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738 results for “Microsatellite”
Data from: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita, however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species M. eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *BEAST and isolation-with-migration (IM) and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.
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.
Data from: Multiplex preamplification PCR and microsatellite validation allows accurate single nucleotide polymorphism (SNP) genotyping of historical fish scales
Incorporating historical tissues into the study of ecological, conservation, and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for preexisting DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for preexisting DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect preexisting DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Preexisting contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The potential for automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.
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>
Nereocystis luetkeana microsatellite data (Genepop format)
<p>In temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe <em>Nereocystis luetkeana</em> genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades. We utilized microsatellite markers to study <em>N. luetkeana</em> genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models. At the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island's outer coast and Juan de Fuca Strait; Washington's inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region. The levels of allelic richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in Haida Gwaii and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.</p>
Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
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>
Isolation and characterization of twelve polymorphic microsatellite markers in the endangered Hopea hainanensis (Dipterocarpaceae)
<p>Using next-generation sequencing technology, 26 microsatellite markers were developed and genotyped by capillary electrophoresis for <i>Hopea</i> <i>hainanensis</i> Merrill & Chun, an endangered tree species in Hainan Island and northern Vietnam. Twelve markers were found to be polymorphic in this species. Primer transferability was tested with <i>H</i>. <i>chinensis</i> Hand.-Mazz. and <i>H</i>.<i> reticulata</i> Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The 12 polymorphic microsatellite markers could be applied to population genetic studies aimed at <i>H</i>. <i>hainanensis</i> as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable <i>Hopea</i> species.</p>
The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa
<p>Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (H<sub>e</sub> : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.</p>
Drakaea glyptodon nuclear microsatellite and chloroplast haplotype data
<p class="CxSpFirst">Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. <span>Ten</span> populations of the common terrestrial orchid <i>Drakaea glyptodon</i> from Southwest Australia were genotyped with ten nuclear and five chloroplast SSR markers. Levels and partitioning of genetic variation, and effective population sizes (<i>N</i><sub>e</sub>), were estimated. Spatial genetic structure of nuclear diversity, together with chloroplast data, are used to infer the effective number of seed parents per population. We found high genetic diversity, <i>N</i><sub>e</sub> values that generally exceed predictions based on the number of flowering individuals, and moderate levels of gene flow. Two populations were founded by < 5 colonists suggesting some populations are colonized by few seeds, with growth largely resulting from <i>in situ</i> recruitment. A value of 3.65 for <i>m</i><sub>p </sub>/<i>m</i><sub>s</sub> indicates that pollinators play a greater role than seed in introducing genetic diversity to populations via gene flow. Our results highlight that <i>D. glyptodon</i> is highly effective at persisting in patchily distributed populations. However, it is important to examine how insights from this common, widespread species transfer to species that are rare and/or occur in fragmented landscapes.</p>
Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
<p class="CuerpoAA">The genetic diversity of a population is the foundation of its adaptability to environmental challenges. The South American fur seal is a widely distributed pinniped in the south cone of South America. However, a large gap in the Pacific coast separates two distinct evolutionary units for the species: the Peruvian and the Southern Pacific/Atlantic populations. Throughout the Pacific, one of the main breeding colonies is located in Guafo Island, in the southern Chilean Patagonia. As the closest reproductive population to the isolated Peruvian group, Guafo's colony may potentially facilitate gene flow, contribute with new alleles and increase genetic variability to Peruvian populations', connecting the entire Pacific's distribution of the species. In this study, Guafo's Island South American fur seal population was characterized by the identification and genotyping of species-specific microsatellite markers. As a result, we confirm that Guafo's colony is a diverse group with mild evidence of genetic structure. Although a couple of family groups among seasons were observed, results indicate that half-siblings are rare and suggest that polygyny in this species is more relaxed than previously thought. Additionally, three full-sibling pairs were genetically identified within the 2017 season, which is the first genetic support that describes the presence of twins for the species. These attributes suggest that the colony at Guafo is a panmictic large group, and could serve as a potential genetic source for other isolated populations.</p>
