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222 results for “genetic interactions”
Data from: The hidden side of a major marine biogeographic boundary: a wide mosaic hybrid zone at the Atlantic–Mediterranean divide reveals the complex interaction between natural and genetic barriers in mussels
The Almeria-Oran Front (AOF) is a recognised hotspot of genetic differentiation in the sea. It is a barrier to dispersal and an ecological boundary, which explain the position of genetic breaks. However, the maintenance of genetic differentiation is likely reinforced by genetic barriers. A general drawback of previous studies is an insufficient density of sampling sites at the transition zone with a conspicuous lack of samples from the southern coastline. We analysed the genetic structure in the mussel Mytilus galloprovincialis with ancestry-informative loci. We discovered a 600 km wide mosaic hybrid zone eastward of the AOF along the Algerian coasts. This mosaic zone provides a new twist to our understanding of the Atlantic-Mediterranean transition because it demonstrates the two lineages can live in sympatry but hardly interbreed. This implies some form of reproductive isolation must exist to maintain the two genetic backgrounds locally cohesive. The zone ends with an abrupt genetic shift at a barrier to dispersal in the Gulf of Bejaia. Simulations in models that account for hydrodynamic features of the region support the hypothesis that sister hybrid zones could have been differentially trapped at two alternative barriers to dispersal or environmental boundaries. A preponderantly unidirectional north-south gene flow next to the AOF can also maintain a patch of an intrinsically maintained genetic background in the south and the mosaic structure. Our results concur with the coupling hypothesis that suggests natural barriers mostly explain the position of genetic breaks while their maintenance must additionally require genetic barriers.
Data from: Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions
The oxidative phosphorylation (OxPhos) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins. The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects and how they may affect human health and disease. In many different organisms, healthy nuclear and mitochondrial genome hybrids between species or among distant populations within a species affect fitness and OxPhos functions. However, what is less understood is whether these interactions impact individuals within a single natural population. The significance of this impact depends on the strength of selection for mito-nuclear interactions. We examined whether mito-nuclear interactions alter allele frequencies for ~11,000 nuclear SNPs within a single, natural Fundulus heteroclitus population containing two divergent mitochondrial haplotypes (mt-haplotypes). Between the two mt-haplotypes, there are significant nuclear allele frequency differences for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of the genome, these 349 outlier SNPs form two groups associated with each mt-haplotype, with a minority of individuals having mixed ancestry. We use this mixed ancestry in combination with mt-haplotype as a polygenic factor to explain a significant fraction of the individual OxPhos variation. These data suggest that mito-nuclear interactions affect cardiac OxPhos function. The 349 outlier SNPs occur in genes involved in regulating metabolic processes but are not directly associated with the 79 nuclear OxPhos proteins. Therefore, we postulate that the evolution of mito-nuclear interactions affects OxPhos function by acting upstream of OxPhos.
Data from: Genetic parameters in subtropical pine F1 hybrids: heritabilities, between-trait correlations and genotype-by-environment interactions
Growth and stem straightness traits of 29 Pinus caribaea var. hondurensis × Pinus tecunumanii (PCH × PTEC) and 26 P. caribaea var. hondurensis × Pinus oocarpa (PCH × POOC) hybrid pair-crosses plus a total of 16 intraspecific families were assessed at ages 5, 8 and 15 years from planting at two sites. The PCH × PTEC hybrid was the most productive, yielding 37 % more than a Pinus elliottii local control and was 21 % superior to either parental species in DBH growth. PCH × POOC hybrid was, on average, 16 % superior to either parental species for DBH. Narrow-sense heritability estimates were low to moderate for growth traits (average of 0.27) and stem straightness (0.16). The estimated additive genetic correlations between growth traits and ages within traits were high (>0.8) and positive, providing confidence in early selection based on diameter at breast height. The high proportion of estimated additive genetic variance compared to dominance variance in the F1 pine hybrids suggests that breeding strategies that maximize the use of additive genetic variance may be effective. The ranking of the 11 PCH parents based on general hybridizing ability predictions (estimated breeding values as hybrids) was somewhat inconsistent between PTEC and POOC hybrid crosses for all traits (r 9 d.f. = 0.38–0.45; p ∼0.15–0.25). There was no evidence of practically important G × E interaction for the hybrids except for PCH × PTEC height growth. This study suggests that a single, multi-hybrid breeding population seems appropriate in Zimbabwe if the trial sites are representative of the planting target zone.
