The occurrence of DChi and new D and B transferrin variants among caste groups of Andhra Pradesh (S. India)

Summary Serum samples from a total of 862 unrelated individuals belonging to seven Hindu endogamous caste groups residing in Hyderabad and Warangal cities of Andhra Pradesh were examined for electrophoretic variation of transferrin (Tf). In four caste groups, namely, Brahmin, Vysya, Padmashali, and Kapu, the Mongoloid genetic marker D_Chi was found, with polymorphic frequencies in Brahmin and Vysya groups. The two new D variants found in individuals of Madiga and Mudiraj castes were designated as D_Madiga and D_Mudiraj. Similarly, two new B variants found in individuals of Goldsmith and Madiga castes were designated as B_Goldsmith and B_Madiga, respectively. These findings suggest a widespread transferrin variation in caste groups of Andhra Pradesh and in the tribal populations of this region.     

Molecular insight into the genesis of ranked caste populations of western India based upon polymorphisms across non-recombinant and recombinant regions in genome

Background

Large-scale trade and cultural contacts between coastal populations of western India and Western-Eurasians paved for extensive immigration and genesis of wide spectrum of admixed gene pool. To trace admixture and genesis of caste populations of western India, we have examined polymorphisms across non-recombining 20 Y-SNPs, 20 Y-STRs, 18 mtDNA diagnostic sites, HVS-1 plus HVS-2 regions; and recombining 15 highly polymorphic autosomal STRs in four predominant caste populations- upper-ranking Desasth-brahmin and Chitpavan-brahmin; a middle-ranking Kshtriya Maratha; and a lower-rank peasant Dhangar.

Results

The generated genomic data was compared with putative parental populations- Central Asians, West Asians and Europeans using AMOVA, PC plot, and admixture estimates. Overall, disparate uniparental ancestries, and l.1% GST value for biparental markers among four studied caste populations linked well with their exchequer demographic histories. Marathi-speaking ancient Desasth-brahmin shows substantial admixture from Central Asian males but Paleolithic maternal component support their Scytho-Dravidian origin. Chitpavanbrahmin demonstrates younger maternal component and substantial paternal gene flow from West Asia, thus giving credence to their recent Irano-Scythian ancestry from Mediterranean or Turkey, which correlated well with European-looking features of this caste. This also explains their untraceable ethno-history before 1000 years, brahminization event and later amalgamation by Maratha. The widespread Palaeolithic mtDNA haplogroups in Maratha and Dhangar highlight their shared Proto-Asian ancestries. Maratha males harboured Anatolianderived J2 lineage corroborating the blending of farming communities. Dhangar heterogeneity is ascribable to predominantly South-Asian males and West-Eurasian females.

Conclusions

The genomic data-sets of this study provide ample genomic evidences of diverse origins of four ranked castes and synchronization of caste stratification with asymmetrical gene flows from Indo-European migration during Upper Paleolithic, Neolithic, and later dates. However, subsequent gene flows among these castes living in geographical proximity, have diminished significant genetic differentiation as indicated by AMOVA and structure.     

Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data

Genetic, ethnographic, and historical evidence suggests that the Hindu castes have been highly endogamous for several thousand years and that, when movement between castes does occur, it typically consists of females joining castes of higher social status. However, little is known about migration rates in these populations or the extent to which migration occurs between caste groups of low, middle, and high social status. To investigate these aspects of migration, we analyzed the largest collection of genetic markers collected to date in Hindu caste populations. These data included 45 newly typed autosomal short tandem repeat polymorphisms (STRPs), 411 bp of mitochondrial DNA sequence, and 43 Y-chromosomal single-nucleotide polymorphisms that were assayed in more than 200 individuals of known caste status sampled in Andrah Pradesh, in South India. Application of recently developed likelihood-based analyses to this dataset enabled us to obtain genetically derived estimates of intercaste migration rates. STRPs indicated migration rates of 1–2% per generation between high-, middle-, and low-status caste groups. We also found support for the hypothesis that rates of gene flow differ between maternally and paternally inherited genes. Migration rates were substantially higher in maternally than in paternally inherited markers. In addition, while prevailing patterns of migration involved movement between castes of similar rank, paternally inherited markers in the low-status castes were most likely to move into high-status castes. Our findings support earlier evidence that the caste system has been a significant, long-term source of population structuring in South Indian Hindu populations, and that patterns of migration differ between males and females.     

