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101 results for “Microsatellite genotyping”
Microsatellite genotypes of Camellia oleifera for GenoDive analysis
<p><i>Camellia oleifera</i>, a hexaploid evergreen broadleaf shrub or small tree, is the dominant woody oilseed crop in China. Understanding the spatial pattern of genetic diversity in wild <i>C. oleifera</i> is essential for conservation and utilization of genetic resources. Six wild <i>C. oleifera</i> populations were sampled along a latitudinal gradient in subtropical evergreen broadleaf forests of Southern China. A new high-throughput sequencing-based microsatellite genotyping method was developed to resolve allele dosage uncertainty in hexaploid wild <i>C. oleifera </i>with 35 microsatellite markers. Finally, the dataset of mcrosatellite genotypes was generated with corrected allele dosages. In addition, another dataset of microsatellite genotypes with uncorrected allele dosages (showing only different alleles) was generated, for mimicking the situation of current microsatellite genotyping methods.</p>
Guppy MHC and microsatellite genotypes, gyrodactylid infection trials, and analysis code
<p>Natural host populations differ in their susceptibility to infection by parasites, and these intra-population differences are still an incompletely understood component of host-parasite dynamics. In this study, we used controlled infection experiments with wild-caught guppies (<em>Poecilia reticulata</em>) and their ectoparasite <em>Gyrodactylus turnbulli</em> to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with Major Histocompatibility Complex (MHC) 'supertypes'. Controlling for intra-population differences and potential inbreeding variance, we found a significant negative relationship between individual-level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype-specific effects. We conclude that population-level differences in host infection susceptibility likely reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.</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
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Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA
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Data from: Mating system of Caiman yacare (Reptilia Alligatoridae) described from microsatellite genotypes
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Data from: Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae)
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Data from: Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle
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Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?
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Microsatellite genotype data for captive and wild Arabian leopards
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Guppy MHC and microsatellite genotypes, gyrodactylid infection trials, and analysis code
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Multi-locus microsatellite genotypes of Pocillopora acuta (Scleractinia: Pocilloporidae) in the Bolinao-Anda Reef Complex, Philippines
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Microsatellite genotypes of Camellia oleifera for GenoDive analysis
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Microsatellite genotypes for Gambusia marshi
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Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
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Microsatellites raw genotypes of Aedes koreicus mosquitoes
<p>Genotypes of single mosquito of the species <em>Aedes koreicus</em>; genotyping was performed using capillary electrophoresis (Fragment Length Analysis) by Eurofins Genomics at 10 loci specific for <em>Ae. koreicus</em>.</p>
Data from: Cost effective microsatellite isolation and genotyping by high throughput sequencing
High throughput sequencing (HTS) has emerged as a valuable tool for the rapid isolation of genetic markers for population genetics and pedigree analysis. HTS-based SNP (single nucleotide polymorphism) genotyping protocols like RAD (Restriction-site associated DNA) sequencing or hybrid capture, allow for the isolation of thousands of markers from any non-model organism. However, these protocols are relatively laborious and expensive and the resulting high marker density is not always necessary. Since HTS technology has also greatly simplified the isolation and genotyping process of microsatellite markers, we develop microsatellite markers as a cost efficient and simple alternative to SNP genotyping. We present low coverage genome sequencing data from seven distantly related spider species (Argiope bruennichi, Larinia jeskovi, Oedothorax restusus, Pisaura mirabilis, Australomisidia ergandros, Cheiracanthium punctorium, Theridion grallator) and show the utility of HTS for microsatellite isolation. We also present a simple Illumina amplicon sequencing protocol to genotype microsatellites from multiplex PCR amplicons in the Hawaiian happy face spider T. grallator. We discuss advantages and drawbacks of the use of microsatellites for a range of research questions, and highlight an unexpectedly fast decay and gain of repeat loci for T. grallator.
Kimberley Fish microsatellite genotypes
<ol> <li>Dispersal is a critically important process that dictates population persistence, gene flow and evolutionary potential and is an essential element for identifying species conservation risks. This project aims to investigate the contributions of dispersal syndromes and hydrographic barriers on patterns of population connectivity and genetic structure in fishes occupying the particularly rugged and fragmented landscape of the Kimberley Plateau, Western Australia.</li> <li>We assessed population genetic structure between three neighbouring catchments (the Mitchell, King Edward and Drysdale rivers) in three congeneric groups of freshwater fishes that exhibit varied dispersal syndromes within and among groups: (1) <i>Melanotaenia australis</i> and <i>M. gracilis</i>; (2) <i>Syncomistes trigonicus </i>and <i>S. rastellus</i>; (3) <i>Hephaestus jenkinsi</i> and <i>H. epirrhinos</i>. Within each species we sampled the upper, middle and lower reaches of each catchment and assessed patterns of gene flow between and within catchments using microsatellite markers.</li> <li>Our results suggest that contemporary connectivity between catchments is greatly limited or absent in all study species, regardless of their dispersal syndromes. However, gene flow within catchments varied in line with predicted dispersal potential with poor dispersers exhibiting limited gene flow and significant genetic structuring.</li> <li>We conclude that the rugged landscape and historical habitat isolation has contributed to patterns of population fragmentation among fish populations from different river catchments. However, it appears dispersal syndromes influence connectivity and gene flow within catchments, where landscape constraints are not as pervasive.</li> <li>This study presents a comparative population genetic analysis of freshwater fishes with differing dispersal syndromes and colonisation ability. Our findings provide new insights into factors shaping patterns of biodiversity on the Kimberley Plateau, and the evolutionary uniqueness of fish communities from different river catchments draining the plateau. The results from this study provide a framework for informing the management of the region's unique freshwater biodiversity.</li> </ol>
Kimberley Fish microsatellite genotypes
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Data from: Cost effective microsatellite isolation and genotyping by high throughput sequencing
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Microsatellite genotypes of Aedes japonicus collected in Belgium and Germany
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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
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.