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104 results for “genotypic variation”
Genotypic variation in an ecologically important parasite is associated with host species, lake, and spore size
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Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression
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Data from: Genotypic variation in the induction and persistence of transgenerational responses to seasonal cues
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Data from: Testing genotypic variation of an invasive plant species in response to soil disturbance and herbivory
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Data from: Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges
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Data from: Genotypic variation in plant traits shapes herbivorous insect and ant communities on a foundation tree species
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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
<p>Several recent studies have shown that ectosymbiotic bacterial microbiota, including gut microbes, affect the growth and reproduction of <span class="MsoSubtleEmphasis">Daphnia</span>, a key organism in lake ecosystems. However, these studies examined specific species, such as the model organism, <i>D. magna,</i> and used green algae as food. It is unclear if symbiotic bacteria affect fitness in other <span class="MsoSubtleEmphasis">Daphnia</span> species common in lakes and ponds in Japan. In this study, we examined the growth rates of sterilized individuals of two <i>D. pulex</i> genotypes with <i>D. magna</i> using the green algae <i>Scenedesmus</i> and the diatom <i>Cyclotella</i> as algal diets. In addition, we examined the growth rate of the sterilized <span class="MsoSubtleEmphasis">Daphnia</span><i> pulex</i> individuals infected by <i>Limnohabitans</i> spp., previously reported to promote the fitness of <i>D. magna</i> as ectosymbiotic bacteria. We found that the effects of ectosymbiotic bacteria on growth rate differed not only between different genotypes of <i>D. pulex</i> but also between individuals fed the different algal diets. The results suggest that the genotype- and diet-specific differences in fitness-dependency on the ectosymbiotic microbiota can be factors affecting the genetic structures of <i>D. pulex</i> populations.</p>
Data from: Connecting thermal performance curve variation to the genotype: a multivariate QTL approach
Thermal performance curves (TPCs) are continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding trade-offs involved in thermal adaptation. While thermal trade-offs such as those between generalists and specialists or between hot- and cold-adapted phenotypes are known to be genetically variable and evolve during thermal adaptation, little is known of the genetic basis to TPCs – specifically, the loci involved and the directionality of their effects across different temperatures. To address this, we took a multivariate approach, mapping QTL for locomotor activity TPCs in the fly, Drosophila serrata using a panel of 76 recombinant inbred lines. The distribution of additive genetic (co)variance in the mapping population was remarkably similar to the distribution of mutational (co)variance for these traits. We detected 11 TPC-QTLs in females and 4 in males. Multivariate QTL effects were closely aligned with the major axes genetic (co)variation between temperatures; most QTL effects corresponded to variation for either overall increases or decreases in activity with a smaller number indicating possible trade-offs between activity at high and low temperatures. QTLs representing changes in curve shape such as the 'generalist-specialist' trade-off, thought key to thermal adaptation, were poorly represented in the data. We discuss these results in light of genetic constraints on thermal adaptation.
Data from: The susceptibility of Echinacea angustifolia to a specialist aphid: eco-evolutionary perspective on genotypic variation and demographic consequences
1. Plants and their herbivores may influence each other's fitness and, hence, genetic dynamics, as well as their demography. Conversely, variation in fitness-related traits may influence the occurrence or intensity of the interaction. Disentangling the fitness consequences of an interaction in nature from the influence of fitness variation on it is challenging, but important to clarifying the ecological and evolutionary dynamics of plants with their herbivores. 2. As part of a larger effort to elucidate eco-evolutionary dynamics in a population of Echinacea angustifolia that is subject to severe fragmentation, we initiated an experiment in 2001 to evaluate differences in fitness among plants of three genotypic classes resulting from matings of plants from different remnant populations ('between', B), plants randomly chosen from the same remnant ('within', W) and maternal siblings ('inbreds', I). The experiment was planted into a field undergoing restoration to a prairie community. Fitness components of individual plants were recorded through 2012. During 2004–2010, each plant was also monitored for its load of Aphis echinaceae, a specialist insect herbivore. 3. Within a season, aphid-load depended consistently on a plant's location and on its load the previous season. Further, flowering individuals generally harboured more aphids than non-flowering plants. In analyses of overall plant fitness, within each genotypic class, fitness was greatest for plants with the greatest aphid-loads, consistent with the preference of aphids for flowering individuals. Inbreeding depression was severe, with I plants producing 60% fewer achenes than W or B plants, and varied with aphid-load. To distinguish the role of aphid choice from the effect of aphid herbivory in the relationship between plant fitness and aphid-load, we evaluated how components of fitness varied with prior aphid-load. Notably, genotype I plants with high aphid-loads the previous year produced far fewer achenes per flower head than those that carried fewer aphids. 4. Synthesis. Sibmating reduces individuals' demographic contribution by 60% over the first 12 years. Outbred individuals tolerate this aphid; each produces on average about 200 achenes per head in a year, despite a heavy aphid-load the previous year. However, inbreeding, which is greater in severely fragmented prairie habitat, results in poor tolerance. Aphid herbivory exacerbates inbreeding depression, further reducing the contribution of those individuals to population growth. This study illustrates an approach that helps to distinguish fitness-dependent attraction of herbivores from the effects of herbivory on plant fitness and demography, a goal that is critically important to eco-evolutionary understanding.