Trends in consanguinity in South India

This study uses data from the 1992-93 National Family Health Survey to assess trends in consanguinity in the South Indian states of Andhra Pradesh, Karnataka, Kerala and Tamil Nadu. In Kerala, the frequency of consanguineous marriages is very low and one type of preferred marriage of the Dravidian marriage system uncle niece marriage--is conspicuously absent. In the other states of South India, consanguinity and the coefficient of inbreeding are high. While no change in consanguinity is observed during the past three to four decades in Karnataka, a definite decline is observed in Andhra Pradesh and Tamil Nadu. Due to recent changes in the demographic and social situation in these states, this decline in consanguinity is likely to continue.     

C3 types in some endogamous populations of Andhra Pradesh

The distribution of C3 phenotypes was studied in some endogamous caste groups of Andhra Pradesh, South India. The C3F allele was found to be at a low frequency and comparable to those found in castes of other regions on the Indian subcontinent.     

Patterns of social and geographical distribution of transferrin subtype polymorphism in India

Transferrin subtypes have been determined by isoelectric focussing of sera from 536 individuals belonging to 9 South Indian populations: Vaidic Brahmins and Vaysya from Andhra Pradesh; Havik Brahmin, Lingayat and Jenu Kuruba from Karnataka; Namboodri Brahmin, Ezhava and Urali from Kerala; and Kallan from Tamil Nadu. C1 and C2 alleles are present in all the populations, whereas C4 is totally lacking and D1 occurs only in 3 populations. The highest frequency of C1 gene (0.814) is found in Havik Brahmins while C2 shows highest incidence among the tribe Urali. C1 occurs in slightly higher frequencies among the Hindu castes (range 0.724-0.814) than the tribal populations (range 0.698-0.703). C2 is more common in the tribes (range 0.281-0.290) compared to the castes (range 0.186-0.269). Strikingly the C3 allele is absent in all the 3 Brahmin samples but is present in 3 non-Brahmin castes and a tribal population. An examination of all the available data on Tf subtypes in India reveals no clear-cut decreasing north-south gradient in C1 gene as suggested by Walter et al. (1983). Interestingly, however, the same is observed when tribal populations are considered separately. Among the castes, in fact, the opposite trend (increasing north to south) is seen. It is suggested that the basic postulate of Walter et al. (1983) will hold good only among the tribal populations of the country. The data do not fully support the observation of Kamboh and Kirk (1983) that C3 is a specific marker of European (Caucasian) populations.     

Genetic admixture studies on four <Emphasis Type="Italic">in situ</Emphasis> evolved,two migrant and twenty-one ethnic populations of Tamil Nadu,south India

We analysed the genetic structure of ~1000 samples representing 27 ethnic groups settled in Tamil Nadu, south India, derived from two linguistic families (Dravidians and Indo–Europeans) representing four religious groups (Hinduism, Islam, Christianity and Jainism) using 11 mtDNA markers. Out of 27 ethnic groups, four are in situ populations (Anglo-Indian, Labbai Muslim, Nadar Christian and south Indian Jain) and two are migrants (Gypsy and north Indian Jain) from north India to Tamil Nadu, and 21 are native ethnic groups. Six of the markers we used were monomorphic (HaeIII663, HpaI3592, AluI5176, AluI7025, AluI13262, 9-bp deletion) and five markers were polymorphic (DdeI10394, AluI10397, HinfI12308, HincII13259 and HaeIII16517). Haplogroup frequencies, genetic affinities and admixture analysis are based on the genotype data of polymorphic markers observed in these populations. Haplogroup frequencies indicate that various ethnic groups entered Tamil Nadu during different time periods. Genetic affinities and admixture estimates revealed that the ethnic groups possessing advanced knowledge of farming cluster in a branch (C), and could be the late arrived settlers as agriculture, was introduced to this region at about 5 to 3 thousand years ago. In situ ethnic groups appear to have arisen at various times as a result of the prevailing dominant socio-cultural forces. Hierarchical Hindu caste system created many ethnic groups in the history of its existence; some of them became isolated for considerable period of time. Over all, among Tamil ethnic groups, in spite of caste systems’ rigidity, built in flexibility in the system in the form of hypergamy and hypogamy had allowed maternal gene flow between them.     

