Microsatellite Analysis of Genetic Population Structure of Zebu Cattle (Bos indicus) Breeds from North-Western Region of India

The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds. Mean estimates of F-statistics: F_IT = 0.144 ± 0.023, F_IS = 0.071 ± 0.021, and F_ST = 0.078 ± 0.014 were significantly different from zero (P < 0.05). The interbreed relationships indicated moderate level of breed differentiation between the six cattle breeds with least differentiation between Kankrej-Mewati pair. The phylogeny structuring further supported close grouping of Kankrej and Mewati breeds. Correspondence analysis plotted Rathi, Tharparkar, and Gir individuals into three separate areas of multivariate space; whereas, Kankrej, Mewati, and Nagori cattle showed low breed specific clustering. This reflected the existence of discrete genetic structure for Tharparkar, Rathi, and Gir, the prominent dairy breeds of the region; whereas, admixture was observed for Kankrej, Mewati, and Nagori individuals.     

Differentiation of four indian aboriginal cattle populations revealed by SIR markers

Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic Variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 ± 0.04 in Binjharpuri to 0.664 ± 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 ± 0.02 and 0.720 ± 0.01, respectively. In the overall population, the homozygote excess (F _IT) of 0.132 ± 0.03, was partly due to the genetic differentiation among breeds (F _ST = 0.044 ± 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F _IS = 0.094 ± 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei??s Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.     

Genetic variability and individual assignment of Chinese indigenous sheep populations (Ovis aries) using microsatellites

The purpose of this study was to assess the genetic characteristics of six breeds of Chinese local sheep using 19 microsatellite loci and to effectively validate statistical methods for individual assignment based on informative microsatellites. All the six breeds deviated from Hardy–Weinberg equilibrium expectations, while the majority of markers complied. The polymorphism information content (PIC) of overall loci for the six populations ranged from 0.283 (SRCRSP5) to 0.852 (OarVH72). Tibetan sheep were the most diverse population with the highest mean allelic richness (6.895), while Ujmuqin (UQ) harboured the lowest allelic richness (6.000). The F‐statistics for the six populations were F_IS = ?0.172, F_IT = ?0.082 and F_ST = 0.077, respectively. Furthermore, the pair‐wise F_IS revealed a moderate genetic differentiation among populations (P < 0.01), indicating that all breeds can be considered genetically independent entities. The lowest genetic differentiation was between Tengchong (TC) and UQ (F_ST = 0.041), and the highest one was between TC and Fat‐tailed Han (F_ST = 0.111). In comparing the three statistical models, we note that the seven microsatellite loci (MAF65, OarJMP58, SRCRSP9, MCM140, OarAE129, BM8125 and SRCRSP5) commonly used for individual assignment will ensure a powerful detection of individual origin, with accuracy up to 91.87%, when the likelihood‐based method is used. Overall, these findings shed light onto the genetic characteristics of Chinese indigenous sheep and offer a set of microsatellite loci that is simple, economic and highly informative for individual assignment of Chinese sheep.     

Analysis of Geographic and Pairwise Genetic Distances Among Sheep Populations

This study assessed the usefulness of geographic and pairwise genetic distances in the characterization of five sheep populations using 15 microsatellite markers. The average F statistics across loci were F _IT = 0.523 ± 0.140, F _ST = 0.363 ± 0.131, and F _IS = 0.263 ± 0.092. The average heterozygosity was 0.716 ± 0.069, polymorphism information content was 0.691 ± 0.070, and effective number of alleles was 3.736 ± 0.998. Sheep populations clustered into group 1 (Hu and Tong breeds) and group 2 (small-tailed Han, Wadi, and Tan breeds). Reynolds’ distance varied from 0.0062 to 0.0499, and the range of gene flow (N _m) was 4.8834–40.0726 among the sheep populations. The results showed that the genetic structure of the five populations was not consistent with their genetic distances, and the population genetic divergence was not linearly related to geographic distance as indicated by a Mantel test (P = 0.7936).     

