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1.
Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.  相似文献   

2.
Data on the distribution of genetic markers in Indian tribal populations as well as in Southwest and Southeast Asiatic populations have been recorded in order to study comparatively the extent of genetic similarity and dissimilarity, respectively, 1. within the various regional tribal groups, and 2. among tribals and the populations from Southwest and Southeast Asia. The--preliminary--results of these comparisons are discussed considering the racial history of the Indian subcontinent.  相似文献   

3.
Aphanius fasciatus is a cyprinodont distributed in the salty coastal water of the central and eastern Mediterranean Sea and occasionally in internal fresh water. In this work, the authors have investigated the genetic structure of eight populations of the killifish A. fasciatus from Sardinia and Sicily. The comparison of the mtDNA control region of 237 individuals revealed a total of 49 haplotypes. Several unique haplotypes were present in each population, and no common haplotype was found among Sicilian and Sardinian populations. Almost all Sardinian populations shared a common haplotype, and indeed the four Sicilian populations examined did not share any as determined by the parsimony network analysis. The analysis of molecular variance showed that the percentage of variation among populations is much higher than within each population of A. fasciatus . The overall F ST value is very high (0·78) and supports an extensive genetic structure of the populations. The observed genetic differentiations of A. fasciatus populations were discussed taking into account the palaeogeographic and palaeoclimatic events that interested the Mediterranean area from Miocenic to Pleistocenic age. The results provide new insight into the knowledge of the pattern of genetic structure and of evolutionary processes occurring in this species.  相似文献   

4.
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.  相似文献   

5.
Fenugreek (Trigonella foenum-graecum) is receiving global attention due to rare medicinal properties of significance to human health. Gene banks possess scanty germplasm and very little background information regarding its genetic variability that has hampered its improvement. We investigated the extent of variability among 17 Indian varieties of fenugreek using phenotypic and genetic markers. Multilocus genotyping by ten random amplified polymorphic DNA (RAPD) primers detected an average of intraspecific variations amounting to 64.7% polymorphism in banding patterns. Analysis of molecular variance indicated that a greater proportion of total genetic variation exists within population (91%) rather than among populations. Higher values of Nei’s gene diversity (h) and Shannon Information Index (i) and genetic distance analysis validate higher genetic diversity among Indian fenugreek varieties. SNPs at 14 sites of rDNA region revealed further lineages of distinct varieties with main RAPD clusters. The representative sequences of each subgroup and all distinct varieties have been submitted to NCBI database and assigned Gen Accession numbers HM 176640–176649. The measures of relative genetic distances among varieties of fenugreek did not completely correlate with the geographical distances of places of their development. The homogeneous phenotypic markers proved insufficient in exhibiting genetic divergence among fenugreek varieties studied. Eventually, the knowledge of their genetic relationships, DNA bar coding and phylogenies might contribute for the designing of intraspecific crosses between cultivars of this fenugreek collection with potential interest in seed spices breeding programme.  相似文献   

6.
Valeriana jatamansi Jones is a natural tetraploid species indigenous to the Indian Himalaya. To assess its genetic diversity and population structure, we analyzed six natural populations from the western Himalayan region using amplified fragment length polymorphism. An analysis of molecular variance found that 93% of the genetic variation of V. jatamansi was within populations and 7% among populations. The correlation between genetic and geographic distances (r = 0.14) was not significant. Though the populations are well separated, the lack of distinct genetic variation between populations may be due to either recent rapid fragmentation from a wide and continuous area resulting in genetically similar populations or wide dispersal of seed by wind, since the follicles are feathery. Polyploidy may be the reason for the lack of genetic impoverishment due to fragmentation.  相似文献   