Genetic serum protein markers (PH,GC, PI) in two South Indian caste populations

The results of HP, GC and PI typings on two caste populations (Relli-I: fruit vendors, Relli-II: scavengers) from Andhra Pradesh (South India) are reported and compared with data obtained on other Indian population samples.     

Book Review

To study the variability and to identify the species of Begomovirus associated with yellow mosaic disease of blackgram in Andhra Pradesh, India, infected blackgram samples were collected from six districts belonging to three regions of Andhra Pradesh. The total DNA was isolated by modified CTAB method and amplified with coat protein gene-specific primers (RHA-F and AC abut) resulting in 900?bp gene product. The PCR products were cloned, sequenced and deposited in GenBank. The sequence analysis of six clones showed that the size of amplified CP gene of YMV was 920?bp. Based on nucleotide sequence identity of six isolates representing three regions of Andhra Pradesh, the isolates from Rayalaseema and Telangana region are the same variant of YMV (>99.5% identity) and isolate from coastal Andhra is another variant of YMV (>95.4%) when compared with other region isolates. Comparison of CP gene sequence of YMV-TPT isolate with 27 other isolates in database revealed more than 93.2 and 86.2% identity with MYMIV isolates and less than 80 and 64% identity with MYMY isolates that originate from Indian sub-continent and South-East Asia at nucleotide and amino acid level, respectively. Phylogenetic tree based on CP gene sequences of six isolates with other isolates from GenBank formed unique cluster with MYMIV. Hence the YMV infecting blackgram in Andhra Pradesh is caused by MYMIV rather than MYMY as reported in Tamil Nadu which is adjoining state in southern India.     

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.     

The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data

We report a comparison of worldwide genetic variation among 255 individuals by using autosomal, mitochondrial, and Y-chromosome polymorphisms. Variation is assessed by use of 30 autosomal restriction-site polymorphisms (RSPs), 60 autosomal short-tandem-repeat polymorphisms (STRPs), 13 Alu-insertion polymorphisms and one LINE-1 element, 611 bp of mitochondrial control-region sequence, and 10 Y-chromosome polymorphisms. Analysis of these data reveals substantial congruity among this diverse array of genetic systems. With the exception of the autosomal RSPs, in which an ascertainment bias exists, all systems show greater gene diversity in Africans than in either Europeans or Asians. Africans also have the largest total number of alleles, as well as the largest number of unique alleles, for most systems. GST values are 11%-18% for the autosomal systems and are two to three times higher for the mtDNA sequence and Y-chromosome RSPs. This difference is expected because of the lower effective population size of mtDNA and Y chromosomes. A lower value is seen for Y-chromosome STRs, reflecting a relative lack of continental population structure, as a result of rapid mutation and genetic drift. Africa has higher GST values than does either Europe or Asia for all systems except the Y-chromosome STRs and Alus. All systems except the Y-chromosome STRs show less variation between populations within continents than between continents. These results are reassuring in their consistency and offer broad support for an African origin of modern human populations.     

Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.     

PGM1 subtype polymorphism in 14 endogamous Dravidian-speaking populations of South India

Red cell hemolysates from 1,004 persons belonging to 14 population groups drawn from four South Indian states, Andhra Pradesh, Tamil Nadu, Karnataka, and Kerala, were tested for PGM1 subtypes. The groups are characterized by a high frequency of phenotype 1+1+ (range 36.98-71.64%) and the allele 1+ (range 60-79%). The groups exhibit marked heterogeneity for PGM1 locus. The results show a clear demarcation between tribes and Brahmin groups.     

Genomic diversity at thirteen short tandem repeat loci in a substructured caste population, Golla, of southern Andhra Pradesh, India.

