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788 results for “genotypic data”
Data from: Genotypic variation in plant traits shapes herbivorous insect and ant communities on a foundation tree species
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Data from: Thermal plasticity in protective wing pigmentation is modulated by genotype and food availability in an insect model of seasonal polyphenism
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Autosomal SNP-genotype data of brown bears (Ursus arctos) in Finland
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Data from: Genotype predicts quantitative song variety in a chickadee hybrid zone despite limited sampling
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Microsatellite Genotype data of <em>Populus fremontii</em> and <em>Populus angustifolia</em>
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Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples
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Genotypic data for Ruditapes decussatus (European clam), including 13,438 SNPs genotyped across 213 individuals
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Data from: Lack of genotype-by-environment interaction suggests limited potential for evolutionary changes in plasticity in the eastern oyster, Crassostrea virginica
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Data from: Genotype and social environment influence female-female interactions in a non-social insect
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Genotype data for: Demographic and genetic consequences of a steelhead supplementation program
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Genotypic data from: Lab-based evaluation of the reproductive performance of trojan (MYY) brook trout (Salvelinus fontinalis)
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Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
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Data for: Russian honey bee genotype identification through enhanced marker panel set
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Data from: Plasticity in hydraulic architecture: Riparian trees respond to increased temperatures with genotype-specific adjustments to leaf traits
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Data from: A socially polymorphic Formica ant species exhibits a novel distribution of social supergene genotypes
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Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status
<p>Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (<em>Crotalus oreganus</em>) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.</p>
Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies
Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes.
Data from: Genotype-specific effects of ericoid mycorrhizae on floral traits and reproduction in Vaccinium corymbosum
PREMISE OF THE STUDY: Most plants interact with mycorrhizal fungi and animal pollinators simultaneously. Yet, the effects of mycorrhizae on pollination are poorly understood. Here, we examined how inoculation with ericoid mycorrhizal fungi affected flowering phenology, floral traits, and reproductive success among eight genotypes of Vaccinium corymbosum (Ericaceae). We asked three overarching questions: 1) do genotypes differ in response to inoculation? 2) How does inoculation affect floral and flowering traits? 3) Are inoculated plants more attractive to pollinators and thus less pollen limited than non-inoculated plants of the same genotype? METHODS: To examine these questions, we experimentally inoculated plants with fungal spores at planting, grew them in the field, and took flowering and floral measurements over two years. In year two, we conducted a hand-pollination experiment to test if plants differed in pollen limitation. KEY RESULTS: Our results demonstrated that inoculated plants had significantly higher levels of colonization for some genotypes but not all, and there were significant floral trait changes in inoculated plants for some genotypes as well. On average, inoculated plants produced significantly larger floral displays, more fruits/inflorescence, and heavier fruits with lower sugar content, than non-inoculated, control plants. Hand pollination enhanced the production of fruits, and fruit mass, for non-inoculated plants but not for those that were inoculated. CONCLUSIONS: Our results demonstrate that ericoid mycorrhizal fungi enhance flowering and alter investment in reproduction in genotype-specific ways. These findings underscore the importance of examining belowground symbionts to fully understand the drivers of aboveground interactions.
Predictive biomarkers of individual trajectories in elderly persons with subtle cognitive decline: APOE genotype data
<p>The mentalizing network (MN) treats social interactions based on our understanding of other people's intentions and includes the medial prefrontal cortex (mPFC), temporoparietal junction (TPJ), posterior cingulate cortex (PCC), precuneus (PC) and amygdala. Not all elders are equally affected by the aging-related decrease of mentalizing abilities. Personality has recently emerged as a strong determinant of functional connectivity in MN areas. However, its impact on volumetric changes across the mentalizing network in brain aging is still unknown. To address this issue, we explored the determinants of volume decrease in MN components including amyloid burden, personality, and APOE genotyping in a previously established cohort of 130 healthy elders with a mean follow-up of 54 months. Personality was assessed with the Neuroticism Extraversion Openness Personality Inventory-Revised. Regression models corrected for multiple comparisons were used to identify predictors of volume loss including time, age, sex, personality, amyloid load, presence of APOE epsilon 4 allele and cognitive evolution. In cases with higher Agreeableness scores, there were lower volume losses in posterior cingulate cortex (PCC), precuneus (PC) and amygdala bilaterally. This was also the case for right medial prefrontal cortex (mPFC) in elders displaying lower Agreeableness and Conscientiousness. In multiple regression models, the effect of Agreeableness was still observed in left PC and right amygdala and that of Conscientiousness in right mPFC volume loss (26.3% of variability, significant age, sex). Several Agreeableness (Modesty) and Conscientiousness (order, dutifulness, achievement striving and self-discipline) facets were positively related to increased volume loss in cortical components of the MN. In conclusion, these data challenge the beneficial role of higher levels of Agreeableness and Conscientiousness in old age showing that they are associated with an increased rate of volume loss within the mentalizing network.</p>
Microsatellite genotypes and ITS2 DNA sequence data for Seriatopora hystrix
<p>Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral, <i>Seriatopora hystrix</i> were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. Seriatopora hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa.As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones.Based on microsatellite analyses three groups could be distinguished within the WIO: (I) north Madagascar, (II) south-west Madagascar together with one site in northern Mozambique (Nacala), and (III) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of <i>S. hystrix,</i> and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.</p> <p> </p>
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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.