Multiple origins of the mtDNA 9-bp deletion in populations of South India

The origins and genetic affinities of the more than 500 tribal populations living in South Asia are widely disputed. This may reflect differential contributions that continental populations have made to tribal groups in South Asia. We assayed for the presence of the intergenic COII/tRNALys 9-bp deletion in human mtDNA in 646 individuals from 12 caste and 14 tribal populations of South India and compared them to individuals from Africa, Europe, and Asia. The 9-bp deletion is observed in four South Indian tribal populations, the Irula, Yanadi, Siddi, and Maria Gond, and in the Nicobarese. Length polymorphisms of the 9-bp motif are present in the Santal, Khonda Dora, and Jalari, all of whom live in a circumscribed region on the eastern Indian coast. Phylogenetic analyses of mtDNA control region sequence from individuals with the 9-bp deletion indicate that it has arisen independently in some Indian tribal populations. Other 9-bp deletion haplotypes are likely to be of Asian and African origin, implying multiple origins of the 9-bp deletion in South India. These results demonstrate varying genetic affinities of different South Indian tribes to continental populations and underscore the complex histories of the tribal populations living in South Asia. Am J Phys Anthropol 109:147–158, 1999. © 1999 Wiley-Liss, Inc.     

Genetic distances among the five tribal populations of Andhra, Pradesh, South India.

In this paper, data on genetic distances among five tribal populations ae given. Among the five tribes, Koya Dora, Raj Gond and Naikpod are autochthonous populations of the Deccan plateau whereas the other two groups, Pardhan and Lambadi are migrants. Kova Doras were sampled from five distant localities. Genetic markers typed are: A1A2B0, Rho(D) blood group systems glucose-6-phosphate dehydrogenase deficiency, transferrin, haptoglobin, groupspecific component, haemoglobin, colour-vision deficiency and tastability to P. T. C. Using frequency data for the above nine genetic loci, genetic distances between the five endogamous tribes, and between the five groups of Koya Dora are calculated by adopting the statistical method of Edwards (1971). While genetic distances between Koya Dora, Raj Gond and Lambadi are minimal, the genetic distance between Pardhans and other tribal groups is maximum. Naikpods occupy an intermediate position. The closeness of Lambadi with Koya Dora and RAJ Gond can be regarded as coincidental. Interestingly, the differences in the genetic distance values between five Koya Dora groups are as great as the differences between the five endogamous tribal populations tested for the same loci. Genetic affinities of these tribal populations are discussed in relation to their ethnic origin migration and geographical isolation.     

Genetic affinities of the central Indian tribal populations

Background

The central Indian state Madhya Pradesh is often called as ‘heart of India’ and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers.

Methodology/Principal Findings

Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results.

Conclusions/Significance

Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn''t unequivocally follow the genetic footprints.     

Microsatellite diversity reveals the interplay of language and geography in shaping genetic differentiation of diverse Proto-Australoid populations of west-central India

Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations.     

Distribution of A1A2BO and Rho (D) blood groups in tribal populations of Andhra Pradesh, South India.

The paper reports the distribution of A1A2BO and Rho (D) blood groups among five tribal populations, Koya Dora, Raj Gond, Naikpod, Pardhan and Lambadi from three districts of Andhra Pradesh, South India. Blood samples from a total of 1090 unrelated individuals were tested. Koya Doras were, however, sampled from five distant localities to find out intratribal variation, if any. In A1A2BO blood group system the combined frequencies of "P1" and "P2" among the five Koya Groups always exceeded the frequency of "q", a characteristic feature of many tribal populations of Andhra Pradesh. However, among Raj Gond, Naikpod, Pardhan and Lambadi tribes the frequency of "q" is higher than "p" with the maximum in Pardhans. The frequency of "r" is always higher than the combined frequencies of "p1" and "p2" except in Raj Gonds. The higher frequency of "q" over "p" among Naikpod, Pardhan and Lambadi tribes is indicative of a tendency towards the distribution pattern found in North India. A few Rh negative persons were detected only in Koya Dora, Raj Gond and Lambadis indicating that the allele r (cde) is present in these populations, although in a low frequency.     

Peopling of South Asia: investigating the caste-tribe continuum in India

In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000-60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations.     

