Distribution, endogamy, and isolation of Malas of Chittoor district, Andhra Pradesh, India

This study investigates the distribution of Malas, a scheduled caste population of Andhra Pradesh, their isolates in different eco-cultural zones, and their endogamy and isolation by marriage district. The Malas, formerly "untouchables," occupy the lowest status in the Hindu hierarchy. The sample consists of 10% of Malas from 10% of the villages in 2 taluks of Chitoor district of Andhra Pradesh. 6 Mala populations--Tangala, Maladasari, Pakanati, Rampala, Murikinati, and Bommanati--live in the area. These populations show a regionality in their distribution, with very little overlapping even when 2 populations inhabit the same village. Of 885 marriages in the 6 endogamous populations, all but 3 have been contracted between individuals belonging to the same Mala group. The 3 exogamous marriages took place between Mala men and women from another caste. Such small exceptions to the general rule do not mean that the Mala populations are not breeding isolates; these 6 populations satisfy Wright's island model. The high incidence of matings between closely related populations also contributes to their genetic and breeding isolation. Consanguineous marriages range from 26.76 to 38.75%. The distance between the birth place of spouses in miles, called marriage distance, shows a range from 7.72 to 15.71 miles. Lower values mean higher population densities. Groups within each population are isolated by distance and form small overlapping Mendelian populations, approaching a stepping stone model with continuous variation of genetic traits between adjacent groups of people.     

Endogamy,consanguinity and community genetics

The population of India is composed of many thousands of subpopulations, divided by geography, language, religion and caste or biraderi (patrilineage) boundaries, with endogamous marriage the norm. The net effect has been the creation of multiple genetic isolates with individual mutation profiles, but to date the clinical consequences of this highly complex differentiation have been largely ignored. In contrast, the topic of consanguinity continues to attract attention among medical and population geneticists, clinicians and social scientists. The significant progress made in India in improving childhood nutritional status and combating infectious disease means that genetic disorders have assumed everincreasing importance. In populations where consanguineous marriage is widely practised, recessive genetic disorders will continue to gain greater prominence in the overall spectrum of ill health. At the same time this increase will in part be negated by urbanization and the move to smaller family sizes, which predictably will result in a decline in the prevalence of consanguineous unions. Developing an understanding of these changes will require a wide-ranging and multidisciplinary investigative approach for which community genetics is ideally suited.     

Genetic studies among seven endogamous populations of the Koshi Zone, Bihar (India)

The distribution of AB0 and Rhesus blood groups, PTC taste sensitivity and colour blindness was studied among seven endogamous populations (Tharu, Mushar, Santal, Dhobi, Julaha, Kulhaiya and Karan Kayastha) in the Koshi Zone of Bihar (India). The phenotype and allele frequencies of the four gene loci (AB0, RH, PTC and colour blindness) show considerable differences between these populations. The measurement of genetic distances revealed, that the lowest genetic distance is seen between Dhobi and Julaha, the highest between Mushar and Tharu. From the genetic distance analysis there is some evidence for a close genetic relationship among the population groups belonging to the same region, irrespective of their caste, religion, linguistic or any other affinities. It may be concluded that all these populations have arisen through a common ancestor and changed gene frequencies among them is due to evolutionary forces like mutation, selection, migration, temporal variation and genetic drift. However, these populations retain their separate entities by practising endogamy. Gene diversity analysis reveals that these populations are at an early stage of genetic differentiation.     

Microsatellite diversity among three endogamous Tamil populations suggests their origin from a separate Dravidian genetic pool

The genetic profiles based on 15 autosomal microsatellite markers were analyzed among three socially distinct endogamous Dravidian populations: Tanjore Kallar, Vanniyar, and Pallar of Tamil Nadu, southern India, in order to understand their origin and the extent of genetic affinity and diversity among them. All loci were highly polymorphic and followed Hardy-Weinberg expectations except for loci D13S317 in Tanjore Kallars and D7S820 in Vanniyars. The SK2 criterion test showed no evidence of association among the 15 loci in the studied populations. The extent of gene differentiation among the three populations was low (G(ST) = 0.012), suggesting proximity between them. The phylogenetic dendrogram based on allele frequencies places them in a separate cluster, away from other compared Indo-European populations. The fit of the Harpending and Ward model of regression was found to be good and consistent with the extent of endogamy followed by the respective populations. These findings support a separate origin of the Dravidians and reveal an overall genetic unity among the studied Tamil populations belonging to different strata of the social hierarchy. The extent of diversity found among them probably resulted from the strict endogamous practices that they follow.     

