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104 results for “genotypic variation”
Data from: Genotypic variation in a foundation tree (Populus tremula L.) explains community structure of associated epiphytes
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Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)
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Data from: Genotype-by-genotype specificity remains robust to average temperature variation in an aphid/endosymbiont/parasitoid system
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Data from: Genetic variation and clonal diversity in introduced populations of Mimulus guttatus assessed by genotyping at 62 single nucleotide polymorphism loci
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Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes (Apiaceae) using genotyping-by-sequencing
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Genetic variation, genotypic and phenotypic correlation, heritability, and path coefficient analysis of yield and yield related traits in bread wheat (Triticum aestivum L.) varieties at Gitilo Dale, western Ethiopia
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Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
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Data from: True colors: commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential
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Data for: Plasticity and co-variation of root traits govern phosphorus acquisition among 20 wheat genotypes
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Data from: Connecting thermal performance curve variation to the genotype: a multivariate QTL approach
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Raw data used in: Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets
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Data from: How to measure maturation: a comparison of probabilistic methods used to test for genotypic variation and plasticity in the decision to mature
Maturation is a developmental trait that plays a key role in shaping organisms' life-history. However, progress in understanding how maturation phenotypes evolve has been held back by confusion over how best to model maturation decisions and a lack of studies comparing genotypic variation in maturation. Here, we fitted probabilistic maturation reaction norms (PMRNs) to data collected from five clones of Daphnia magna and five of Daphnia pulex collected from within and between different populations. We directly compared the utility of modeling approaches that assume maturation to be a process with an instantaneous rate with those that do not by fitting maturation rate and logistic regression models, and emphasize similarities and differences between them. Our results demonstrate that in Daphnia, PMRNs using a logistic regression approach were simpler to use and provided a better fit to the data. The decision to mature was plastic across a range of growth trajectories and dependent upon both body size and age. However, the age effect was stronger in D. magna than D. pulex and varied considerably between clones. Our results support the idea that maturation thresholds can evolve but also suggest that the notion of a threshold based on a single fixed state is an oversimplification that underestimates the adaptability of these important traits.
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.
Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon
<p>Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population histories and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism (SNP) genotypic data from archival scale samples, and demonstrate its application to a study of kokanee salmon (<i>Oncorhynchus nerka</i>) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (>90% average genotyping across all individuals) and low genotyping error (<0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrate GT-seq as a valuable tool for genome-wide data collection from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.</p>
Data from: Phytochemical traits underlie genotypic variation in susceptibility of quaking aspen (Populus tremuloides) to browsing by a keystone forest ungulate
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Data from: Genotypic and phenotypic variation in transmission traits of a complex life cycle parasite
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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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Genotypic variation in parasite avoidance behavior and other mechanistic, non-linear components of transmission
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Data from: Grain of environment explains variation in the strength of genotype × environment interaction
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Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.