7.
Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.  相似文献   

8.
Small, isolated populations are prone to genetic drift and high levels of inbreeding that can threaten their long-term survival. Alnus maritima persists exclusively in three groups of small, highly disjunct, regional populations in the Delmarva Peninsula, Georgia, and Oklahoma. Trees in the three regions are recognized as separate subspecies. Microsatellite markers were used to measure fine-scale population genetic diversity and structure (1) within and among regions and (2) within and among populations in each region. Compared to a previous study utilizing allozymes, microsatellite data show higher levels of variation, lower levels of inbreeding, but similar levels of genetic differentiation among regions. Significant genetic differentiation was detected among regions and among distinct populations within regions. Genetic differentiation was significantly correlated with geographic distance among regional populations, but not among populations within regions. Populations, therefore, likely represent fragments of formerly extensive networks of populations that have decayed and retracted due to competition with other species better adapted to the shadier habitats of late-succession environments. The unique genetic features of populations within different regions should be considered as part of future conservation efforts.  相似文献   

9.
The combination of founder events, random drift and new selective forces experienced by introduced species typically lowers genetic variation and induces differentiation from the ancestral population. Here, we investigate microsatellite differentiation between introduced and native populations of the small Indian mongoose (Herpestes auropunctatus). Many expectations based on introduction history, such as loss of alleles and relationships among populations, are confirmed. Nevertheless, when applying population assignment methods to our data, we observe a few specimens that are incorrectly assigned and/or appear to have a mixed ancestry, despite estimates of substantial population differentiation. Thus, we suggest that population assignments of individuals should be viewed as tentative and that there should be agreement among different algorithms before assignments are applied in conservation or management. Further, we find no congruence between previously reported morphological differentiation and the sorting of microsatellite variation. Some introduced populations have retained much genetic variation while others have not, irrespective of morphology. Finally, we find alleles from the sympatric grey mongoose (Herpestes edwardsii) in one small Indian mongoose within the native range, suggesting an alternative explanation for morphological differentiation involving a shift in female preferences in allopatry.  相似文献   

10.
Population-based genetic association studies, popularly known as case-control studies, have continued to be the most preferred method for deciphering the genetic basis of various complex diseases, even in the post-human genome sequencing era. However, interpopulation differences in allele, genotype, and haplotype frequencies and linkage disequilibrium patterns lead to inconsistent results in candidate gene association studies. Therefore, for any meaningful disease association study, knowledge of the normative genetic background of the baseline population is a prerequisite. In addition, such genetic variation data also provide a ready-made menu of allele frequencies and linkage disequilibrium patterns of various polymorphisms in specific candidate genes in a particular population, which is a useful reference for further genetic association studies. Such genetic variation data are lacking for the Indian population, which represents about one-sixth of the world's population. In the present study we have reported the allele, genotype, and haplotype frequencies, Hardy-Weinberg equilibrium status, and linkage disequilibrium patterns of 12 polymorphisms in six candidate genes from the renin-angiotensin-aldosterone system among Indians. Because of their different history of origin, the Indian population is broadly divided into two subpopulations: North Indians (Caucasian Europeans) and South Indians (Dravidians). Considering this well-documented difference in gene pools, we have presented a comparative account of the normative genetic data of North Indian and South Indian populations with at least four individuals of urban and suburban origin from each of the representative states of northern and southern India.  相似文献   

11.
RAPD markers provide a powerful tool for the investigation of genetic variation in natural and domesticated populations. Recent studies of strain/cultivar identification have shown extensive RAPD divergence among, but little variation within, inbred species or cultivars. In contrast, little is known about the pattern and extent of RAPD variation in heterogeneous, outcrossing species. We describe the population genetic variation of RAPD markers in natural, diploid sources of dioecious buffalograss [Buchloë dactyloides (Nutt.) Engelm.]. Buffalograss is native to the semi-arid regions of the Great Plains of North America, where it is important for rangeland forage, soil conservation, and as turfgrass. Most sources of buffalograss germplasm are polyploid; diploid populations are previously known only from semi-arid Central Mexico. This is the first report of diploids from humid Gulf Coastal Texas. These two diploid sources represent divergent adaptive ecotypes. Seven 10-mer primers produced 98 polymorphic banding sites. Based on the presence/ absence of bands, a genetic distance matrix was calculated. The new Analysis of Molecular Variance (AMOVA) technique was used to apportion the variation among individuals within populations, among populations within adaptive regions, and among regions. There was considerable variation within each of the four populations, and every individual was genetically distinct. Even so, genetic divergence was found among local populations. Within-population variation was larger and among-population variation smaller in Mexico than in Texas. The largest observed genetic differences were those between the two regional ecotypes. These patterns of genetic variation were very different from those reported for inbred species and provide important baseline data for cultivar identification and continuing studies of the evolution of polyploid races in this species.  相似文献   

