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210 results for “phenotypic effects”
Data and R script for Neville, Andrews, Nettle and Bateson, 'Dissociating the effects of alternative early-life feeding schedules on the development of adult depression-like phenotypes'
<p>The R script and raw data files for the paper 'Dissociating the effects of alternative early-life feeding schedules on the development of adult depression-like phenotypes', by Vikki Neville, Clare Andrews, Daniel Nettle and Melissa Bateson.</p>
Effects of phenotypic plasticity on species coexistence
<p>Data generated during a study on the effects of phenotypic plasticity on species coexistence.</p> <p>Hess_etal_Data_Competition_01.csv contains data generated during competition trials between two species (Lemna minor and Spirodela polyrhiza). Prior to the competition trials, replicate populations of these species were subject to one of two different levels of an experimental treatment - either low-frequency plasticity-induction or a high-frequency plasticity-induction. Refer to manuscript for full details.</p> <p>Hess_etal_Data_Traits_01.csv contains data on morphological traits of Lemna minor and Spirodela polyrhiza subject to either low- or high-frequency plasticity-induction. Refer to manuscript for full details.</p> <p> </p> <p> </p>
Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana
<p>Data and code from: "Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana" published at Annals of Botany PLANTS. This is a dataset on phenotypic traits of Arabidopsis in response to different abiotic stresses and a reproducible R script to generate all figures and tables in the publication.</p>
Direct and indirect phenotypic effects on sociability indicate potential to evolve
<p class="MsoNormal">The decision to leave or join a group is important as group size influences many aspects of organisms' lives and their fitness. This tendency to socialise with others, sociability, should be influenced by genes carried by focal individuals (direct genetic effects) and by genes in partner individuals (indirect genetic effects), indicating the trait's evolution could be slower or faster than expected. However, estimating these genetic parameters is difficult. Here, in a laboratory population of the cockroach <em>Blaptica dubia</em>, I estimate phenotypic parameters for sociability: repeatability (<em><span>R</span></em>) and repeatable influence (<em><span>RI</span></em>), which indicate whether direct and indirect genetic effects respectively are likely. I also estimate the interaction coefficient (<em><span>Ψ</span></em><em>)</em>, which quantifies how strongly a partner's trait influences the phenotype of the focal individual and is key in models for the evolution of interacting phenotypes. Focal individuals were somewhat repeatable for sociability across a three-week period (<em><span>R</span></em> = 0.080), and partners also had marginally consistent effects on focal sociability (<em><span>RI</span></em> = 0.053). The interaction coefficient was non-zero, although in the opposite sign for the sexes; males preferred to associate with larger individuals (<em><span>Ψ</span></em><sub>male </sub>= -0.129) while females preferred to associate with smaller individuals (<em><span>Ψ</span></em><sub>female</sub><strong><sub> </sub></strong>= 0.071). Individual sociability was consistent between dyadic trials and in social networks of groups. These results provide phenotypic evidence that direct and indirect genetic effects have limited influence on sociability, with perhaps the most evolutionary potential stemming from heritable effects of the body mass of partners. Sex-specific interaction coefficients may produce sexual conflict and the evolution of sexual dimorphism in social behaviour.</p>
Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly
<p><span>In alpine systems, cushion plants act as foundation species by ameliorating local environmental conditions. Empirical studies indicate that contrasting phenotypes of alpine cushion species have different effects on understory plant species, either facilitative or competitive. Furthermore, dependent species within each community type might also exhibit different responses to each cushion phenotype, which can be clustered into several "response groups". Additionally, these species-groups specific responses to alpine cushion species phenotypes could alter community assembly. However, very few studies have assessed responses of dependent communities at species-group levels, in particular for both above- and below-ground communities. Here, we selected a loose and a tight phenotype of the alpine cushion species <em>Thylacospermum</em> <em>caespitosum</em> in two sites in northwest China, and use the relative intensity of interactions index to quantify cushion plant effects on subordinate communities of plants and soil fungi and bacteria. We assessed variations in responses of both above- and below-ground organisms to cushion plant effects at species-group level. Species-group level analyses showed that the effects of the phenotype varied among groups of each of the three community types, and different species-groups were composed of unique taxa. Additionally, we found that loose cushions enhanced stochastic processes in community assembly, for plants and soil fungi but not for soil bacteria. These variations of phenotypic effects on different species-group induced contrasting taxonomic composition between groups and altered community assembly thereby. Our study highlights the occurrence of contrasting effects of two phenotypes of a foundation cushion plant on understory plants, soil fungi and bacteria community composition, but not necessarily on their richness. We also showed that assessing responses of understory species at the species-group level allows a more realistic and mechanistic understanding of biotic interactions both for above- and below-ground communities.</span></p>
