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83 results for “microsatellite loci”
Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.
Data from: Development of nuclear microsatellite loci and mitochondrial single nucleotide polymorphisms for the natterjack toad, Bufo (Epidalea) calamita (Bufonidae), using next generation sequencing and Competitive Allele Specific PCR (KASPar)
Amphibians are undergoing a major decline worldwide and the steady increase in the number of threatened species in this particular taxa highlights the need for conservation genetics studies using high-quality molecular markers. The natterjack toad, Bufo (Epidalea) calamita, is a vulnerable pioneering species confined to specialized habitats in Western Europe. To provide efficient and cost-effective genetic resources for conservation biologists, we developed and characterized 22 new nuclear microsatellite markers using next-generation sequencing. We also used sequence data acquired from Sanger sequencing to develop the first mitochondrial markers for KASPar assay genotyping. Genetic polymorphism was then analyzed for 95 toads sampled from 5 populations in France. For polymorphic microsatellite loci, number of alleles and expected heterozygosity ranged from 2 to 14 and from 0.035 to 0.720, respectively. No significant departures from panmixia were observed (mean multilocus F IS = −0.015) and population differentiation was substantial (mean multilocus F ST = 0.222, P < 0.001). From a set of 18 mitochondrial SNPs located in the 16S and D-loop region, we further developed a fast and cost-effective SNP genotyping method based on competitive allele-specific PCR amplification (KASPar). The combination of allelic states for these mitochondrial DNA SNP markers yielded 10 different haplotypes, ranging from 2 to 5 within populations. Populations were highly differentiated (G ST = 0.407, P < 0.001). These new genetic resources will facilitate future parentage, population genetics and phylogeographical studies and will be useful for both evolutionary and conservation concerns, especially for the set-up of management strategies and the definition of distinct evolutionary significant units.
Data from: Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)
Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent–offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop-out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent–offspring pairs and unintentionally recaptured individuals, respectively. By direct-count error estimates, the recapture and known parent–offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent–offspring comparisons. Furthermore, there was no correlation in locus-specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus-specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent–offspring comparisons in parentage studies).
Data from: Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia
Microsatellite markers are important tools in population, conservation and forensic studies and are frequently used for species delineation, the detection of hybridization and introgression. Therefore, marker sets that amplify variable DNA regions in two species are required; however, cross-species amplification is often difficult, as genotyping errors such as null alleles may occur. In order to estimate the level of potential misidentifications based on genotyping errors, we compared the occurrence of parental alleles in laboratory and natural Daphnia hybrids (Daphnia longispina group). We tested a set of twelve microsatellite loci with regard to their suitability for unambiguous species and hybrid class identification using F1 hybrids bred in the laboratory. Further, a large set of 44 natural populations of D. cucullata, D. galeata and D. longispina (1715 individuals) as well as their interspecific hybrids were genotyped to validate the discriminatory power of different marker combinations. Species delineation using microsatellite multi-locus genotypes produced reliable results for all three studied species using assignment tests. D. galeata x cucullata hybrid detection was limited due to three loci exhibiting D. cucullata specific null alleles which most likely are caused by differences in primer binding sites of parental species. Overall discriminatory power in hybrid detection was improved when a subset of markers was identified that amplifies equally well in both species.
Data from: Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)
Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
Allele scores and frequencies of 66 microsatellite locus loci in Solenopsis invicta
<p>Allele scores and frequencies of 66 microsatellite loci in <em>Solenopsis invicta </em>samples were analyzed from 65 populations and 1,074 individuals.</p> <p>65 populations were collected from South Korea, China, Taiwan, and the United States.</p>
Microsatellite (13 loci) and plastid DNA haplotypes in a population of Antirrhinum charidemi
<p>Genotype matrix of 182 Antirrhinum charidemi individuals sampled in 2007-2009 in the Barranco del Dragoncillo Blanco population in Cabo de Gata, Almería, Spain. Genotypes are given for 13 microsatellite loci and also include 3 plastid DNA haplotypes. Details on loci and genotyping conditions can be found in Forrest et al. 2017, https://doi.org/10.1093/botlinnean/bow002. Each individual is geolocated. Additional information include its corolla colour, its ancestry score in four gene pools obtained in Bayesian genetic cluster analysis (STRUCTURE), and its assignment to geo-genetic subpopulations. Metadata are available in a separate tab in the submitted spreadsheet. The data are analysed in a paper expected to be published in AoB Plants in 2025, titled: "Fine-scale genetic differentiation in the bee-specialized Antirrhinum charidemi covaries more strongly with microenvironment than with corolla colour"</p>
12 nuclear microsatellite loci scores for 543 adult trees of Tilia cordata in Lithuainia
