maternallineages has been reported to be not specific to aparticular language or caste (Mountain et al. 1995;Kivisild et al. 1999; Bamshad et al. 2001). Morethan 60% of the Indians have their maternal rootsin Indian specific branches of haplogroup M.Because of its great time depth and virtual absencein western Eurasians, it has been suggested thathaplogroup M was brought to Asia from EastAfrica along the southern route by earliestmigration wave of AMH ~ 60000 years ago

(Mountain et al. 1995; Kivisild et al. 1999, 2000;Quintana Murci et al. 1999; Sun et al. 2006).Haplotype U was found to connect westernEurasian and Indian populations. Both macroha-plogroup M and N suggest deep ancestry ofIndian population dating back to 40,000-60,000years (Metspalu et al. 2004 and Palanichamy et al.2004). More than one wave of migration of people


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bearing West Eurasian haplogroups from westAsia into India has been reported.

Cordaux et al. (2003) reported that mtDNAvariation indicated strong affinity of Indian tribaland caste groups to east Eurasians, whileBamshad et al. (2001) and Barnabas et al. (1996)reported that west Eurasian haplotypes werefound to represent about a quarter of Caste mtDNAhaplotypes. Baig et al. (2004), Kivisild et al. (2003),Cordaux et al. (2003), Roychoudhury et al. (2000),reported that both caste and tribal groups sharethe same maternal lineages. In contrast, Watkinset al. (1999) based on mtDNA 9bp deletion reporteddifferent origins for caste and tribal populations,whereas Kumar et al. (2006) inferred Asian andnon-Asian origins of MonKhmer and Mundari

groups of Austro-Asiatic tribes. Some of thestudies have reported correlation of social rankwith the mtDNA distances among the castepopulations (Thanseem et al. 2006; Sahoo andKashyap 2006). Relatively greater affinity of north-west Indian populations to West Eurasians hasalso been observed (Passarino et al. 1996a;Bamshad et al. 1996, 2001; Quintana-Murci 2004).High mtDNA diversity and deep coalescencedates (~56-63k ybp) suggest that Austo-Asiaticspeaking groups might be original inhabitants of

India (Kumar et al. 2006; Basu et al. 2003;Roychoudhuri et al. 2001; Kivisild et al. 1999).

Overall, thus, the studies based on mtDNAsuggest deep rooted maternal lineages for bothcaste and tribal populations and support singleinitial origin. The present population structuremight have therefore resulted from subsequentadmixture and drift. However, the estimatedamount of west Eurasian or East Eurasianhaplotype sharing of the different Indianpopulations has been vastly different amongdifferent studies. The mtDNA variation reportedin India is largely explained as due to differentlevel of admixture and genetic drift.

In contrast to mtDNA variation the conclu-sions based on Y-Chromosome variation have

been quite varied. Ramana et al. (2001), Thanseemet al. (2003), Cordaux et al. (2004b) reported thatthe patterns of variation based on frequencies ofsome haplogroups are distinct among castes andtribal groups. While Bamshad et al. (1998) andBhattacharya et al. (1999) reported very little orno paternal gene flow among Indian populations,Ramana et al. (2001) suggest possibility of malegene flow between tribal and caste populations.Concurrent to this, Kumar et al. (2006) observedthat Y-Chromosome variants are not localized

Table 2: Coalescence age for different haplotypes and populations in different studies in Indianpopulations

Diagnos tic Codi ng Coal escence Coalescence years Population Expansion times/Region Marker (ye ars ) (X 10 00 ) TMRCA (confidence interval )