Data from: Testing the evolutionary potential of an alpine plant: Phenotypic plasticity in response to growth temperature outweighs parental environmental effects and other genetic causes of variation
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The effect of urbanisation and local environmental heterogeneity on phenotypic variability of a tropical treefrog
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Data from: The city and forest bird flock together in a common garden: Genetic and environmental effects drive urban phenotypic divergence
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Direct and indirect phenotypic effects on sociability indicate potential to evolve
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Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly
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Data from: Genetic and environmental effects on morphological traits of social phenotypes in wasps
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Data from: Phenotype-environment matching predicts both positive and negative effects of intraspecific variation
Natural populations can vary considerably in their genotypic and/or phenotypic diversity. Differences in this intraspecific diversity can have important consequences for contemporary ecological dynamics, but the direction and magnitude of these effects appear inconsistent across studies and systems. Here we proposed and tested the hypothesis that context-dependent ecological effects of altering phenotypic variance are predictable and arise from the relationship between a population's mean phenotype and the local environmental optimum. By factorially manipulating the mean and variance of a key host trait in environments with and without a lethal parasite, we demonstrate that increasing phenotypic variance can have beneficial effects for host populations (e.g. smaller disease epidemics), but only when the population's initial phenotype was poorly-matched to the local environment. When phenotypes were initially well-suited to environmental conditions, in contrast, greater phenotypic variance led to larger disease epidemics. Significant reductions in individual susceptibility occurred in both contexts over time, but the mechanisms leading to those reductions differed; strong selection was caused by either a 'suboptimal' trait mean and insufficient trait variance, or a 'near-optimal' trait mean and too much trait variance. Increasing intraspecific variation is clearly not always beneficial for populations, instead producing predictable ecological and evolutionary effects that depend on environmental context and biological interactions.
Data from: Transgenerational effects in an ecological context: conditioning of adult sea urchins to upwelling conditions alters maternal provisioning and progeny phenotype
Transgenerational plasticity occurs when the conditions experienced by the parental generation influences the phenotype of their progeny. This may in turn affect progeny performance and physiological tolerance, providing a means by which organisms cope with rapid environmental change. We conditioned adult purple sea urchins, Strongylocentrotus purpuratus, to combined pCO2 and temperature conditions reflective of in situ conditions of their natural habitat, the benthos in kelp forests of nearshore California, and then assessed the performance of their progeny raised under different pCO2 levels. Adults were conditioned during gametogenesis to treatments that reflected static non-upwelling (~650 μatm pCO2, ~17°C) and upwelling (~1300 μatm pCO2, ~13°C) conditions. Following approximately 4 months of conditioning, the adults were spawned and embryos were raised under low pCO2 (~450 μatm pCO2) or high pCO2 (~1050 μatm pCO2) treatments to determine if differential maternal conditioning impacted the progeny response to a single abiotic stressor: pCO2. We examined the size, protein content, and lipid content of eggs from both sets of conditioned female urchins. Offspring were sampled at four stages of early development: hatched blastula, gastrula, prism, and echinopluteus. This resulted in four sets of offspring: (1) progeny from non-upwelling-conditioned mothers raised under low pCO2, (2) progeny from non-upwelling-conditioned mothers raised under high pCO2, (3) progeny from upwelling-conditioned mothers raised under low pCO2, and (4) progeny from upwelling-conditioned mothers raised under high pCO2. We then assessed the effects of maternal conditioning along with the effects of developmental pCO2 levels on body size of the progeny. Our results showed that differential maternal conditioning had no impact on average egg size, although non-upwelling females produced eggs that were more variable in size. Maternal conditioning did not affect protein content but did have a modest impact on egg lipid content. Developing embryos whose mothers were conditioned to simulated upwelling conditions (~1300 μatm pCO2, ~13°C) were greater in body size, although this effect was no longer evident at the echinopluteus larval stage. Although maternal conditioning affected offspring body size, the pCO2 levels under which the embryos were raised did not. Overall, this laboratory study provides insight into how transgenerational effects may function in nature. The impacts of parental environmental history on progeny phenotype during early development have important implications regarding recruitment success and population-level effects.
