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394 results for “Microsatellite data”
Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)
Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall heterozygosity was markedly consistent between populations (from 0.54 to 0.57). All loci also amplified in the endangered congener P. fitzgeraldii but only five of the loci had more than one allele. Conclusions: These 15 loci are the first microsatellite markers developed in the genus Pherosphaera. These loci will be useful for investigating the species' extant genetic diversity and structure, the impact of past environmental change and the significance of asexual reproduction.
Data from: Dissimilarity of individual microsatellite profiles under different mutation models: empirical approach
Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.
Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments
High levels of intra-specific variation are commonly observed in natural microbial populations, yet the consequences of this variation for ecological and evolutionary processes remains poorly understood. Protists are excellent experimental models for investigating fundamental and applied questions in ecology and evolution, but studying intra-specific variation remains a challenge due to a lack of molecular resources to aid in quantifying and distinguishing strains during experiments. Here we present a molecular method, quantitative microsatellite genotyping, to accurately quantify strain specific frequencies from microcosm experiments of the marine flagellate Oxyrrhis marina, both between many pairs of strains and between strains in a multi-strain mixture. We find that for pairs of strains the method is effective for relative frequencies as low as 0.02 and with around 99% accuracy. The method is able to quantify four strains reasonably well, though less accurately than for pairs (range 92%-97% accuracy). This makes accessible a cheap and easy to implement method for quantifying strain (or allele) frequencies, and is suitable for use in a broad range of single celled eukaryotes (Protists) where copy number should correlate well with number of individuals (i.e. cells). This opens up the possibility of examining the role of intra-specific variation using experimental protist microcosms.
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>
Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape
<p>The dataset consists of 9 microsatellite markers used to analyze reticulated flatwoods salamanders' (<em>Ambystoma bishopi</em>) population structure on Eglin AFB. Samples came from various breeding ponds and allele sizes were scored using GeneMapper (GeneMapper v4.0; Applied Biosystems). Data was collected via allele scoring in GeneMapper by two independent researchers. Allele sizes for each individual have been re-formatted for various programs using the microsatellite Add-in in Excel as well as by using the GenAlEx extension in Excel. </p>
Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence
<p><span><span><span><span><span><span><span><span><span><span><span>Three subspecies of Northern Bahamian Rock Iguanas, <i>Cyclura cychlura</i>, are currently recognized: <i>C. c. cychlura,</i>restricted to Andros Island, and <i>C. c. figginsi</i> and <i>C. c. inornata,</i> native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of <i>C. cychlura</i> are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: <i>C. cychlura</i> iguanas, their ticks (genus <i>Amblyomma</i>, preferentially parasitizing these reptiles), and <i>Rickettsia </i>spp. endosymbionts (within tick ectoparasites). Our results indicate that while <i>C. c. cychlura</i> on Andros is consistently supported as a separate clade, patterns of relatedness among populations of <i>C. c. figginsi</i> and <i>C. c. inornata</i> within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and <i>Rickettsia</i> spp., supports the evolutionary independence of <i>C. c. inornata</i>. Further, these patterns are also consistent with two independent evolutionarily significant units within <i>C. c. figginsi</i>. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.</span></span></span></span></span></span></span></span></span></span></span></p>
Microsatellite genotypes and associated data for: Tetrasporophyte bias coupled with heterozygote deficiency in Antarctic Plocamium sp. (Rhodophyta)
<p>Meiosis and syngamy generate an alternation between two ploidy stages, but the timing of these two processes varies widely across taxa, thereby generating life cycle diversity. One hypothesis suggests that life cycles with long-lived haploid stages are correlated with selfing, asexual reproduction, or both. Though mostly studied in angiosperms, selfing and asexual reproduction are often associated with marginal habitats. Yet, in haploid-diploid macroalgae, these two reproductive modes have subtle, but unique consequences whereby predictions from angiosperms may not apply. Along the western Antarctic Peninsula, there is a thriving macroalgal community, providing an opportunity to explore reproductive system variation in haploid-diploid macroalgae at high latitudes where endemism is common. <em>Plocamium </em>sp. is a widespread and abundant red macroalga found within this ecosystem. We sampled twelve sites during 2017 and 2018 field seasons and