Microsatellite marker data for Chernobyl Daphnia populations
<p>Populations experiencing varying levels of ionising radiation provide an excellent opportunity to study the fundamental drivers of evolution. Radiation can cause mutations, and thus supply genetic variation; it can also selectively remove individuals that are unable to cope with the physiological stresses associated with radiation exposure, or non-selectively cull swathes of the population, reducing genetic variation. Since the nuclear power plant explosion in 1986, the Chernobyl area has experienced a spatially heterogeneous exposure to varying levels of ionising radiation. We sampled <em>Daphnia pulex</em> (a freshwater crustacean) from lakes across the Chernobyl area, genotyped them at ten microsatellite loci, and also calculated the current radiation dose rates. We then investigated whether the pattern of genetic diversity was positively associated with radiation dose rates, consistent with radiation-mediated supply of de novo mutations, or negatively associated with radiation dose rates, as would be expected with strong radiation-mediated selection. We found that measures of genetic diversity, including expected heterozygosity and mean allelic richness (an unbiased indicator of diversity) were significantly higher in lakes that experienced the highest radiation dose rates. This suggests that mutation outweighs selection as the key evolutionary force in populations exposed to high radiation dose rates. We also found significant but weak population structure, indicative of low genetic drift, and clear evidence for isolation by distance between populations. This further suggests gene flow between nearby populations is eroding population structure, and that mutational input in high radiation lakes could, ultimately, supply genetic variation to lower radiation sites.</p>
Supplementary Materials for Evaluation role of ferroptosis long non-coding RNAs for immune microenvironment and microsatellite instability in colon cancer
<p>Supplementary Materials for "Evaluation role of ferroptosis long non-coding RNAs for immune microenvironment and microsatellite instability in colon cancer"</p>
Orchis nuclear microsatellite data
<p><b>Premise of the study </b>The genetic structure of hybrid zones provides an insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (<i>Orchis anthropophora</i>, <i>O. militaris</i>, <i>O. purpurea</i> and <i>O. simia</i>) hybridize when they co-occur. We aimed to characterize patterns of hybridization in <i>O. militaris – O. purpurea</i>, <i>O. purpurea – O. simia</i> and <i>O. anthropophora – O. simia</i> hybrid zones using molecular and morphological data.</p> <p><b>Methods </b>We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape.</p> <p><b>Key Results </b>Backcrossing was asymmetric towards <i>O. militaris</i> in multiple <i>O. militaris – O. purpurea</i> hybrid zones. Hybrids in <i>O. purpurea – O. simia</i> and <i>O. anthropophora – O. simia</i> hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data which correlated strongly with nuclear microsatellite data in all three species combinations.</p> <p><b>Conclusions </b>The co-existence of parental and admixed individuals in these <i>Orchis</i> hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa.</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>
Field data and microsatellite genotypes of Cercidiphyllum japonicum
<p>Field data and genotypes at five microsatellite loci of 281 <i>Cercidiphyllum japonicum </i>adults of a population distributed over a ca. 80 ha along a stream and 755 <i>C. japonicum </i>current-year seedlings sampled at approximate center of the populatoin. The population is located in Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan.</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>
Microsatellite data set
<p>Microsatellite data set for article RADICAL TEMPORAL SHIFT IN THE GENETIC COMPOSITION OF NEW ENGLAND CHICORY POPULATIONS published in Journal of Ecology.</p>
Microsatellites of Desmophyllum dianthus - Patagonia
<p>Final dataset of microsatellites used in Addamo et al., 2022 "The shrunk genetic diversity of coral populations in North-Central Patagonia calls for management and conservation plans for marine resources" Scientific Reports 2022, 12:14894 DOI: 10.1038/s41598-022-19277-3:</p> <p>28 microsatellites, 223 individuals,12 sampling locations</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.