12.
Plethodon shermani comprises a series of geographically disjunct populations occupying high-elevation mountain isolates. These populations hybridize at their borders with salamanders of the Plethodon glutinosus species complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions between P. shermani and species of the P. glutinosus complex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions between P. shermani, its close relative Plethodon cheoah, and species of the P. glutinosus complex. Ongoing hybridization with the P. glutinosus-complex species Plethodon teyahalee is accompanied by extensive mitochondrial introgression in some Unicoi populations of P. shermani, but it has little genetic impact on P. shermani populations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations of P. shermani exhibit mtDNA evidence of past hybridization with diverse lineages from P. aureolus and P. glutinosus. The Tusquitee isolate of P. shermani is also characterized by mtDNA haplotypes most closely related to Plethodon aureolus and P. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of Unicoi P. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates of P. shermani appears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate that P. shermani isolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts between P. shermani and other species permits a fine-level resolution of evolutionary lineages not evident from allozymic data.  相似文献   

13.
Labeo rohita, popularly known as rohu is a widely cultured species in the whole Indian subcontinent. Knowledge of the genetic diversity of this species is important to support management and conservation programs which will subsequently help in sustainable production of this species. DNA markers, mostly microsatellite markers are excellent tool to evaluate genetic variation of populations. Genetic variation of three wild and one farm population was assessed using eleven microsatellite loci. In analyzing 192 samples, the number of alleles ranged from 4 to 23; observed heterozygosity 0.500 to 0.870 and expected heterozygosity from 0.389 to 0.878. Exact test for Hardy Weinberg disequilibrium revealed that each riverine sample had at least one locus not in equilibrium except one river. Negative inbreeding coefficients (FIS) were observed across populations indicating very high level of genetic diversity but little genetic differentiation among populations.  相似文献   

14.
Identification and study of genetic variation in recently admixed populations not only provides insight into historical population events but also is a powerful approach for mapping disease loci. We studied a population (OG-W-IP) that is of African-Indian origin and has resided in the western part of India for 500 years; members of this population are believed to be descendants of the Bantu-speaking population of Africa. We have carried out this study by using a set of 18,534 autosomal markers common between Indian, CEPH-HGDP, and HapMap populations. Principal-components analysis clearly revealed that the African-Indian population derives its ancestry from Bantu-speaking west-African as well as Indo-European-speaking north and northwest Indian population(s). STRUCTURE and ADMIXTURE analyses show that, overall, the OG-W-IPs derive 58.7% of their genomic ancestry from their African past and have very little inter-individual ancestry variation (8.4%). The extent of linkage disequilibrium also reveals that the admixture event has been recent. Functional annotation of genes encompassing the ancestry-informative markers that are closer in allele frequency to the Indian ancestral population revealed significant enrichment of biological processes, such as ion-channel activity, and cadherins. We briefly examine the implications of determining the genetic diversity of this population, which could provide opportunities for studies involving admixture mapping.  相似文献   