<p>Genetic signature of the natural genepool of <i>Tilia cordata</i> Mill. in Lithuania: compound evolutionary and anthropogenic effects</p> <p><i>Tilia cordata</i> Mill. is a valuable tree species enriching the ecological values of the coniferous dominated boreal forests in Europe. Following the historical decline, spreading of <i>Tilia</i> sp. is challenged by the elevated inbreeding and habitat fragmentation. We studied the geographical distribution of genetic diversity of <i>Tilia cordata</i> populations in Lithuania. We used 14 genomic microsatellite markers to genotype 543 individuals from 23 wild growing populations. We found that <i>Tilia cordata</i> retained high levels of genetic diversity (population F<sub>is</sub> = 0 to 0.15, H<sub>o </sub>= 0.53 to 0.69, H<sub>e </sub>= 0.56 to 0.75). AMOVA, Bayesian clustering and Monmonier's barrier detection indicate weak but significant differentiation among the populations (F<sub>st</sub> = 0.037***) into geographically interpretable clusters of (a) western Lithuania with high genetic heterogeneity but low genetic diversity, bottleneck effects, (b) relatively higher genetic diversity of <i>Tilia cordata</i> on rich and most soils of midland lowland, and (c) the most differentiated populations on poor soils of the coolest north-eastern highland possessing the highest rare allele frequency but elevated inbreeding and bottleneck effects. Weak genetic differentiation among the <i>Tilia cordata</i> populations in Lithuania implies common ancestry, absence of strong adaptive gradients and effective genetic exchange possible mediated via the riparian networks. A hypothesis on riparian networks as geneflow mediators in <i>Tilia cordata</i> was raised based on results of this study.</p>
Scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu (Philippines) based on the fragment length size of their respective alleles
<p>Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.</p>
Allele scores and frequencies of 66 microsatellite locus loci in Solenopsis geminata
<p>Allele scores and frequencies of 66 microsatellite loci in <em>Solenopsis geminata</em> samples were analyzed from 18 populations and 131 individuals.</p> <p>Eighteen populations were collected from South Korea, Laos, Myanmar, Thailand, and the United States.</p>
Primers designed for red deer microsatellite loci
<p>Primers designed for microsatellite loci in the red deer genome</p>
Microsatellite loci in the red deer genome
<p>Position of microsatellite motifs in the red deer genome. </p>
Genotype data of 14 nuclear microsatellite loci for 18 Quercus chenii populations in China
<p>This dataset includes genotype data of 14 nuclear microsatellite loci for 419 individuals of Quercus chenii from 18 natural populations in China.</p>
Data from: Stabilising selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci
The loci arginine vasopressin receptor 1a (avpr1a) and oxytocin receptor (oxtr) have evolutionarily conserved roles in vertebrate social and sexual behavior. Allelic variation at a microsatellite locus in the 5' regulatory region of these genes is associated with fitness in the bank vole Myodes glareolus. Given the low frequency of long and short alleles at these microsatellite loci in wild bank voles, we used breeding trials to determine whether selection acts against long and short alleles. Female bank voles with intermediate length avpr1a alleles had the highest probability of breeding, while male voles whose avpr1a alleles were very different in length had reduced probability of breeding. Moreover, there was a significant interaction between male and female oxtr genotypes, where potential breeding pairs with dissimilar length alleles had reduced probability of breeding. These data show how genetic variation at microsatellite loci associated with avpr1a and oxtr is associated with fitness, and highlight complex patterns of selection at these loci. More widely, these data show how stabilising selection might act on allele length frequency distributions at gene-associated microsatellite loci.
Lampsilis siliquoidea and L. radiata seven microsatellite loci data set
<p>The data set corresponds to genotypes of individuals belonging to <i>Lampsilis siliquoidea</i> and <i>L. radiata </i>which are two closely related freshwater mussel species [Bivalvia: Unionidae]. Individual genotypes consist of seven microsatellite loci developed by Eackles and King 2002. Genotypes were used to asses population genetic structure above and below waterfalls in the lower Great Lakes (USA) and to investigate the degree of hybridization between these two species. </p>
Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa
<p>Many highly social species show plasticity in their social structure in response to different environmental conditions. For example, typical colonies of the yellowjacket wasp <i>Vespula squamosa </i>are headed by a single reproductive queen and survive for only a single season. However, in warmer climates, <i>V. squamosa</i> colonies sometimes persist for multiple years and can grow to extremely large size. We used genetic markers to understand patterns of reproduction and recruitment within these perennial colonies. We genotyped <i>V. squamosa</i> workers, pre-reproductive queens, and males from perennial colonies in the southeastern United States at 10 polymorphic microsatellite loci and one mitochondrial DNA locus. We found that <i>V. squamosa</i> from perennial nests were produced by multiple reproductives, in contrast to typical annual colonies. Relatedness of nestmates from perennial colonies was significantly lower than relatedness of nestmates from annual colonies. Our analyses of mitochondrial DNA indicated that most <i>V. squamosa</i> perennial colonies represented semi-closed systems whereby all individuals belonged to a single matriline despite the presence of multiple reproductive females. However, new queens recruited into perennial colonies apparently mated with non-nestmate males. Notably, perennial and annual colonies did not show significant genetic differences, supporting the hypothesis that perennial colony formation represents an instance of social phenotypic plasticity. Overall, our results indicate that perennial <i>V. squamosa</i> colonies show substantial changes to their social biology compared to typical annual colonies.</p>
Lampsilis siliquoidea and L. radiata seven microsatellite loci data set
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Data from: Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)
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Data from: A suite of potentially amplifiable microsatellite loci for ten reptiles of conservation concern from Africa and Asia
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Data from: SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)
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