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101 results for “Microsatellite genotyping”
Data from: Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model
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Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery
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Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments
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Genotypes of Swan Geese Anser cygnoides using 17 nuclear microsatellite loci at 14 locations.
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Data from: Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping
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Microsatellite genotypes and ITS2 DNA sequence data for Seriatopora hystrix
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Data from: Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations
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Microsatellite genotypes from non-invasive monitoring of hazel dormouse
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Data from: Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites
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Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa
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Microsatellite genotypes, cluster membership and metadata of Central European wolves (Canis lupus)
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Field data and microsatellite genotypes of Cercidiphyllum japonicum
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Microsatellite genotypes and extraction plate positions from publication: Genetic structure across urban and agricultural landscapes reveals evidence of resource specialization and philopatry in the Eastern carpenter bee, Xylocopa virginica L.
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Multi-locus microsatellite genotypes of Pocillopora acuta (Scleractinia: Pocilloporidae) in the Bolinao-Anda Reef Complex, Philippines
<p>This repository contains genotype data and sampling metadata used for the manuscript "Shifts in coral clonality along a gradient of disturbance: insights on reproduction and dispersal of <em>Pocillopora acuta</em>". The dataset contains genotypes of 428 <em>P. acuta </em>colonies using 16 polymorphic microsatellite loci, colony sizes, in-transect locations of each coral, and geographic coordinates of reef sites. These were used to examine clonal richness and structure, population genetic differentiation, and demographic and genetic connectivity within the reef system. In the study, we estimated the relative contribution of sexual and asexual modes of reproduction to population maintenance, and inferred the species' spatial scale of realized dispersal all against a backdrop of varying levels of wave exposure. </p>
Microsatellite genotype data from seven loci for a phylogeographic/population genetic study of the South African endemic freshwater crab Potamonautes lividus sampled from eight localities in the KwaZulu-Natal and Eastern Cape provinces in South Africa
<ol> <li>During the present study, the phylogeography of the only southern African IUCN Red Listed vulnerable (VU) freshwater crab, <i>Potamonautes lividus</i> was investigated by surveying several localities in the Eastern Cape and KwaZulu-Natal provinces in South Africa. Both nuclear and mitochondrial DNA markers were used, and it was hypothesized, that marked genetic differentiation should be present, while niche modeling was undertaken to explore the distribution of the species along the east coast of South Africa. <span><span>Further, the shortfalls in the present approach to IUCN Red Listing, as illustrated by a vulnerable species of crabs are discussed</span></span>.</li> <li>Results from the mtDNA revealed the presence of two haploclades confined to specimens from the two provinces respectively and the general absence of maternal dispersal; a fact that was further validated by the marked <i>F</i><sub>ST</sub> data and high F<sub>ST</sub>. Within the Eastern Cape haploclade, low frequency maternal dispersal occurred, corroborated by the low F<sub>ST</sub>. In contrast, no haplotypes were shared in the KwaZulu-Natal haploclade a fact corroborated by marked F<sub>ST</sub> differences. </li> <li>The microsatellite data demonstrated the presence of higher frequency, possibly paternally biased dispersal of specimens between the Eastern Cape and KwaZulu-Natal provinces. Our results suggest that presence of two distinct management units within <i>P. lividus</i>. Divergence time estimation suggest a late Pleistocene cladogenesis between the Eastern Cape and KwaZulu-Natal haploclades. </li> <li>Considering the presence of <i>P. lividus</i> in several newly collected nature conservation areas in both provinces, and its potential presence in the intermediary area based on the MAXENT niche modeling, our data suggest the species IUCN Red Listing status should be downgraded to LC.</li> <li>A comparison of all the EN, VU and CR IUCN Red Listed freshwater crabs for the entire Afrotropical region reveals the lack of recent sampling in the three biodiversity hotspots in West, Central and East Africa, with mountainous areas containing a disproportionate number of species with most species being devoid of phylogeographic study. </li> </ol>
Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?