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
Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
Data from: True colors: commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential
<p>Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANEL<sup>TM</sup> data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e<sup>-7</sup> and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to trace the mode by which characteristics have spread across breeds during historical breed formation; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial.</p>
Data for: Plasticity and co-variation of root traits govern phosphorus acquisition among 20 wheat genotypes
<p>Trait plasticity (variation of a trait under environmental variability or gradients) and trait integration are both crucial for plant adaption to environmental change. Variations in different suite of root traits such as biomass allocation, morphology and physiology underlie diverse phosphorus (P) acquisition strategies among plants. Yet, how the intraspecific plasticity and integration of root traits influence plant adaptation to different P supply remains obscure. To characterize diverse adaptive strategies in relation to plant P acquisition, eight root traits were assessed in 20 wheat (<em>Triticum aestivum</em> L.) genotypes grown in a culture room with low and high P supply. High P supply increased shoot P accumulation and biomass of all wheat genotypes. The shoot P accumulation in genotypes with high P sensitivity (PS: calculated as shoot P content at low P / shoot P content at high P supply) was higher with high P supply and lower with low P supply compared with that in the genotypes with low PS. The high-PS genotypes exhibited larger variation in root length, root/shoot ratio and rhizosphere pH across P supplies than the low-PS genotypes, suggesting an integrated response at the whole-plant level. At low P supply, the high-PS genotypes had greater root length and specific root length, but lower acid phosphatase activity than the low-PS genotypes, which suggests contrasting P-acquisition strategies across the genotypes. Strong co-variation of root traits occurred across low-PS genotypes regardless of P supply; conversely, the high-PS genotypes only exhibited strong trait integration at low P supply, whereas high P supply sharply reduced root trait co-variation. Our findings suggest that P stress may strengthen root trait integration in wheat plants, and that both plasticity and integration of root traits drive plant adaptive strategies and tolerance to P-deficiency stress.</p>
Life-history genotype explains variation in migration activity in Atlantic salmon (Salmo salar)
<p>Data and R-script used in the paper titled in the title.</p>
Data from: A set of plastid loci for use in multiplex fragment length genotyping for intraspecific variation in Pinus (Pinaceae)
Premise of the study: Recently released Pinus plastome sequences support characterization of 15 plastid Simple Sequence Repeat (ptSSR) loci originally published for P. contorta and P. thunbergii. This allows selection of loci for single-tube PCR multiplexed genotyping in any subsection of the genus. Methods: Unique placement of primers and primer conservation across the genus were investigated, and a set of six loci were selected for single-tube multiplexing. We compare interspecific variation between ptSSRs and nucleotide sequences of ycf1 then test intraspecific variation for ptSSRs using 911 samples in the P. ponderosa species complex. Results: The ptSSR loci contain mononucleotide and complex repeats with additional length variation in flanking regions. They are not located in hypervariable regions and most primers are conserved across the genus. A single PCR per sample multiplexed for six loci yielded 45 alleles in 911 samples. Discussion: The protocol allows efficient genotyping of many samples. The ptSSR loci are too variable for Pinus phylogenies but are useful for the study of genetic structure within and among populations. The multiplex method could easily be extended to other plant groups by choosing primers for ptSSR loci in a plastome alignment for the target group.
FIG. 3. Conchological diOEerentiation among the homozygous genotypes Aat 1 in Selection and habitat-speci®c allozyme variation in the self-fertilizing land snail Cochlicopa lubrica (O. F. MuÈller)
FIG. 3. Conchological diOEerentiation among the homozygous genotypes Aat 1`20 ' and Aat 1`80' of Cochlicopa lubrica. The two groups are very similar with respect to the four shell dimensions. Discriminant scores are extracted with`shell height',`shell diameter',`diameter of the last whorl' and`diameter of the penultimate shell whorl'. Data of 316 shells are incorporated.
Therapy With High Clopidogrel Dose or Prasugrel Standard Dose Reduces the Platelet Reactivity in Patients With Genotype Variation RESET GENE Trial
ClinicalTrials.gov study NCT01465828. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Human Genomic Population Structure and Phenotype-genotype Variation in ADME Genes in Four Populations
ClinicalTrials.gov study NCT02789527. IPD Sharing: UNDECIDED. Countries: 4. Publications: 1.
Phenotypic and Genotypic Variations of Enterococcus Spp
ClinicalTrials.gov study NCT05751317. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Genotype x environment interaction obscures genetic sources of variation in seed size in Dithyrea californica but provides the opportunity for selection on phenotypic plasticity
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Data from: The susceptibility of Echinacea angustifolia to a specialist aphid: eco-evolutionary perspective on genotypic variation and demographic consequences
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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.