Molecular genetic diversity in 5 populations of Madhya Pradesh, India

This paper presents data on the distribution of 3 amplified fragment length polymorphisms (D1S80, APOB, and YNZ22) in 5 populations of Central India. Using the polymerase chain reaction technique, 3 caste (Brahmin, Khatri, and Dhimer) and 2 tribal (Gond and Baiga) populations were studied for the 3 loci. The allelic variations observed in the caste populations are compatible with those of many Caucasian populations, but the caste populations showed significant overall and interpopulation variability within the region. D1S80 allele *24 varied from 32% (Dhimers) to 42% (Brahmins). Allele *18 was not observed in Baiga tribal populations, but in caste populations it varied from 11% (Dhimers) to 24% (Brahmins). Both tribal populations showed higher frequencies of allele *31 (17%-18%). For APOB, caste populations again showed bimodal distribution of alleles *35 and *37, but in tribal populations higher allele numbers (*47, *49) were also frequent. For YNZ22, extensive variation was observed for all populations studied. Allele *4 was the most common in caste populations, while alleles *2, *7, and *10 were prominent in tribal populations. The level of gene differentiation is not very high for the 3 systems studied in the 5 populations. Overall, allele frequency distribution, heterozygosity, and genetic diversity analysis show that the genetic diversity observed is socially and geographically structured.     

A microsatellite study to disentangle the ambiguity of linguistic,geographic, ethnic and genetic influences on tribes of India to get a better clarity of the antiquity and peopling of South Asia

An understanding of the genetic affinity and the past history of the tribal populations of India requires the untangling of the confounding influences of language, ethnicity, and geography on the extant diverse tribes. The present study examines the genetic relationship of linguistically (Dravidian, Austro‐Asiatic, and Tibeto‐Burman) and ethnically (Australian and East Asian) diverse tribal populations (46) inhabiting different regions of the Indian subcontinent. For the purpose, we have utilized the published data on allele frequency of 15 autosomal STR loci of our study on six Adi sub‐tribes of Arunachal Pradesh and compared the same with the reported allele frequency data, for nine common autosomal STR loci, of 40 other tribes. Phylogenetic and principal component analyses exhibit geography based clustering of Tibeto‐Burman speakers and separation of the Mundari and Mon‐Khmer speaking Austro‐Asiatic populations. The combined analyses of all 46 populations show clustering of the groups belonging to same ethnicity and inhabiting contiguous geographic regions, irrespective of their different languages. These results help us to reconstruct and understand three plausible scenarios of the antiquity of Indian tribal populations: the Dravidian and Austro‐Asiatic (Mundari) tribes were possibly derived from common early settlers; the Tibeto‐Burman tribes possibly belonged to a different ancestry and the Mon‐Khmer speaking Austro‐Asiatic populations share a common ancestry with some of the Tibeto‐Burman speakers. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.     

Tracking the genetic imprints of lost Jewish tribes among the gene pool of Kuki-Chin-Mizo population of India

Background  

The Kuki-Chin-Mizo population comprising traditionally endogamous tribal groups residing in the state of Mizoram, India claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians. To ascertain their oral history, we analysed DNA markers comprising 15 autosomal microsatellite markers, 5 biallelic and 20 microsatellite markers on Y-chromosome and the maternally inherited mitochondrial DNA sequence variations on 414 individuals belonging to 5 tribal communities from Mizoram (Hmar, Kuki, Mara, Lai and Lusei). The genetic profiles obtained were compared either with populations sharing Jewish ancestry or with local populations along the probable route of migration of the Jewish ancestry claimant Mizoram tribes.     

A genetic survey in the Bhil tribe of Madhya Pradesh,Central India

Examination of blood groups, plasma proteins and red cell enzyme types (23 loci), in a sample of 145 Bhils, a tribal group of Madhya Pradesh, Central India, demonstrates their genetic uniqueness. They differ in a number of systems from the nearby nontribal groups both of Hindus and Muslims. The results suggest that the Bhil frequencies include vestiges of the ancestral genepool of a more widespread aboriginal population whose influence is detectable in the gene frequencies of some other populations in India.     