15.
The black tiger shrimp (Penaeus monodon) is an ecologically and economically important penaeid species and is widely distributed in the Indo-Pacific region. Here we investigated the genetic diversity of P. monodon (n = 355) from eight geographical regions by genotyping at 10 microsatellite loci. The average observed heterozygosity at various loci ranged from 0.638 to 0.743, indicating a high level of genetic variability in this region. Significant departures from Hardy-Weinberg equilibrium caused by heterozygote deficiency were recorded for most loci and populations. Pairwise F(ST) and R(ST) values revealed genetic differentiation among the populations. Evidence from the assignment test showed that the populations in the West Indian Ocean were unique, whereas other populations examined were partially admixed. In addition, the non-metric multidimensional scaling analysis indicated the presence of three geographic groups in the Indo-Pacific region, i.e. the African populations, a population from western Thailand and the remaining populations as a whole. We also sequenced and analysed the mitochondrial control region (mtCR) in these shrimp stocks to determine whether the nuclear and mitochondrial genomes show a similar pattern of genetic differentiation. A total of 262 haplotypes were identified, and nucleotide divergence among haplotypes ranged from 0.2% to 16.3%. Haplotype diversity was high in all populations, with a range from 0.969 to 1. Phylogenetic analysis using the mtCR data revealed that the West Indian Ocean populations were genetically differentiated from the West Pacific populations, consistent with the microsatellite data. These results should have implications for aquaculture management and conservation of aquatic diversity.  相似文献   

16.
The genetic diversity among ten Indian cultivars of cowpea was analyzed using 18 sets of RAPD markers. A total of 181 bands with an average of 15 bands per primer were obtained. Out of 181 bands, 148 showed polymorphism (81.7%). The variation in genetic diversity among these cultivars ranged from 0.1742 to 0.4054. Cluster analysis based on Jaccard’s similarity coefficient using UPGMA with high bootstrap values revealed two distinct clusters I and II comprised of two and seven cultivars, respectively. Cluster II was further differentiated into various subclusters. Cultivar IC-9883 was found to be unique based on its altogether distinct position in the dendrogram and two-dimensional space projections.  相似文献   

17.
Both mtDNA variation and allozyme data demonstrate that geographic groupings of different color morphs of the starfish Linckia laevigata are congruent with a genetic discontinuity between the Indian and Pacific Oceans. Populations of L. laevigata sampled from Thailand and South Africa, where an orange color morph predominates, were surveyed using seven polymorphic enzyme loci and restriction fragment analysis of a portion of the mtDNA including the control region. Both allozyme and DNA data demonstrated that these populations were significantly genetically differentiated from each other and to a greater degree from 23 populations throughout the West Pacific Ocean, where a blue color morph is predominant. The genetic structure observed in L. laevigata is consistent with traditional ideas of a biogeographic boundary between the Indian and Pacific Oceans except that populations several hundreds kilometers off the coast of north Western Australia (Indian Ocean) were genetically similar to and had the same color morphs as Pacific populations. It is suggested that gene flow may have continued (possibly at a reduced rate) between these offshore reefs in Western Australia and the West Pacific during Pleistocene falls in sea level, but at the same time gene flow was restricted between these Western Australian populations and those in both Thailand and South Africa, possibly by upwellings. The molecular data in this study suggest that vicariant events have played an important role in shaping the broadscale genetic structure of L. laevigata. Additionally, greater genetic structure was observed among Indian Ocean populations than among Pacific Ocean populations, probably because there are fewer reefs and island archipelagos in the Indian Ocean than in the Pacific, and because present-day surface ocean currents do not facilitate long-distance dispersal.  相似文献   