On the utility of Cas13d for genetic interaction mapping
<p>Scripts to calculate tau values and genetic interaction (GI) scores in knockdown experiments using Cas13d. </p>
Evaluation of Cas13d as a tool for genetic interaction mapping
<p>This zenodo upload contains the scripts for the calculation of tau values and genetic interaction scores (GI) in knockdown experiments with Cas13d. In addition to the scripts for determining the tau values and GI scores (Calculate_tau_and_GI.zip), the script for creating the plots used and the reference files for the publication “On the utility of Cas13d for genetic interaction mapping” are also provided. Further information can be found in the README. </p>
Data from: The many dimensions of diet breadth: phytochemical, genetic, behavioral, and physiological perspectives on the interaction between a native herbivore and an exotic host
From the perspective of an herbivorous insect, conspecific host plants are not identical, and intraspecific variation in host nutritional quality or defensive capacity might mediate spatially variable outcomes in plant-insect interactions. Here we explore this possibility in the context of an ongoing host breadth expansion of a native butterfly (the Melissa blue, Lycaeides melissa) onto an exotic host plant (alfalfa, Medicago sativa). We examine variation among seven alfalfa populations that differed in terms of colonization by L. melissa; specifically, we examined variation in phytochemistry, foliar protein, and plant population genetic structure, as well as responses of caterpillars and adult butterflies to foliage from the same populations. Regional patterns of alfalfa colonization by L. melissa were well predicted by phytochemical variation, and colonized patches of alfalfa showed a similar level of inter-individual phytochemical diversity. However, phytochemical variation was a poor predictor of larval performance, despite the fact that survival and weight gain differed dramatically among caterpillars reared on plants from different alfalfa populations. Moreover, we observed a mismatch between alfalfa supporting the best larval performance and alfalfa favored by ovipositing females. Thus, the axes of plant variation that mediate interactions with L. melissa depend upon herbivore life history stage, which raises important issues for our understanding of adaptation to novel resources by an organism with a complex life history.
FIGURE 1 in An interactive identification key for genets and oyans (Carnivora, Viverridae, Genettinae, Genetta spp. and Poiana spp.) using Xper²
FIGURE 1. Xper² interface showing the three columns with adjustable labels: (left) identification procedure, with character partitions ("Groups"), characters ("Descriptors"), character states ("States") and characters used ("Description in progress"); (central) contextual information on taxa and characters, with "Definition" and "Images"; (right) list of "Remaining taxa" and "Dismissed taxa".
Data from: Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts
<p>Several studies have demonstrated the ecological consequences of genetic variation within a single plant species. For example, these studies show that individual plant genotypes support unique composition of the plants' associated arthropod community. By contrast, fewer studies have explored how plant genetic variation may influence evolutionary dynamics in the plant's associated species. Here, we examine how aphids respond evolutionarily to genetic variation in their host plant. We conducted two experiments to examine local adaptation and rapid evolution of the free-feeding aphid <i>Chaitophorus populicola</i> across genetic variants of its host plant, <i>Populus angustifolia</i>. To test for local adaptation, we collected tree cuttings and aphid colonies from three sites along an elevation / climate gradient and conducted a reciprocal transplant experiment. In general, home aphids (aphid transplanted onto trees from the same site) produced 1.7-3.4 times as many offspring as foreign aphids (aphids transplanted onto trees from different sites). To test for rapid evolution, we used 4 clonally replicated aphid genotypes and transplanted each onto 5 clonally replicated <i>P. angustifolia</i> genotypes. Each tree genotype started with the same aphid genotype composition. After 21 days (~two aphid generations), aphid genotype composition changed (i.e. aphids evolved) and some tree genotypes supported unique evolutionary trajectories of aphids. These results suggest that plant evolution in response to human perturbation, such as climate change and invasive species will also result in evolutionary responses in strongly interacting species that could cascade to affect whole communities.</p>
The genotype data accompanying the paper titled "Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia"
<p>The newly generated genome-wide genotype data for 10 Lao individuals used in the paper "Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia" ( https://www.nature.com/articles/s41598-023-35507-8 )</p>
Interaction Between Genetic Factors and Maternal Stressors During Pregnancy in the Risk of Postpartum Depression
ClinicalTrials.gov study NCT01648816. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Breast Cancer in Poland: An Expanded Study to Assess Occupational and Environmental Factors and Interactions With Genetics
ClinicalTrials.gov study NCT00341458. IPD Sharing: Not stated. Countries: 1. Publications: 4.
DIetary plAnt Extracts, Colonic MicrObes, and Apoe geNetics Interactions stuDy
ClinicalTrials.gov study NCT05905822. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Drug & Gene Interaction Risk Analysis With & Without Genetic Testing Among Patients Undergoing MTM
ClinicalTrials.gov study NCT02428660. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Genetic, Environment and Its Interaction Analysis for Cardiovascular Autonomic Neuropathy
ClinicalTrials.gov study NCT02461342. IPD Sharing: Not stated. Countries: 1. Publications: 14.
Prospective Study of VEGFR-2 /IL-8 Genetic Interaction in MBC Treated With Paclitaxel and Bevacizumab vs. Chemotherapy
ClinicalTrials.gov study NCT02329639. IPD Sharing: Not stated. 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: Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change
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Data from: Social interactions predict genetic diversification: an experimental manipulation in shorebirds
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Data from: Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts
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Data from: Effects of arbuscular mycorrhizal fungi on aboveground tri-trophic interactions are contingent upon plant genetic effects of cross type in the perennial herb Ruellia nudiflora
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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.