used ten microsatellite loci to describe the reproductive system. Overall genotypic richness and evenness were high, suggesting sexual reproduction. Eight sites were dominated by tetrasporophytes, but there was strong heterozygote deficiency, suggesting intergametophytic selfing. We found slight differences in the prevailing reproductive mode among sites, possibly due to local conditions (e.g., disturbance) that may contribute to site-specific variation. It remains to be determined whether high levels of selfing are characteristic of macroalgae more generally at high latitudes or due to the haploid-diploid life cycle. Further investigations of algal life cycles will likely reveal the processes underlying the maintenance of sexual reproduction more broadly across eukaryotes, but more studies of natural populations are required.</p>
Data of the paper "The ionospheric exploration based on TJU#01 meteorological microsatellite mission: initial results"
<p>Ionospheric occultation data of the paper "The ionospheric exploration based on TJU#01 meteorological microsatellite mission: initial results"</p>
Microsatellite and morphological data for Carpobrotus species sampled from 40 different populations
<p>Microsatellite data for six loci and 698 individuals of Carpobrotus species sampled from 40 different population</p> <p>Morphological data for individuals of Carpobrotus species from 40 different populations</p>
Aardvark microsatellite data for southern and east Africa
<p><strong>Aim:</strong> As climate change accelerates, assessing how climate shapes gene flow and neutral and adaptive genetic differentiation on landscapes is increasingly important. Aardvarks (<em>Orycteropus</em> <em>afer</em>) are ecologically important in sub-Saharan Africa but are sensitive to human pressures and increasing aridity. We used individual, population, and landscape genetic approaches to infer the influence of landscape, climate, and potential adaptive differences on gene flow.</p> <p><strong>Location</strong>: We surveyed 8 protected and 4 privately owned areas in South Africa, 2 protected areas in Eswatini, and one location in Kenya during 2016–2018.</p> <p><strong>Methods</strong>: We developed microsatellite markers and methods for DNA extraction from feces, collected and genotyped fecal samples from focal areas, and estimated genetic structure. We inferred space use from individual redetections, tested for close relatives, and estimated genetic neighborhood distance. We applied individual-based landscape genetic analyses at multiple scales across South Africa to test hypotheses about genetic differentiation by landscape resistance and potential adaptive differences.</p> <p><strong>Results</strong>: We developed 19 variable microsatellite loci and collected 253 fecal samples from 13 focal areas. We genotyped 104 samples successfully at ≥8 loci as needed for individual identification. Genetic structure suggested 3 regional divisions in South Africa. We detected individuals at locations ≤7.3 km distant and closely related individuals at ≤44 km; genetic neighborhood distance was <55 km. Lower precipitation increased landscape resistance and strongly predicted genetic differentiation at most spatial scales. Temperature differences at sampling sites also influenced structure, suggesting climate-associated adaptive differences.</p> <p><strong>Main Conclusions</strong>: Genetic structure of aardvarks in South Africa and Eswatini is strongly shaped by climate, with arid areas limiting gene flow, and reflects apparent isolation by adaptation associated with temperature. Dispersal distances likely are <45 km. The markers we developed will facilitate studies of space use, dispersal, population density, or survival. Aridification will increase fragmentation and we recommend monitoring aardvark presence as an indicator of ecosystem change associated with aridification.</p>
Microsatellite marker data for Chernobyl Daphnia populations
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Data from: Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs.
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Data from: Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers
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Data from: Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri
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Data from: Mitochondrial and microsatellite DNA markers reveal a Balkanic origin for the highly invasive Horse-Chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae)
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Data from: Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances
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Screening and microsatellite data for Varroa infesting resistant honey bee pupae
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Lampsilis siliquoidea and L. radiata seven microsatellite loci data set
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Data from: Conservation genetics of Neotropical pollinators revisited: microsatellite analysis suggests that diploid males are rare in orchid bees
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Data from: Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)
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OpenNeuro
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