Genetic studies on Gadaba: a tribal population of Andhra Pradesh, India.

Blood samples were collected from Gadaba, a tribal population of Andhra Pradesh, South India, in order to examine the distribution of blood groups, red cell enzymes and the gammaglobulin polymorphism. Out of 20 genetic markers studied seven protein loci exhibited monomorphism. Surprisingly a case of a rare homozygous variant and twenty-one heterozygous variants at the phosphogluconate dehydrogenase locus (6-PGD), six variants at the phosphohexose isomerase locus (PHI) and a single case of phosphoglucomutase locus 1 (PGM 1) variant were observed. Further, the tribal populations of South India reveal higher frequencies of rare variants than the caste populations. However, the presence of rare variants that are phenotypically neutral may be plausibly due to their high selective value.     

Phylogeography of mitochondrial DNA and Y-chromosome haplogroups reveal asymmetric gene flow in populations of Eastern India

Polymorphisms in mitochondrial (mt) DNA and Y-chromosomes of seven socially and linguistically diverse castes and tribes of Eastern India were examined to determine their genetic relationships, their origin, and the influence of demographic factors on population structure. Samples from the Orissa Brahmin, Karan, Khandayat, Gope, Juang, Saora, and Paroja were analyzed for mtDNA hypervariable sequence (HVS) I and II, eight Y-chromosome short tandem repeats (Y-STRs), and lineage-defining mutations diagnostic for Indian- and Eurasian-specific haplogroups. Our results reveal that haplotype diversity and mean pairwise differences (MPD) was higher in caste groups of the region (>0.998, for both systems) compared to tribes (0.917-0.996 for Y-STRs, and 0.958-0.988 for mtDNA haplotypes). The majority of paternal lineages belong to the R1a1, O2a, and H haplogroups (62.7%), while 73.2% of maternal lineages comprise the Indian-specific M*, M5, M30, and R* mtDNA haplogroups, with a sporadic occurrence of West Eurasian lineages. Our study reveals that Orissa Brahmins (a higher caste population) have a genetic affinity with Indo-European speakers of Eastern Europe, although the Y-chromosome data show that the genetic distances of populations are not correlated to their position in the caste hierarchy. The high frequency of the O2a haplogroup and absence of East Asian-specific mtDNA lineages in the Juang and Saora suggest that a migration of Austro-Asiatic tribes to mainland India was exclusively male-mediated which occurred during the demographic expansion of Neolithic farmers in southern China. The phylogeographic analysis of mtDNA and Y-chromosomes revealed varied ancestral sources for the diverse genetic components of the populations of Eastern India.     

Independent origins of Indian caste and tribal paternal lineages

The origins of the nearly one billion people inhabiting the Indian subcontinent and following the customs of the Hindu caste system are controversial: are they largely derived from Indian local populations (i.e. tribal groups) or from recent immigrants to India? Archaeological and linguistic evidence support the latter hypothesis, whereas recent genetic data seem to favor the former hypothesis. Here, we analyze the most extensive dataset of Indian caste and tribal Y chromosomes to date. We find that caste and tribal groups differ significantly in their haplogroup frequency distributions; caste groups are homogeneous for Y chromosome variation and more closely related to each other and to central Asian groups than to Indian tribal or any other Eurasian groups. We conclude that paternal lineages of Indian caste groups are primarily descended from Indo-European speakers who migrated from central Asia approximately 3,500 years ago. Conversely, paternal lineages of tribal groups are predominantly derived from the original Indian gene pool. We also provide evidence for bidirectional male gene flow between caste and tribal groups. In comparison, caste and tribal groups are homogeneous with respect to mitochondrial DNA variation, which may reflect the sociocultural characteristics of the Indian caste society.     

Microsatellite diversity among the primitive tribes of India

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.     