Endogamy among the Dogon of Boni, Mali

This paper examines factors influencing endogamy in a Dogon population in Mali. Situated in Boni district, this population of about 5000 individuals is distributed over fifteen villages located on four independent massifs. This population is strongly endogamous (only 4% of all marriages are contracted with neighbouring ethnic groups), and each massif shows high endogamy. The roles of lineage, residence in the same village, and geographical distance in mating choice are examined. These different factors are successively analysed using log-linear statistical models and the results offer a more precise interpretation of endogamy in this population.     

Skin colour in north Indian populations

The skin colour of six endogamous groups of north India has been studied reflectometrically. The percentage reflectance at upper arm and forchead of 650 adult males (20–25 years) is described and discussed using 601 (425 nm), 605 (545 nm) and 609 (685 nm) filters of the “EEL” spectrophotometer. The inter-group heterogeneity is revealed by variance-ratio test. The t-test has been applied to study inter-group differences in pigmentation. Some correspondence has been found in skin colour with caste hierarchy, which holds only when the populations living in the same region are compared. These differences are assigned to adaptive adjustments superimposed by caste endogamy and assortative mating for skin colour.     

GENETIC DRIFT AND COLLECTIVE DISPERSAL CAN RESULT IN CHAOTIC GENETIC PATCHINESS

Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free‐living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex dispersal patterns to create chaotic genetic patchiness. Here we use a coancestry model and individual‐based simulations to test this idea. We found that chaotic genetic patterns (qualified by global F_ST and spatio‐temporal variation in F_ST's between pairs of samples) arise from the combined effects of (1) genetic drift created by the small local effective population sizes of the sessile phase and variance in contribution among breeding groups and (2) collective dispersal of related individuals in the larval phase. Simulations show that patchiness levels qualitatively comparable to empirical results can be produced by a combination of strong variance in reproductive success and mild collective dispersal. These results call for empirical studies of the effective number of breeders producing larval cohorts, and population genetics at the larval stage.     

Genetic Structure and Kinship Patterns in a Population of Black Howler Monkeys, Alouatta pigra, at Palenque National Park, Mexico

We investigated the genetic structure and kinship patterns of black howler monkeys (Alouatta pigra) at Palenque National Park, Mexico. Fecal samples from 49 individuals residing in eight social groups were successfully genotyped for 19 polymorphic microsatellite markers known to be variable in other ateline primates. Overall, genetic diversity was low (H_o = 0.588) with an average of 4.2 alleles per loci (range = 2–8). We found that intergroup genetic variation among adults was relatively high (mean between‐group F_ST = 0.119), largely due to the genetic divergence of one study group from the others. Intragroup kinship patterns showed that in most social groups, either adult males, adult females, or individuals of both sexes resided with same‐sexed adult kin, suggesting that some black howler males and females may not disperse from their natal group or may disperse with related individuals. Of the six sampled immigrant males, two males joined established groups by themselves, and four males formed two pairs that each took over the social group they joined after evicting the resident males. Males in both these coalitions were genetically closely related, while the two solitary immigrants were not closely related to any of the resident males present in the group they joined. Am. J. Primatol. 74:948‐957, 2012. © 2012 Wiley Periodicals, Inc.     