18.
Although quite a lot is known about the genetic structure of the polytypic species Mus musculus at the periphery of its range, the centre of origin and dispersion of the species remains unknown. To investigate the amount of genetic subdivision that occurs in the central parts of its range, we analysed the genetic variation in four new samples of mice coming from Iran, Pakistan, northern and southern India using 35 autosomal protein loci and restriction fragment length polymorphisms of three genes of the Vβ gene complex of the immune system. The variation was then compared with that found in the subspecies occupying the peripheral regions of the species range. The two samples from the northern part of the Indian subcontinent were shown to be more heterozygous than the samples from any of the other regions. They also contain the majority of the alleles that exist in the differentiated subspecies at the periphery of the species range. A neighbour-joining analysis on Nei's genetic distances and a factorial analysis of correspondences on the allelic composition of each sample both place the Pakistani and Indian populations in a phylogenetically and genetically central position compared to the peripheral subspecies. These results suggest that the populations in this geographically central area have retained most of the ancestral polymorphisms, which in turn indicates that the Indian subcontinent is probably the cradle of the species. The nature of the genetic relationships between the various populations throughout the species range and the possibility that they form an incipient ring species are also discussed. Our results are in agreement with the classical model of geographic differentiation where genetic divergence in allopatry is considered to be the prime cause of subspecies formation that may eventually lead to partial reproductive isolation on secondary contact.  相似文献   

19.
Gene flow among invertebrate populations inhabiting bodies of nonflowing freshwater such as ponds or lakes must at some stage involve transport across habitat unsuitable for adult stages. Consequently the potential for interpopulational differentiation is high in these species, yet empirical studies of lake populations of Cladocerans such as Daphnia have failed to reveal high levels of genetic distinctiveness among populations and have led to much speculation about how these populations exchange genes and remain cohesive evolutionary units. In this study we surveyed 42 Oregon lake populations of Daphnia from the D. pulex species complex for genetic variation within the mitochondrial DNA control region. We have used this data to test the relative abilities of various ecological factors to explain the observed patterns in genetic differentiation among lakes. Despite limited genetic variation detected among our samples--11 very similar RFLP-defined mtDNA genotypes from 388 individuals--analyses of nucleotide variance using analogs to Wright's F statistics indicate that when multilake populations are defined in terms of the river drainage basin to which they belong, strong and significant amounts of among-population genetic variation can be detected at this locus (F(ST) estimates between 0.5 and 0.6). In contrast, we fail to detect consistent significant among-population variation when populations are defined on the basis of regional physical geography, bird migratory flyways, or lake trophic status. The manner in which the data are compiled, that is, whether RFLPs or nucleotide sequences are used, has little effect on the overall conclusions, yet it is clear that nucleotide sequence data would lower the standard errors of F(ST) estimates. We propose that periodic widescale flooding during the late Pleistocene may be an important mechanism to homogenize genetic differences among lake Daphnia continent-wide south of the southern-most extent of Pleistocene glaciation.  相似文献   

20.
Enzyme electrophoresis was employed to examine genetic variation at 20 loci in 16 populations of Lasthenia minor and 18 populations of its presumed derivative species L. maritima. The purposes of the study were to ascertain levels of genetic variation in each species, to assess how the variation at enzyme-coding genes is apportioned within and among populations of each species, and to determine the level of divergence between the two species. The two species are both diploid annuals, similar morphologically, and produce fertile F1 hybrids when crossed. Lasthenia minor is self-incompatible and restricted to mainland California, whereas L. maritima is self-compatible and probably largely autogamous; it occurs on seabird rocks from central California to British Columbia. Mean genetic identities for pair-wise comparisons of populations of the two species are similar to values for populations of the same species, indicating they have not diverged at the 20 genes coding for soluble enzymes. Despite its more extensive geographical range, L. maritima exhibits only 50% of the genetic diversity of L. minor. The latter species apportions a greater amount of its diversity within populations, whereas the former harbors more diversity among populations than within them. This is probably a reflection of the different breeding systems of the two species. Six unique alleles were detected in L. minor, whereas only one novel allele was found in a single individual of L. maritima. The electrophoretic data are concordant with the suggestion that L. maritima is relatively recently derived from L. minor. The switch from outcrossing to selfing and selection of genotypes adapted to the chemically and physically unusual substrate on the seabird rocks are considered the critical steps in the evolution of L. maritima.  相似文献   

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