Data from: Phenotypic plasticity and the effects of thermal fluctuations on specialists and generalists
<p>Classical theories predict that relatively constant environments should generally favor specialists, while fluctuating environments should select for generalists. However, theoretical and empirical results have pointed out that generalist organisms might on the contrary perform poorly under fluctuations. In particular, if generalism is underlaid by phenotypic plasticity, performance of generalists should be modulated by the temporal characteristics of environmental fluctuations. Here, we used experiments in microcosms and a mathematical model to test whether the period or autocorrelation of thermal fluctuations mediate links between the level of generalism and the performance of organisms under fluctuations. In the experiment, thermal fluctuations consistently impeded performance compared to constant conditions. However, the intensity of this effect depended on the level of generalism: while the more specialists strains performed better under fast or negatively autocorrelated fluctuations, plastic generalists performed better under slow or positively autocorrelated fluctuations. Our model suggests that these effects of fluctuations on organisms' performance may result from a time delay in the expression of plasticity, restricting its benefits to slow-enough fluctuations. This study points out the need to further investigate the temporal dynamics of phenotypic plasticity to better predict its fitness consequences under environmental fluctuations.</p>
Wildfire as a natural stressor and its effect on female phenotype and ornament development
<p>Controlled low-intensity fires are commonly used in ecosystem management for both habitat restoration and wildfire management. Animals in those ecosystems may respond to fire by shifting energy allocation away from reproduction and growth, and toward maintenance. Stress-induced shifts in energy allocation may affect expression of condition-dependent sexual signals, which are sensitive to energetic and physiological trade-offs mediated by glucocorticoids. Here, we examine the effect of fire on ornament expression, corticosterone, and other phenotypic traits in a population of striped plateau lizards, <i>Sceloporus virgatus</i>, affected by the Horseshoe 2 Fire in the Chiricahua Mountains, Arizona, USA. The condition-dependent female ornament was significantly smaller the month following the fire than two years prior, and was both smaller and less orange on the burned site relative to a nearby unburned site. These patterns are similar to those found in a previous experimental study examining the response of the ornament to corticosterone manipulations. Yet, in the current study, corticosterone levels were not different in lizards on the burned and unburned sites. Perhaps glucocorticoid levels already returned to baseline, or do not adequately track environmental change. Females tended to be smaller and lighter on the burned site than the unburned site, however the year after the fire, body condition was higher for females on the burned site, indicating a rapid recovery and potential long-term benefits in response to low-intensity fires in this fire-adapted ecosystem. We found that the lizards adjusted energy allocation away from sexual signaling and growth in response to low-intensity fires. As fires and fire management are likely to increase in response to changing fire regimes across the globe, it will be important to consider behavioral and physiological responses of impacted species, as well as population, community, and ecosystem level responses.</p>
Effects of semi-constant temperature on embryonic and hatchling phenotypes of six-tubercled Amazon River turtles, Podocnemis sextuberculata
<p><strong>Purpose:</strong> We evaluated how constant incubation temperatures affect life-history traits pre-hatching and post-hatching of the six-tubercled Amazon River turtle, <em>Podocnemis sextuberculata</em>.</p> <p><strong>Methods:</strong> We incubated eggs from natural nests at ten semi-constant temperatures between 22.26±1.01°C and 37.37±0.38°C (2013) and at six temperatures between 25.75±0.22°C and 36.17±0.15°C (2016). In 2013, we raised hatchling for 90 days to evaluate effects of temperature on early hatchling growth. We evaluated maternal effects in 2016.</p> <p><strong>Results:</strong> <em>P. sextuberculata</em> displays temperature-dependent sex determination and produces males at colder and females at warmer temperatures (TSD Ia). The estimated pivotal temperature was 33.73 ± 0.15°C and the transitional range of temperatures (TRT) 1.16 ± 0.59°C. Semi-constant temperatures below 26°C and above 38°C were lethal. Intermediate temperatures (32.25°C and 31.5°C, respectively) were optimal for hatching success and produced larger hatchlings that grew slower early in life compared to colder or warmer conditions, which produced smaller hatchlings. Warmer incubation temperatures within the optimal range (28°C-37°C) accelerated embryonic development. In contrast, comparisons of 30, 60 and 90 days-old suggests that warmer incubation temperatures reduced growth and mass gain rates post-hatching, such that incubation temperature effects on body size at emergence disappeared by 3 months of age.</p> <p><strong>Conclusions</strong>: Six-tubercled Amazon River turtles showed the highest pivotal temperature reported for any turtle. The relatively narrow TRT may limit the evolutionary potential of this vulnerable turtle in the face of global warming. Future incubation experiments at a finer scale (33°C-36°C) are warranted to refine the sex-ratio reaction norm. Field studies that monitor natural nests are imperative to evaluate conservation measures and the effect of female-biased illegal hunting and climate change. By providing data about the thermal biology of an understudied lineage of non-model species, our study helps fill gaps in our understanding of the evolution of vertebrate sex determination and its potential adaptive value.</p>
The diverse effects of phenotypic dominance on hybrid fitness