M2 70,600 21,0001 Austro-Asiatic 56098 (51220-60975)2

M2a 48,300 20,1001 70.23 Dravidian 39024 (34146-43902)2

M2b 77.13 Tibeto-Burman 51220 (48780-53659)2

M3 24.03

M3a 17,300 7,4001 TMRCAM4a 19,200 9,0001 Munda 65,730 (25,442-132,230)5

M5* 46.33 Khasi 57,252 (27,644-92,201)5

M6 33,000 13,9001 Nicobarese 16,578 ( 4, 565-51,377)5

M6a 19,100 7,6001 Austro-Asiatc 68,098 (25,992-146,833)5

M6b 6,000 2,1001 92.53

M18 9,400 3,2001 41.13 Age estimate of M HaplogroupM25 19,400 7,2001

M33 43.73 South Asia 44600 33003

M35a 36.03 East Asia 69300 54003

M38 54.03 Oceania 73000 79003

M39 39.1

3

South East Asia 55700 7400

3

M40 38.63

M* 41.13 Coalescence age forMaharastrian populations

Total M 54.13

R2e 40,400 14,3001 M Total 45082 6414

R5 66,100 22,0001 U Total 25628 16244

R6 30,000 11,0001 R Total 45001 10394

1 Metspalu 2004, 2 Majumder 2001, 3 Sun et al. 2006, 4 Baig et al. 2004, 5 Kumar et al. 2007


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geographically and also suggest the possibilityof male gene flow. Kivisild et al. (2003), on theother hand, suggested ancient and shared geneticheritage of male lineages in India. Genetic affinitywith west Eurasian gene pool was found to becorrelated with caste rank by Bamshad et al. (1998)and Sahoo and Kashyap (2006). Bamshad et al.(2001) further suggested that this affinity with westEurasians is proportionate to caste rank. WhileMukherjee et al. (2001) placed North Indians bet-ween west Asian and Central Asian populations,Cordaux et al. (2004b) placed Indian castepopulations closer to Central Asian populations.On the other hand, while Bamshad et al. (2001)placed caste populations of southern Indian statescloser to East Europeans, Sahoo et al. (2006) and

Sengupata et al. (2006) suggest no recentadmixture in the Indian caste populations. Thisconclusion is similar to most of the mtDNA studies.However, Cordaux et al. (2004b) infer a relativelyrecent migration of Indo-European speakers toIndia lending support to the Aryan invasion/migration theory.

Y-Chromosome sharing between northeastIndia and South China is inferred as due toNeolithic expansion via northeast Indian corridor(Su et al. 2000; Basu et al. 2003). Kumar et al.(2007) on the other hand suggested migration ofAustro-Asiatic males from India to SoutheastAsia via northeast Indian corridor, as the missinggenetic link is evident in the form of Austro-Asiatic Khasi that were not genetically exploredearlier.

Autosomal markers have been used mostlyfor studying the genetic affinities among differentpopulations and are generally not used forestimating the time of common origin. The studiesbased on Autosomal markers have also providedsome contrasting results. Some studies whichfocused on populations in a small geographicalregion found that genetic distances are notcorrelated with geographical distance(Viswanathan et al. 2004; Reddy et al. 2005), andothers reported that they are correlated withgeographical distance and/or ethnic affiliation

(Kashayap et al. 2004; Kritika et al. 2006; Bamshadet al. 2001; Reddy et al. 2001a, 2001b). Whenpopulations were compared at broader level(Reddy et al.. 2005; Langstieh et al.. 2005; Majumderet al. 1999) the clusteres were formed consistentto geographic affiliation of the groups.Roychoudury et al. (2001), on the other hand,reported close affinity of the populations of similar

linguistic background, Basu et al. (2003) found notangible clustering based on social, geographicor linguistic criteria. Studies of Kivisild et al. (2003),Watkins et al. (2005) and Kashyap et al. (2006) onthe contrary suggest common ancestry of Indiancaste and tribal populations.

With the emergence of molecular genetictechniques the general expectation had been thatthe riddles of physical anthropology will besolved. Indeed, these techniques have beenextensively used to study human evolution andvariation and to trace the routes of migration ofthe humans from Out of Africa to the rest of theworld, in conjunction with the data from paleo-anthropology and archaeology. One of theadvantages of these studies has been that the

Time of Most Recent Common Ancestor(TMRCA) could be estimated using more robustassumptions in comparison to the traditionalmarkers. However, these studies have their shareof pitfalls as well; for example, the TMRCAestimated from quite a few studies have been foundto be less than the time estimated from the fossilor archeological finds. Nevertheless, at the globallevel, many of the finer details of major populationrelationships and routes of migration have beenelucidated with fair degree of confidence.