Heterozygote excess through life history stages in Cestrum miradorense Francey (Solanaceae), an endemic shrub in a fragmented cloud forest habitat

Comparisons of genetic diversity and population genetic structure among different life history stages provide important information on the effect of the different forces and micro‐evolutionary processes that mould diversity and genetic structure after fragmentation. Here we assessed genetic diversity and population genetic structure using 32 allozymic loci in adults, seeds, seedlings and juveniles of eight populations of the micro‐endemic shrub Cestrum miradorense in a highly fragmented cloud forest in central–eastern Mexico. We expected that due to its long history or rarity, this species may have endured the negative effects of fragmentation and would show moderate to high levels of genetic diversity. High genetic diversity (H_e = 0.445 ± 0.03), heterozygote excess (F_IT = ?0.478 ± 0.034, F_IS = ?0.578 ± 0.023) and low population differentiation (F_ST = 0.064 ± 0.011) were found. Seeds had higher genetic diversity (H_e = 0.467 ± 0.05) than the later stages (overall mean for adults, seedlings and juveniles H_e = 0.438 ± 0.08). High gene flow was observed despite the fact that the fragmentation process began more than 100 years ago. We conclude that the high genetic diversity was the result of natural selection, which favours heterozygote excess in all stages, coupled with a combination of a reproductive system and seed/pollen dispersal mechanisms that favour gene flow.     

Genetic variability of dromedary camel populations based on microsatellite markers

Understanding existing levels of genetic variability of camel populations is capital for conservation activities. This study aims to provide information on the genetic diversity of four dromedary populations, including Guerzni, Harcha, Khouari and Marmouri. Blood samples from 227 individuals belonging to the aforementioned populations were obtained and genotyped by 16 microsatellite markers. A total of 215 alleles were observed, with the mean number of alleles per locus being 13.4 ± 6.26. All loci were polymorphic in the studied populations. The average expected heterozygosity varied from a maximum of 0.748 ± 0.122 in Guerzni population to a minimum of 0.702 ± 0.128 in Harcha population; Guerzni population showed the highest value of observed heterozygosity (0.699 ± 0.088), whereas Harcha population the lowest (0.646 ± 0.130). Mean estimates of F-statistics obtained over loci were F_IS = 0.0726, F_IT = 0.0876 and F_ST = 0.0162. The lowest genetic distance was obtained between Guerzni and Khouari (0.023), and the highest genetic distance between Harcha and Marmouri (0.251). The neighbour-joining phylogenetic tree showed two groups of populations indicating a cluster of Guerzni, Khouari and Marmouri, and a clear isolation of Harcha. The genetic distances, the factorial correspondence analysis, the analysis of genetic structure and the phylogenetic tree between populations revealed significant differences between Harcha and other populations, and a high similarity between Guerzni, Khouari and Marmouri. It is concluded from this study that the camel genetic resources studied are well diversified. However, the herd management, especially the random selection of breeding animals, can increase the level of genetic mixing between different populations, mainly among Guerzni, Khouari and Marmouri, that live in the same habitat and grazing area.     

Microsatellite analysis of genetic population structure of zebu cattle (Bos indicus) breeds from north-western region of India

The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds. Mean estimates of F-statistics: F(IT) = 0.144 ± 0.023, F(IS) = 0.071 ± 0.021, and F(ST) = 0.078 ± 0.014 were significantly different from zero (P < 0.05). The interbreed relationships indicated moderate level of breed differentiation between the six cattle breeds with least differentiation between Kankrej-Mewati pair. The phylogeny structuring further supported close grouping of Kankrej and Mewati breeds. Correspondence analysis plotted Rathi, Tharparkar, and Gir individuals into three separate areas of multivariate space; whereas, Kankrej, Mewati, and Nagori cattle showed low breed specific clustering. This reflected the existence of discrete genetic structure for Tharparkar, Rathi, and Gir, the prominent dairy breeds of the region; whereas, admixture was observed for Kankrej, Mewati, and Nagori individuals.     