Culture modifies expectations of kinship and sex‐biased dispersal patterns: A case study of patrilineality and patrilocality in tribal yemen

Studies of the impact of post‐marital residence patterns on the distribution of genetic variation within populations have returned conflicting results. These studies have generally examined genetic diversity within and between groups with different post‐marriage residence patterns. Here, we directly examine Y chromosome microsatellite variation in individuals carrying a chromosome in the same Y haplogroup. We analyze Y chromosome data from two samples of Yemeni males: a sample representing the entire country and a sample from a large highland village. Our results support a normative patrilocality in highland Yemeni tribal populations, but also suggest that patrilocality is violated often enough to break down the expected correlation of genetic and geographic distance. We propose that a great deal of variation in male dispersal distance distributions is subsumed under the “patrilocal” label and that few human societies are likely to realize the idealized male dispersal distribution expected under strict patrilocality. In addition, we found almost no specific correspondence between social kinship and genetic patriline at the level of the clan (large, extended patrilineal kinship group) within a large, highland Yemeni village. We discuss ethnographic accounts that offer several cultural practices that explain exceptions to patrilocality and means by which social kinship and genetic patriline may become disentangled. © 2013 Wiley Periodicals, Inc.     

Complex genetic origin of Indian populations and its implications

Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000?years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.     

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwise F_ST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and F_ST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables and F_ST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.     

Genomic diversity and affinities in population groups of North West India: An analysis of Alu insertion and a single nucleotide polymorphism

The North West region of India is extremely important to understand the peopling of India, as it acted as a corridor to the foreign invaders from Eurasia and Central Asia. A series of these invasions along with multiple migrations led to intermixture of variable populations, strongly contributing to genetic variations. The present investigation was designed to explore the genetic diversities and affinities among the five major ethnic groups from North West India; Brahmin, Jat Sikh, Bania, Rajput and Gujjar. A total of 327 individuals of the abovementioned ethnic groups were analyzed for 4 Alu insertion marker loci (ACE, PV92, APO and D1) and a Single Nucleotide Polymorphism (SNP) rs2234693 in the intronic region of the ESR1 gene. Statistical analysis was performed to interpret the genetic structure and diversity of the population groups. Genotypes for ACE, APO, ESR1 and PV92 loci were found to be in Hardy–Weinberg equilibrium in all the ethnic groups, while significant departures were observed at the D1 locus in every investigated population after Bonferroni's correction. The average heterozygosity for all the loci in these ethnic groups was fairly substantial ranging from 0.3927 ± 0.1877 to 0.4333 ± 0.1416. Inbreeding coefficient indicated an overall 10% decrease in heterozygosity in these North West Indian populations. The gene differentiation among the populations was observed to be of the order of 0.013. Genetic distance estimates revealed that Gujjars were close to Banias and Jat Sikhs were close to Rajputs. Overall the study favored the recent division of the populations of North West India into largely endogamous groups. It was observed that the populations of North West India represent a more or less homogenous genetic entity, owing to their common ancestral history as well as geographical proximity.     

Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata

The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self‐fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within‐ and among‐population variation at 3928 SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among‐group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U‐shaped distribution of pairwise F_ST values reflecting “islands” of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density‐dependent attack by species‐specific strains of pathogenic fungi and/or root‐nodulating bacteria specializing on distinct genotypes.     

Demography, and genetic and morphological variability of the endangered Sophronitis sincorana (Orchidaceae) in the Chapada Diamantina, Brazil

We carried out a demographic study and evaluated the genetic and morphological variability in five populations of the endangered Sophronitis sincorana (Orchidaceae) endemic to Northeastern Brazil, based on allozyme and morphometric analyses. Plant density was approximately 0.5 plants/m², and the projected total number of plants was approximately 50,000 individuals. However, fruit set and recruitment of individuals are rare. The genetic variability was very high in all populations (P = 100, A = 3.0−3.5, H _e = 0.33−0.48), and all populations presented similar values of morphological variability. Low genetic and morphological structuring were found in the species (F _ST = 0.053, A_MRPP = 0.018). The elevated coefficient of endogamy encountered in populations of S. sincorana indicates the occurrence of structuring within the populations. The lack of correlation between morphological and genetic variation in this species indicates that none of the markers examined should be used separately for either conservation purposes.     

