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.     

Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations

Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.     

Red cell enzyme polymorphism: Gene differentiation in three populations of Maharashtra,India

Blood samples of 1,266 individuals were collected from three caste populations; Nava Budha (Mahar), Maratha, and a mixed group of Scheduled castes from each of three districts of Maharashtra, Nagpur, Akola, and Thane. The samples were tested for 12 enzyme systems, viz., AcPh, AK, CA-I, CA-II, Est-D, LDH, MDH, Oxidase, PGM-1, PGM-2, 6-PGD, and PHI. The gene frequencies of these loci are within the ranges observed among the Indian populations so far studied. The total differences in gene frequencies for each polymorphic locus was partitioned into three components, i.e., the differences between caste populations, the differences between regions, and the differences due to interaction between caste populations and regions. The results show that besides caste variation for two loci, Est-D and PGM-1, the gene frequencies for AK, Est-D, and G-6PD loci have different geographical distributions.     

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.     

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.     

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.     

Extreme genetic differences between queens and workers in hybridizing Pogonomyrmex harvester ants

The process of reproductive caste determination in eusocial insect colonies is generally understood to be mediated by environmental, rather than genetic factors. We present data demonstrating unexpected genetic differences between reproductive castes in a variant of the rough harvester ant, Pogonomyrmex rugosus var. fuscatus. Across multiple loci, queens were consistently more homozygous than expected, while workers were more heterozygous. Adult colony queens were divided into two highly divergent genetic groups, indicating the presence of two cryptic species, rather than a single population. The observed genetic differences between castes reflect differential representation of heterospecific and conspecific patrilines in these offspring groups. All workers were hybrids; by contrast, winged queens were nearly all pure-species. The complete lack of pure-species workers indicates a loss of worker potential in pure-species female offspring. Hybrids appear to be bipotential, but do not normally develop into reproductives because they are displaced by pure-species females in the reproductive pool. Genetic differences between reproductive castes are expected to be rare in non-hybridizing populations, but within hybrid zones they may be evolutionarily stable and thus much more likely to occur.     

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.     

Y-chromosomal insights into the genetic impact of the caste system in India

The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Tatiana Zerjal and Arpita Pandya contributed equally to this work.     

Gene differentiation among the Dhangar caste-cluster of Maharashtra, India

Genetic differentiation among the 22 Dhangar castes of Maharashtra, India, is studied using data on several polymorphic serological and biochemical loci employing Nei's distance measures. The intercaste genetic distances and the coefficient of gene diversity among these caste groups are found to be rather small. The relationship between gene identity and geographic distance is also studied empirically from the gene frequency data. All these analyses indicate that genetic differentiation among the Dhangar castes is at its very early stage only. It is also suggested that these caste groups probably originated from a common stock and are in the process of differentiation by fission with very little intercaste migration in the recent past.     

A population genetic study of the Vania Soni in Western India.

A total of 267 blood samples from persons belonging to the Shrimali Vania Soni caste group in Gujarat State, Western India have been analyzed for 6 blood group, 4 serum protein and 19 red cell enzyme systems, for haemoglobin and beta-thalassaemia and for red-green colour blindness. A number of rare genetic variants were detected, including a unique electrophoretically fast variant of superoxide dismutase. Genetic distance comparisons with other caste groups in Gujarat State show that Vania Soni from Surat are a distinctive group clustering with another subdivision of the Vania. The remaining Vania Soni cluster together and are distinct from the other caste groups examined in Gujarat. However, on the basis of individual genetic markers the Vania Soni appear not to be genetically differentiated in any remarkable way from other Hindu populations in western and northern India.     

Geographic variation of caste structure among ant populations

Morphologically distinct worker castes of eusocial insects specialize in different tasks. The relative proportions of these castes and their body sizes represent the demography of a colony that is predicted to vary adaptively with environments. Despite strong theoretical foundations, there has been little empirical evidence for the evolution of colony demography in nature. We show that geographically distinct populations of the ant Pheidole morrisi differ in worker caste ratios and worker body sizes in a manner consistent with microevolutionary divergence. We further show that the developmental mechanism for caste determination accounts for the unique pattern of covariation observed in these two traits. Behavioral data reveal that the frequency of different tasks performed by workers changes in a caste-specific manner when caste ratios are altered and demonstrate the importance of the major caste in colony defense. The population-level variation documented here for P. morrisi colonies supports the predictions of adaptive demography theory and illustrates that developmental mechanisms can play a significant role in shaping the evolution of phenotype at the colony level.     

Restriction isotyping of apolipoprotein E among populations of Punjab, northwestern India

The molecular polymorphism displayed by apolipoprotein E (apoE, protein; APOE, gene) has been listed as a risk factor for susceptibility to various disorders, such as those associated with lipid metabolism and arteriosclerosis. Data from many population groups are available. The present study endeavors to add to the world population database for alleles encountered at this locus. One hundred sixty-five individuals representing four castes and a mixed group from Punjab, a state in northwestern India, were analyzed for APOE isotyping. Intercaste group comparisons of allele frequencies revealed statistically insignificant differences, pointing to homogeneity at this locus among Punjabi caste groups, which can be considered as one Punjabi population. A further comparison of this Punjabi sample with other populations of the world revealed the Punjabi population to be closer to some European populations than to either African or Asian populations, a pointer to the ethnic origins of the Punjabi population.     

Demographic history of India and mtDNA-sequence diversity.

The demographic history of India was examined by comparing mtDNA sequences obtained from members of three culturally divergent Indian subpopulations (endogamous caste groups). While an inferred tree revealed some clustering according to caste affiliation, there was no clear separation into three genetically distinct groups along caste lines. Comparison of pairwise nucleotide difference distributions, however, did indicate a difference in growth patterns between two of the castes. The Brahmin population appears to have undergone either a rapid expansion or steady growth. The low-ranking Mukri caste, however, may have either maintained a roughly constant population size or undergone multiple bottlenecks during that period. Comparison of the Indian sequences to those obtained from other populations, using a tree, revealed that the Indian sequences, along with all other non-African samples, form a starlike cluster. This cluster may represent a major expansion, possibly originating in southern Asia, taking place at some point after modern humans initially left Africa.     

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.     

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.     

Consanguinity, caste and deaf-mutism in Punjab, 1921

The effects of religion, population sub-division and geography on the prevalence of deaf-mutism were investigated using information collected in the 1921 Census of Punjab. The total sample size was 9.36 million, and comprised data on thirteen Hindu castes, seventeen Muslim biraderis and two Sikh castes. A two-way analysis of variance comparing males in Hindu castes in which consanguineous marriage was prohibited, with males in Muslim biraderis which favoured first cousin marriage, indicated major differences with respect to the patterns of deaf-mutism within each religion. In the Muslim population 9.1% of the relative variation in the prevalence of deaf-mutism was inter-biraderi, 36.8% between geographical regions, and 48.8% an interaction between biraderi and region, whereas among Hindus 46.8% of the observed variation was inter-caste, 12.8% inter-region and 33.6% due to caste region interaction. From a wider disease perspective the results obtained with the Hindu community indicate the significant genetic differentiation associated with caste endogamy. As the overwhelming majority of Hindu marriages continue to be within-caste, it can be predicted that similar levels of inter-caste differences in disease frequency currently exist. By comparison, the lower level of inter-biraderi variation among Muslims is probably indicative of the dissolution of pre-existing caste boundaries and the resultant gene pool mixing that followed the large-scale conversion of Hindus to Islam during Muslim rule in North India from the 13th to the 19th centuries.     

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.     

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.     

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.