Heterozygote excess in ancient populations of the critically endangered Dioon caputoi (Zamiaceae,Cycadales) from central Mexico

Dioon caputoi is a long‐lived cycad known from only four populations that range in size from 50 to 120, mostly adult individuals. Dioon caputoi has the most narrow geographical range of all Dioon spp. (less than 10 km), existing completely within the boundaries of the Tehuacán–Cuicatlán Biosphere Reserve, Mexico. Negative inbreeding values were found in all four populations (F_IT = ?0.242) and within subpopulations (F_IS = ?0.379). Only c. 10% of the total genetic variation was partitioned among populations (F_ST = 0.099). We also found that most mean values of genetic variation (A = 1.91 ± 0.12; P = 78.9 ± 10.2; H_E = 0.35 ± 0.01) are within the range reported for other Dioon species with larger populations and with wider geographical ranges. These results support recent findings that rare plant species maintain high levels of genetic diversity. The heterozygote excess found at all loci is discussed in detail from a neutral evolutionary perspective, leaving arguments as working hypotheses for further research. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158 , 436–447.     

Estimation,variance and optimal sampling of gene diversity II. Diploid locus

Nei's analysis of diversity at a diploid locus is extended to a population subdivided into a large number of subpopulations. The diversities and the heterozygotes frequency are defined with respect to the total population and unbiasedly estimated in a two-stage random cluster sampling. The fixation indices F _IS, F _IT andF _ST are derived, then inter- and intra-population variances of the estimated parameters are studied. We show that there is a unique sample size per population which yields the best accuracy in estimatingF _ST and F _IS, respectively, at a given locus. These results are illustrated with an analysis of DNA diversity in a forest tree and compared to those obtained under the Hardy-Weinberg assumption.     

Diversity and genetic structure of three species of Dioon Lindl. (Zamiaceae, Cycadales) from the Pacific seaboard of Mexico

We have estimated levels of genetic diversity and partitioning in the Mexican endemic cycad species Dioon sonorense, Dioon tomasellii, and Dioon holmgrenii, whose populations are exclusively distributed along the Pacific seaboard. For the three species, the patterns of variation at 19 allozyme loci in a total of 11 populations were evaluated. The average number of alleles per locus was in the range 2.05–1.68, corresponding to the northernmost population of D. sonorense (Mazatán), and the southernmost population of Dioon holmgrenii (Loxicha), respectively. In turn, the percentage of polymorphic loci peaked (94.73) in the El Higueral and Altamirano populations of Dioon tomasellii, and was estimated to be lowest (57.89) in the Loxicha population of D. holmgrenii. The mean expected heterozygosis varied markedly between taxa, with relatively high indices for D. sonorense and D. tomasellii (H_E = 0.314 and 0.295, respectively) and substantially lower values for D. holmgrenii (H_E = 0.170). Comparison of the inferred genetic structure based on F‐statistics for the three species also indicated differences along the north‐south Pacific seaboard axis. For D. sonorense and D. tomasellii, local inbreeding (F_IS) was zero but global inbreeding (F_IT) values were positive and significantly different from zero (0.130 and 0.116, respectively). By contrast, values of both F_IT and F_IS were negative and significantly different from zero (?0.116 and ?0.201, respectively) for D. holmgrenii. The genetic differentiation between populations (F_ST) had positive values in all taxa and corresponded with their geographic location along the north‐south axis: according to this statistic, D. sonorense was the most differentiated species (F_ST = 0.151), D. tomasellii had intermediate values (F_ST = 0.145), and D. holmgrenii was the less differentiated taxon (F_ST = 0.069). Finally, a phenogram representing Nei's genetic distances among populations displayed three major groups, each one corresponding to each of the studied species. Within D. tomasellii (of intermediate geographic distribution), a further division into two clusters corresponded precisely to the pair of populations that are geographically divided by the Trans Mexican Neovolcanic Mountains. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94 , 765–776.     

Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F_ST=0.126–0.138), and from DP (F_ST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F_ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.     

Population genetics of the people of Iran II. Genetic differentiation and population structure

The genetic structure of six populations of Iran (Turks, Kurds, Lurs, Zabolis, Baluchis and Zoroastrians) was examined using data on blood groups, serum proteins and cell enzymes. Our results show conclusively that there are genetic differences among the six populations and the analysis of superimposed R and S matrices defined Harpending & Jenkins (1973) show by that the dispersion of some of the alleles correspond to the dispersion of the populations. The F_ST estimates are not large enough to favour selection on any of the loci studied. The F_IT and F_IS estimates are positive and moderately high suggesting that the genetic differentiation to some extent is influenced by inbreeding.     

HLA gene and haplotype frequencies in galicia (NW Spain)

The genetic structure of six populations of Iran (Turks, Kurds, Lurs, Zabolis, Baluchis and Zoroastrians) was examined using data on blood groups, serum proteins and cell enzymes. Our results show conclusively that there are genetic differences among the six populations and the analysis of superimposed R and S matrices defined by Harpending & Jenkins (1973) show that the dispersion of some of the alleles correspond to the dispersion of the populations. The F_ST estimates are not large enough to favour selection on any of the loci studied. The F_IT and F_IS estimates are positive and moderately high suggesting that the genetic differentiation to some extent is influenced by inbreeding.     

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale,Merino and Creole sheep

The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip^®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F_ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F_ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F_ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.     

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations

Nonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (F_IS or F_ST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, F_IS or F_ST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro ‐checker .     

DEMOGRAPHIC GENETICS OF A PIONEER TROPICAL TREE SPECIES: PATCH DYNAMICS,SEED DISPERSAL,AND SEED BANKS

We consider whether changes in population-genetic structure through the life cycle of Cecropia obtusifolia, a tropical pioneer tree, reflect its gap-dependent demography and the role of evolutionary processes that are important for this species. We asked whether the spatial scale at which population-genetic subdivision occurs corresponds to the scale of habitat patchiness created by gap dynamics; whether patterns of seed dispersal and storage in the soil affect spatial genetic patterns; and whether spatial genetic patterns change through the species life cycle. We estimated Wright's F-statistics for six successive life-history stages for individuals grouped into subpopulations according to occurrence in natural gaps, physical proximity, or occurrence within large quadrats. For each life stage, F_ST-statistics were significantly higher when individuals were grouped by gaps, although concordant patterns across life stages for the three grouping methods were obtained. This supports the hypothesis that patchy recruitment in gaps or among-gap heterogeneity influences the species' genetic structure. F-statistics of seeds collected from females before dispersal (tree seeds), seed-rain seeds, soil seeds, seedlings, juveniles, and adults grouped by gaps, were, respectively: F_IT = 0.004, 0.160, 0.121, 0.091, –0.0002, –0.081; F_IS = –0.032, 0.124, 0.118, 0.029, –0.016, –0.083; and F_ST = 0.035, 0.041, 0.003, 0.063, 0.015, 0.002. Spatial genetic differentiation in rain seeds was not significantly lower than that of tree seeds. The loss of genetic structure in the soil seed bank, relative to that found in the seed rain may be due to sampling artifacts, but alternative explanations, such as microsite selection or temporal Wahlund effect are also discussed. If structure among soil seeds is unbiased, the peak in seedling F_ST may be due to microsite selection. F_IS of seeds in the rain and soil were significantly greater than zero. A Wahlund effect is the most likely cause of these positive F_IS values. Such fine-scale substructuring could be caused by correlated seed deposition by frugivores. The decrease in F_IS from seedlings to adults could result from loss of fine-scale genetic structure during stand thinning or from selection.     