The origins and genetic structure of three co-resident Chinese Muslim populations: the Salar,Bo'an and Dongxiang

A genome-based investigation of three Muslim populations, the Salar, Bo'an, and Dongxiang, was conducted on 212 individuals (148 males, 64 females) co-resident in Jishisan County, a minority autonomous region located in the province of Gansu, PR China. The Salar are believed to be of Turkic origin, whereas the Bo'an and Dongxiang both speak Mongolian. Biparental dinucleotide markers on chromosomes 13 and 15 indicated elevated mean homozygosity in the Salar (0.32), Bo'an (0.32), and Dongxiang (0.27), equivalent to inbreeding coefficients ( F(is) ) of 0.16; 0.12; 0.01, confirming varying levels of endogamous and consanguineous marriage in all three communities. Y-chromosome unique event polymorphisms (UEPs) showed that males in the three communities shared common ancient origins, with 80-90% of haplotypes in common. However, the high levels of community-specific Y-chromosome STR haplotypes strongly suggested the action(s) of founder effect, genetic drift and preferential consanguinity during more recent historical time. By comparison with the marked inter-community differentiation revealed by the Y-chromosome STRs (29.4%), the mtDNA data indicated similarity between the female lineages of each community with just 1.2% inter-community variation. The combined use of these different marker systems gives an in-depth historical perspective, and provides evidence of past inter-marriage between genetically diverse male founders of each community and Han Chinese females with subsequent community endogamy.     

Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

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.     

Genetic polymorphism of six DNA loci in six population groups of India

The genetic profile based on autosomal markers, four microsatellite DNA markers (D8S315, FES, D8S592, and D2S1328) and two minisatellite DNA markers (TPMT and PDGFA), were analyzed in six endogamous populations to examine the effect of geographic and linguistic affiliation on the genetic affinities among the groups. The six populations are from three different states of India and are linguistically different. Marathas from western India speak Marathi, an Indo-European language. Arayas, Muslims, Ezhavas, and Nairs from Kerala state of South India speak Malayalam, and Iyers from Tamil Nadu state speak Tamil. Genomic DNA was extracted from peripheral blood samples of random, normal, healthy individuals. Locus-specific PCR amplification was carried out, followed by electrophoresis of the amplicons and genotyping. All the loci were highly polymorphic and followed Hardy-Weinberg equilibrium, except for loci D8S315 and PDGFA in Iyers and Marathas, respectively. All six loci had high heterozygosity (average heterozygosity ranged from 0.73 to 0.76) and high polymorphism information content (0.57-0.90). The extent of gene differentiation among the six populations (G(ST) = 0.030) was greater than that for four Kerala populations (G(ST) = 0.011), suggesting proximity between the four Kerala populations. This result conforms with the cultural and linguistic background of the populations. The extent of diversity found among the populations probably resulted from the strict endogamous practices that they follow.     

Population genetics of Wolbachia‐infected,parthenogenetic and uninfected,sexual populations of Tetrastichus coeruleus (Hymenoptera: Eulophidae)

Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. These manipulations are expected to have consequences on the population genetics of the host, such as heterozygosity levels, genetic diversity and gene flow. The parasitoid wasp Tetrastichus coeruleus has populations that are infected with parthenogenesis‐inducing Wolbachia and populations that are not infected. We studied the population genetics of T. coeruleus between and within Wolbachia‐infected and uninfected populations, using nuclear microsatellites and mitochondrial DNA. We expected reduced genetic diversity in both DNA types in infected populations. However, migration and gene flow could introduce new DNA variants into populations. We therefore paid special attention to individuals with unexpected (genetic) characteristics. Based on nuclear and mitochondrial DNA, two genetic clusters were evident: a thelytokous cluster containing all Wolbachia‐infected, parthenogenetic populations and an arrhenotokous cluster containing all uninfected, sexual populations. Nuclear and mitochondrial DNA did not exhibit concordant patterns of variation, although there was reduced genetic diversity in infected populations for both DNA types. Within the thelytokous cluster, there was nuclear DNA variation, but no mitochondrial DNA variation. This nuclear DNA variation may be explained by occasional sex between infected females and males, by horizontal transmission of Wolbachia, and/or by novel mutations. Several females from thelytokous populations were uninfected and/or heterozygous for microsatellite loci. These unexpected characteristics may be explained by migration, by inefficient transmission of Wolbachia, by horizontal transmission of Wolbachia, and/or by novel mutations. However, migration has not prevented the build‐up of considerable genetic differentiation between thelytokous and arrhenotokous populations.     

Integrating Linguistics,Social Structure,and Geography to Model Genetic Diversity within India

India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.