Brief communication: Allelic and haplotypic structure at the DRD2 locus among five North Indian caste populations

The dopamine D2 receptor (DRD2) gene, with its known human‐specific derived alleles that can facilitate haplotype reconstruction, presents an important locus for anthropological studies. The three sites (TaqIA, TaqIB, and TaqID) of the DRD2 gene are widely studied in various world populations. However, no work has been previously published on DRD2 gene polymorphisms among North Indian populations. Thus, the present study attempts to understand the genetic structure of North Indian upper caste populations using the allele and haplotype frequencies and distribution patterns of the three TaqI sites of the DRD2 gene. Two hundred forty‐six blood samples were collected from five upper caste populations of Himachal Pradesh (Brahmin, Rajput and Jat) and Delhi (Aggarwal and Sindhi), and analysis was performed using standard protocols. All three sites were found to be polymorphic in all five of the studied populations. Uniform allele frequency distribution patterns, low heterozygosity values, the sharing of five common haplotypes, and the absence of two of the eight possible haplotypes observed in this study suggest a genetic proximity among the selected populations. The results also indicate a major genetic contribution from Eurasia to North Indian upper castes, apart from the common genetic unity of Indian populations. The study also demonstrates a greater genetic inflow among North Indian caste populations than is observed among South Indian caste and tribal populations. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Population structure of indigenous inhabitants of Arabia

Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world’s major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world’s major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.     

A sero-biochemical genetic study of Jalari and Brahmin caste populations of Andhra Pradesh, India

Blood specimens from Jalari and Brahmin caste populations of Andhra Pradesh, India, were examined for blood groups, red cell enzymes, and serum proteins. Of 33 genetic loci studied, 16 were observed to be invariant among both the castes, while common polymorphism or rare variants were observed in one or both populations for the other loci. Three rare heterozygotes at the phosphoglucoisomerase locus, two different peptidase A variants occurring once each and single cases of rare 6-phosphogluconate dehydrogenase and transferrin variants were recorded. Also a few cases of hemoglobin AS and anhaptoglobinemia were observed. The difference in rare variants between the two castes is conspicuous but large differences in their gene frequencies at the polymorphic loci were not observed. It is pointed out that the frequency of rare variants in the tribal and caste populations of Southern India appears to be higher than observed in temperate-dwelling civilized populations.     

Fertility and mortality differentials among selected tribal population groups of north-western and eastern India

Selection potential based on differential fertility and mortality has been computed for six tribal groups inhabiting different geo-climatic conditions, namely: Sahariya, Mina and Bhil of the State of Rajasthan, north-western India, and Munda, Santal and Lodha of the State of West Bengal, eastern India. Irrespective of the methodology, the total index of selection was found to be highest among Lodhas (0.668), followed by Sahariyas (0.524), Santals (0.462), Bhils (0.386), Mundas (0.353) and Minas (0.334). Incidentally, Lodha and Sahariya are two of the seventy-four notified primitive tribal groups of India, and these two study populations show the highest index of total selection, mainly because of a higher embryonic and postnatal mortality. The relative contribution of the fertility component to the index of total selection is higher than the corresponding mortality component in all tribal groups. The analysis of postnatal mortality components indicates that childhood mortality constitutes the bulk of postnatal mortality, suggesting that children under 5 years need better health care in these tribal groups.     

Anthropometric and genetic distance between Gonds of Central India

A morphological and genetic study was undertaken on five Gondi-speaking populations of Central India (Andhra Pradesh and Maharashtra States). There has been no systematic biological study on this large Dravidian-speaking tribal group, 4 million in number, amounting to 13% of the total tribal population of India. Data was collected on 16 anthropometric measurements and seven genetic markers (blood groups, hemoglobin, G6PD and plasma protein polymorphisms) on the Raj Gonds, Kolams, Manne, Koyas and Plains Maria Gonds. Various genetic distance measures such as Mahalanobis's D2 and Nei's and Sanghvi's measures and cluster analysis techniques were used to determine the relationship between these groups based on anthropometrics and genetic variables. The statistical analysis revealed the Gonds to be a heterogenous group in both morphology and genetic characteristics. The morphological and genetic distances between these five groups when projected graphically revealed that the spatial distribution of these Gonds generally corresponds to their present geographical distribution. However, the actual relationships among each of the Gond populations show differences when based on these two biological variables, the possible reasons for this being discussed in the paper. The emphasis of this study is on the importance of geographical proximity in producing morphological and genetic similarity between populations, brought about by a short distance as well as similar geographical factors (such as soil, terrain, flora, etc.) drawing these populations together under a common ecocultural umbrella.