At micro-level, molecular anthropologicalstudies on Indian populations have indeed comeup with quite interesting but sometimes withcontrasting results. Some of the results likecommon and deep genetic heritage of Indiancaste and tribal populations have stronglycontradicted the previous hypothesis of recententry of Indo-European speakers in India. Manystudies have also come up with dates of commonancestry and/or for initial colonization of Indiansubcontinent as ~60,000 years which roughlycorresponds with the first wave of migration ofhumans out of Africa. Some of the studiessubstantiated the findings of classical markers,like the greater affinity of caste populations ofhigher social hierarchy to the Europeans and alsothat of geographically closer population aregenetically closer as well.

In spite of these interesting results, there havebeen quite contrasting conclusions from differentstudies. Contrasting conclusions on populationaffinities and coalescence dates from the commonancestors are reported in different studies. Table2 presents the age of coalescence for differenthaplogroups and populations from differentstudies. Although, the dates seem quite interes-


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ting, they are accompanied by very largeconfidence intervals which make the conclusionsequivocal. Also the same haplotype is assignedquite contrasting dates in different studies. Acritical apprisal of the literature makes one towonder what is going wrong. Are their some gravemethodological problems or is it because theIndian population structure is too complex to bedescribed in simple terms as different studies haveattempted to do? One striking aspect of thesemolecular anthropology studies is the fact thatvery often the sweeping conclusions are madewith inappropriate study frame, compounded byinadequate samples and sampling. Often thesampling details and/or population details werenot furnished and one is prompted to surmise if

the investigators really knew and/or care aboutthese aspects which are crucial in populationgenetics research. Sometimes, the samples usedfor the study does not even match the requirementof the hypothesis being tested. For example,including geographically and ethnically/linguis-tically disparate populations without even remotepossibility of exchange of genes, either currentlyor historically, to test the hypothesis of male geneflow between them is far from being a suitablestudy frame given that India offers immensepossibilities to find appropriate situations to testmany such hypotheses. Identification of suitablepopulation units has also been a problem in somestudies; populations groups as diverse as Hindispeaking, North Indian, etc have been used asunits of study. Quite a few studies lack properdescription of the populations investigated, whichis of great importance in such studies. One reviewin fact wrongly defines Scheduled caste (SC)population and then describes the tribal populationas most disadvantaged group in SC (Chaubey etal. 2006). One of the major reasons behind thesemishaps might be lack of anthropologicalinsights into Indian population structure, as manyof the papers have been written by people ofnon-Anthropology (especially Indian Anthro-pology) background. This may be the reason whywe find one of the studies describing the process

of Hypergamy as a process which has resulted insimilar maternal gene pools of the Indian popula-tion. The process of Hypergamy though descri-bed in religious text and other records has notbeen reported to be a commonly practiced by themasses to cause such systematic genetic patterns.

The importance of population based app-roach has been realized in the emerging fields of

Genetic Epidemiology and pharmacogeneticswhere the focus is on identifying genesassociated with complex diseases and in turn usethis information in individual and/or populationspecific treatment. Thus, a proper knowledge ofpopulation and/or population structure is crucialin all forms of molecular genetic research. Popu-lation based approach has been the hallmark ofanthropological research from the beginning.Anthropologists can thus make a major contri-bution in the emerging research fields of mole-cular genetics. Unfortunately anthropologistshave been marginalized because of the advent ofsophisticated and resource intensive techno-logies of modern genetics. It is highly imperativethat fruitful research can be conducted if mole-

cular biologists practicing anthropologicalgenetics work in mutual collaboration withbiological anthropologists.

ACKNOWLEDGEMENT

The authors are thankful to the Director,Indian Statistical Institute, Kolkata and Chairman,Mahathma Gandhi National Institute of Researchand Social Action (MGNIRSA), Hyderabad forlogistic support.

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15 microsatellites of four caste groups of the easternIndian state, Bihar. Ann Hum Biol, 30: 570-578.

Baig MM, Khan AA, Kulkarni KM 2004. MitochondrialDNA diversity in tribal and caste groups ofMaharashtra (India) and its implication on theirgenetic origins. Ann Hum Genet, 68: 453-460.

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