<p>When divergent populations interbreed, their alleles are brought together in hybrids. In the initial F1 cross, most divergent loci are heterozygous. Therefore, F1 fitness can be influenced by dominance effects that could not have been selected to function well together. We present a systematic study of these F1 dominance effects by introducing variable phenotypic dominance into Fisher's geometric model. We show that dominance often reduces hybrid fitness, which can generate optimal outbreeding followed by a steady decline in F1 fitness, as is often observed. We also show that "lucky" beneficial effects sometimes arise by chance, which might be important when hybrids can access novel environments. We then show that dominance can lead to violations of Haldane's Rule (reduced fitness of the heterogametic F1) but strengthens Darwin's Corollary (F1 fitness differences between cross directions). Taken together, results show that the effects of dominance on hybrid fitness can be surprisingly difficult to isolate because they often resemble the effects of uniparental inheritance or expression. Nevertheless, we identify a pattern of environment-dependent heterosis that only dominance can explain, and for which there is some suggestive evidence. Our results also show how existing data set upper bounds on the size of dominance effects. These bounds could explain why additive models often provide good predictions for later-generation recombinant hybrids, even when dominance qualitatively changes outcomes for the F1.</p>
Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies
<p>Examining how environmental factors influence phenotypic distribution might provide valuable information about local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of <em>Heliconius</em> butterflies displays a wide range of color patterns across the Neotropics and is involved in several hybrid zones, making it an excellent system to study color phenotypic distribution. Using a multiscale distribution strategy, we studied whether different phenotypes of the distantly related species <em>H. erato</em> and <em>H. melpomene,</em> belonging to the red-yellow mimetic ring, are associated with different environmental conditions. We show that environmental gradients (particularly heat and precipitation factors) drive <em>Heliconius</em> phenotypic distributions, but that phenotype and environmental correlations vary with spatial scale. While co-mimics are frequently found in similar environments at a broad scale, patterns at the local level are not necessarily consistent (different variables are the best predictors of phenotypic occurrence in different areas) or congruent (co-mimic pairs show distinct associations with the environment). Thus, large-scale analysis may help to identify how environmental heterogeneity influences broad mimic phenotypic distributions, but local studies are needed to understand the context-dependent biotic, abiotic, and historical mechanisms that drive finer-scale phenotypic shifts.</p>
Adaptive effects of parental and developmental environments on offspring survival, growth, and phenotype
<p><span>Phenotypic adjustments to environmental variation are particularly relevant to cope with putative environmental mismatches often imposed by natal dispersal.</span></p> <p><span>We used an inter-generational cross-transplant field-based experiment to evaluate the morphological and physiological effects of parental and post-settlement water flow environments on the orange-fin anemonefish <em>Amphiprion chrysopterus</em> through ontogeny (at pre- and post-settlement stages).</span></p> <p><span>Offspring born from parents under high water flow had an 18% higher caudal fin aspect ratio (</span><span>a compound measure of shape) at the pre-settlement stage, 10% slower growth after settlement, and 55% lower survival after settlement compared to offspring from low-water-flow parents. At the pre-settlement stage, caudal fin length was determined by parental caudal fin length. At the post-settlement stage, fish survived equally well with similar phenotypes in both high- and low-developmental-flow environments. However, results suggest potential developmental phenotypic plasticity in caudal fin length, which increases more under low water flow during development. After settlement growth was the only morphological or physiological trait that was associated with parental water flow, which was lower from parents under high flow, as was survival.</span></p> <p><span>These results give important insights into the parental contribution, both genetic and non-genetic, in determining early offspring phenotype and subsequent growth and survival. Our results also suggest that offspring may possess the flexibility </span><span>to cope with a wide range of local environments including those different from their parents. Overall, the findings of this study show the fitness consequences of living in different environments and the likely trade-offs between parental and offspring fitness in a wild population.</span></p>
Data and Results for: Cost-effective, high-throughput fruit phenotyping system for three-dimensional reconstruction of fruit form
<p>The dataset contains the raw data used for generating the results in the paper, and the reconstructed results at 1mm and 2mm voxel resolution.</p> <p><strong>Raw data</strong>: Samples are gathered into groups of five, DataObjects1-5.zip, ... , DataObjects56-59.zip.</p> <p>Once uncompressed, each directory holds the images and configuration information used for each sample. For instance, '1_obj' is for the first sample, and the 'data' folder has the image files by camera. In this case one camera was used, 'cam2', and there are 62 images. 'pattern_square_mm_external.txt', 'pattern_square_mm_internal.txt', and 'rotate_specification_file.txt' are all configuration files needed for the calibration step.</p> <p> </p> <p><strong>Results</strong>: Reconstructions results are in compressed folders 'reconstruction-results-1mm.zip' and 'reconstruction-results-2mm.zip' for 1 mm and 2 mm voxel resolutions, respectively. These results are three-dimensional model files than can be viewed with a variety of software, we have used the free MeshLab: https://www.meshlab.net/ .</p> <p> </p> <p> </p> <p> </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.