Craniometric variation among modern human populations

Previous studies of genetic markers and mitochondrial DNA have found that the amount of variation among major geographic groupings of Homo sapiens is relatively low, accounting for roughly 10% of total variation. This conclusion has had implications for the study of human variation and consideration of alternative models for the origin of modern humans. By contrast, it has often been assumed that the level of among-group variation for morphological traits is much higher. This study examines the level of among-group variation based on Craniometric data from a large sample of modern humans originally collected by W. W. Howells. A multivariate method based on quantitative genetics theory was used to provide an estimate of F_ST — a measure of among-group variation that can be compared with results from studies of genetic markers. Data for 57 Craniometric variables on 1,734 crania were analyzed. These data represent six core areas: Europe, Sub-Saharan Africa, Australasia, Polynesia, the Americas, and the Far East. An additional set of analyses was performed using a three-region subset (Europe, Sub-Saharan Africa, and the Far East) to provide comparability with several genetic studies. The minimum F_ST (assuming complete heritability) for the three-region analysis is 0.065, and the minimum F_ST for the six-region analysis is 0.085. Both of these are less than the average F_ST from genetic studies (average estimates of 0.10–0.11). The smaller value of the minimum F_ST estimates is expected since it provides an estimate of F_ST expected under complete heritability. Using an estimate of average craniometric heritability from the literature provides an estimate of F_ST of 0.112 for the three-region analysis and 0.144 for the six-region analysis. These results show that genetic and craniometric data are in agreement, qualitatively and quantitatively, and that there is limited variation in modern humans among major geographic regions. © 1994 Wiley-Liss, Inc.     

Genetic structure of lions (Panthera leo L.) in the Selous Game Reserve: implications for the evolution of sociality

Abstract We use 14 microsatellites to examine the genetic structure of a lion (Panthera leo L.) population in southern Tanzania. Heterozygosity levels were high (0.75 ± 0.08). Relatedness estimates showed that prides often had close relatives in neighbouring prides, whereas few relatives were found in prides not sharing a border. The drop‐off in relatedness with distance was highly significant. Female pridemates exhibited a higher mean relatedness (0.26 ± 0.07) to one another than did pride males (0.11 ± 0.07). Mean relatedness among females was significantly higher in small prides than in large ones. Prides exhibited significant inbreeding avoidance (F_IL: ?0.11). Mating did not detectably differ from random across prides (F_IT: ?0.02 ns). In addition to being recognizable behavioural and demographic units, prides were statistically distinct genetic units (F_LT: 0.07). Some neighbouring prides grouped together both geographically and genetically, forming ‘superprides’ in the population (F_ZT = 0.05). Thus, although individual prides were genetically distinct, there was an important genetic structure above the level of social groups.     

Genetic Demographic Description of the Ust-Aldan Rural Population of Sakha Republic (Yakutia): Migrations and Marriage Structure

Migrations, dynamics of the gametic structure of rural populations, and marriage structure with respect to birthplaces and inbreeding estimated from isonymy have been studied in the Ust-Aldan ulus (administrative district) of Sakha Republic (Yakutia). The villages studied (Byadi, Dyupsya, and Cheriktey) are characterized by intense migration; however, the migration radius is small (most migrations occur within the district). The rural populations studied differ in the intensities and directions of gamete flows and their dynamics. There is no substantial gamete flow into the Ust-Aldan population from outside Sakha Republic. About 50% of marriages contracted in this population are homolocal (between residents of the same district); the endogamy is low (15%). In most cases of heterolocal marriages (contracted between residents of different districts), one of the spouses is a local resident. The inbreeding estimated from isonymy is F _IT = 0.002930 in Yakuts; it is mainly accounted for by the nonrandom component (F _IS = 0.002232 and F _ST = 0.000700).