Genomic diversity based on 13 short tandem repeat (STR) loci was studied in seven population groups of a substructured Golla caste from Chittoor district in southern Andhra Pradesh, India. These groups are traditionally pastoral, culturally homogeneous, and strictly endogamous. Blood samples were drawn from 317 individuals from 30 Golla villages. The 13 STR loci analyzed in five standard multiplex polymerase chain reactions were: (1) CSF1R, TH01, and PLA2A; (2) F13A1, CYP19, and LPL; (3) D21S1446 and D21S1435; (4) D20S481, D20S473, and D20S604; and (5) D5S1453 and D6S1006. The average heterozygosity was found to be low among the Golla subgroups (0.64-0.70) in comparison to that of groups at the upper levels of the hierarchy. The coefficient of gene differentiation was found to be moderate (average GST = 0.031; range between 0.018 and 0.049 among the loci) when compared to that observed for a similar class of markers among populations with relatively higher levels of hierarchy, for example, among castes. It is, however, much higher when compared to the average observed for Indian caste and tribal populations, based on classical markers. Genetic distance measures revealed clusters of populations that are consistent with the known ethnohistorical and geographical backgrounds of the groups. We claim that these hypervariable markers are quite useful in understanding the process of substructuring within the Indian castes, leading to the formation of smaller breeding isolates, the basic Mendelian units within which microevolutionary forces operate.     

Role of Community Group Exposure in Reducing Sexually Transmitted Infection-Related Risk among Female Sex Workers in India

Background

Empowering female sex workers (FSWs) to address structural barriers and forming community groups (CGs) through community mobilization are seen as essential components of HIV prevention programs in India. Taking the membership of a CG as an exposure intervention, we hypothesized whether participation in a CG lead to reduced sexually transmitted infections (STIs) and increased treatment-seeking behavior among FSWs in three selected states of India — Andhra Pradesh, Maharashtra and Tamil Nadu.

Methods and Findings

The propensity score matching (PSM) approach examined the effect of CG membership, as against no membership, on STI-related risk, described as selected outcome measures — presence of any STI, self-reported STI symptoms, and treatment-seeking behavior among FSWs. A cross sectional bio-behavioral survey was administered in 2009–2010 and covered 7,806 FSWs through two-stage probability-based conventional and time location cluster sampling in 23 administrative districts of Andhra Pradesh, Maharashtra and Tamil Nadu. Only 2,939 FSWs were reported to be members of a CG and among them 4.5% had any STIs. A majority of FSWs were aged above 24 years (86.4%), had ever been married (73%), operated from a public place for solicitation (81.5%), and had ever received HIV test results (75.6%). The average effect of CG exposure was reduction in STI prevalence by 4%, while self-reported STI symptom treatment-seeking behavior increased by 13.7%.

Conclusion

FSWs who were exposed to a CG were at a substantially lower risk of STIs than those who were unexposed. The FSWs exposed to a CG had a higher chance of seeking STI treatment from public and private health facilities. Collectivization related challenges must be overcome to provide access to tailored STI prevention and care services.     

Correlates of female sterilization regret in the southern states of India

This study analyses factors associated with the incidence of sterilization regret in the four south Indian states of Andhra Pradesh, Karnataka, Kerala and Tamil Nadu. Using data from the National Family Health Surveys, in all four states the incidence of regret was found to be less than 10% and the factors significantly associated with it were child loss experience and quality of services. Hence, there is a need to improve the quality of services, both in terms of counselling and service provision, and women need to be counselled about the permanent nature of sterilization in order to avoid future regret.     

The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations

Two tribal groups from southern India--the Chenchus and Koyas--were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup. Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools.     

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.     

Molecular insight into the genesis of ranked caste populations of western India based upon polymorphisms across non-recombinant and recombinant regions in genome

Background  

Large-scale trade and cultural contacts between coastal populations of western India and Western-Eurasians paved for extensive immigration and genesis of wide spectrum of admixed gene pool. To trace admixture and genesis of caste populations of western India, we have examined polymorphisms across non-recombining 20 Y-SNPs, 20 Y-STRs, 18 mtDNA diagnostic sites, HVS-1 plus HVS-2 regions; and recombining 15 highly polymorphic autosomal STRs in four predominant caste populations- upper-ranking Desasth-brahmin and Chitpavan-brahmin; a middle-ranking Kshtriya Maratha; and a lower-rank peasant Dhangar.     

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.