Refugia are expected to preserve genetic variation of relict taxa, especially in polyploids, because high gene dosages could prevent genetic erosion in small isolated populations. However, other attributes linked to polyploidy, such as asexual reproduction, may strongly limit the levels of genetic variability in relict populations. Here, ploidy levels and patterns of genetic variation at nuclear microsatellite loci were analysed in Prunus lusitanica, a polyploid species with clonal reproduction that is considered a paradigmatic example of a Tertiary relict. Sampling in this study considered a total of 20 populations of three subspecies: mainland lusitanica (Iberian Peninsula and Morocco), and island azorica (Azores) and hixa (Canary Islands and Madeira). Flow cytometry results supported an octoploid genome for lusitanica and hixa, whereas a 16-ploid level was inferred for azorica. Fixed heterozygosity of a few allele variants at most microsatellite loci resulted in levels of allelic diversity much lower than those expected for a high-order polyploid. Islands as a whole did not contain higher levels of genetic variation (allelic or genotypic) than mainland refuges, but island populations displayed more private alleles and higher genotypic diversity in old volcanic areas. Patterns of microsatellite variation were compatible with the occurrence of clonal individuals in all but two island populations, and the incidence of clonality within populations negatively correlated with the estimated timing of colonization. Our results also suggest that gene flow has been very rare among populations, and thus population growth following founder events was apparently mediated by clonality rather than seed recruitment, especially in mainland areas. This study extends to clonal taxa the idea of oceanic islands as important refugia for biodiversity, since the conditions for generation and maintenance of clonal diversity (i.e. occasional events of sexual reproduction, mutation and/or seed immigration) appear to have been more frequent in these enclaves than in mainland areas.
Microsatellite genotypes for Gambusia marshi
<p>1. The valley of Cuatro Ciénegas in Coahuila, Mexico has the highest degree of local endemism of any habitat in North America. Despite the arid desert climate, the Cuatro Ciénegas basin harbors an extensive system of permanent streams, wetlands, and spring fed pools.</p> <p>2. Microsatellite loci were surveyed to infer genetic diversity and population structure of <i>Gambusia marshi</i>, a poeciliid fish endemic to the desert springs of the Cuatro Ciénegas basin and its outflow the Río Salado de Nadadores in Mexico.</p> <p>3. The Sierra de San Marcos and long-term isolation have played a vital role in shaping the current pattern of phylogeographic structure in<i> G. marshi</i>, and Bayesian clustering analysis revealed four genetic populations within <i>G. marshi</i> as well as a major east-west division of the of the species corresponding to the Sierra de San Marcos.</p> <p>4. Most sample sites exhibited high levels of genetic differentiation, although there is evidence for recent gene flow between some of these locations, presumably facilitated by irrigation canals. Although all populations exhibit genetic differentiation, the population of <i>G. marshi</i> in Poza Anteojo is extremely divergent and should be considered as an independent management unit.</p>
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
Microsatellite genotype data for captive and wild Arabian leopards
<p>Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbour genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (<em>Panthera pardus nimr</em>) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modelling approaches. We estimated a population size of 51 (95% CI: 32–79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population, as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realised load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. The next step in the recovery plan of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimise a strategy for genetic rescue as a tool to recover Arabia's last big cat.</p>
Data from: Mating system of Caiman yacare (Reptilia Alligatoridae) described from microsatellite genotypes
The yacare caiman (Caiman yacare) is a reptile from South America and 1 of the 2 crocodilian species present in Argentina. The degradation of their natural habitat and strong hunting pressure led to a sharp numerical decline of wild populations. Nowadays, C. yacare is included in Appendix II of CITES, and ranching practices in some areas in Argentina are helping hatching success. In this context, it is important to better understand the population structure and mating system of the species. To do this, we amplified 10 microsatellite markers (SSRs) in 148 individuals of 13 C. yacare nests. All of the markers were polymorphic with 2–12 alleles per locus, with allelic sizes ranging between 154 and 400 bp and medium levels of polymorphism (H o = 0.152–0.551 and H e = 0.221–0.621). We were able to determine the maternal genotype in 9 out of 13 nests. In 6 of them we found more than 1 paternal genotype, with a maximum of 3 fathers for a single nest. This study is the first to provide evidence of multiple paternity behavior. These findings will be useful to improve management and conservation strategies for the species.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.