Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
4,669
datasets available to search
ShareScore release 0.9.0
Dataset results
4,669 results for “Environment;”
Data from: Shifting fitness landscapes in response to altered environments
The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of adaptation. We thus demonstrate that an essential protein can harbor adaptive potential upon an environmental challenge, and report a remarkable fit of the data to a version of Fisher's geometric model that focuses on the fitness trade-offs between mutations in different environments.
Data from: A new method of Bayesian causal inference in non-stationary environments
Bayesian inference is the process of narrowing down the hypotheses (causes) to the one that best explains the observational data (effects). To accurately estimate a cause, a considerable amount of data is required to be observed for as long as possible. However, the object of inference is not always constant. In this case, a method such as exponential moving average (EMA) with a discounting rate is used to improve the ability to respond to a sudden change; it is also necessary to increase the discounting rate. That is, a trade-off is established in which the followability is improved by increasing the discounting rate, but the accuracy is reduced. Here, we propose an extended Bayesian inference (EBI), wherein human-like causal inference is incorporated. We show that both the learning and forgetting effects are introduced into Bayesian inference by incorporating the causal inference. We evaluate the estimation performance of the EBI through the learning task of a dynamically changing Gaussian mixture model. In the evaluation, the EBI performance is compared with those of the EMA and a sequential discounting expectation-maximization algorithm. The EBI was shown to modify the trade-off observed in the EMA.
Data from: Egg-laying environment modulates offspring responses to predation risk in an amphibian
Predator-induced plasticity has been in the focus of evolutionary ecological research in the last decades, but the consequences of temporal variation in the presence of cues predicting offspring environment have remained controversial. This is partly due to the fact that the role of early environmental effects has scarcely been scrutinized in this context while also controlling for potential maternal effects. In this study we investigated how past environmental conditions, i.e. different combinations of risky or safe adult (pre-natal) and oviposition (early post-natal) environments affected offspring's plastic responses in hatching time and locomotor activity to predation risk during development in the smooth newt (Lissotriton vulgaris). We found that females did not adjust their reproductive investment to the perceived level of risk in the adult environment, and this pre-natal environment had generally negligible effect on offspring phenotype. However, when predator cues were absent during oviposition, larvae raised in the presence of predator cues delayed their hatching and exhibited a decreased activity compared to control larvae developing without predator cues, which responses are advantageous when predators pose a threat to hatched larvae. In the presence of predator cues during oviposition, the difference in hatching time persisted,but the difference in general locomotor activity disappeared between risk-exposed and control larvae. Our findings provide clear experimental evidence that fine-scale temporal variation in a predictive cue during and after egg-laying interactively affect offspring phenotype, and highlight the importance of the early post-natal environment, which may exert a substantial influence on progeny's phenotype also under natural conditions.
Data from: Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments
Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p<0.05) and broader optimum thermal window for aerobic scope (>3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multi-variate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.
Data from: Pair bonding prevents reinforcing effects of testosterone in male California mice in an unfamiliar environment
Testosterone (T) can be released by stimuli such as social interactions, and thereby influence future social behaviours. Because the reinforcing effects of T can induce preferences for specific environmental locations, T has the potential to alter behaviour through space use. In a monogamous species, this T pulse may contribute differently to space use in sexually naive (SN) and pair-bonded (PB) males: SN males may be more likely to explore new areas to set up a territory than PB males, which are more likely to defend an existing, established territory. In this study, we test for variation in T-driven space use by examining variation in the formation of conditioned place preferences (CPPs) in SN and PB male California mice. In the three-chambered CPP apparatus, subcutaneous administrations of physiological levels of T were used to repeatedly condition SN and PB males to a side chamber, which is an unfamiliar/neutral environment. The final tests revealed that T-induced CPPs in the side chamber are developed in SN, but not PB males. This study fills a gap in our knowledge about plasticity in the rewarding nature of T pulses, based on past social experience.
Data from: Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments
Reaction norms or tolerance curves have often been used to predict how organisms deal with fluctuating environments. A potential drawback is that reaction norms measured in different constant environments may not capture all aspects of organismal responses to fluctuating environments. We examined growth of the filamentous fungus Neurospora crassa in fluctuating temperatures and tested if growth in fluctuating temperatures can be explained simply by growth in different constant temperatures or if more complex models are needed. In addition, as previous studies on fluctuating environments have revealed that past temperatures that organisms have experienced can affect their response to current temperature, we tested the roles of different epigenetic mechanisms in response to fluctuating environments using different mutants. We found that growth of Neurospora can be predicted in fluctuating temperatures to some extent if acclimation times are taken into account in the model. Interestingly, while fluctuating environments have been linked with epigenetic responses we found only some evidence of involvement of epigenetic mechanisms on tolerating fluctuating temperatures. Mutants which lacked H3K4 or H3K36 methylation had slightly impaired response to temperature fluctuations, in addition the H3K4 methylation mutant and a mutant in the RNA interference pathway had altered acclimation times.
Data from: Feedback between environment and traits under selection in a seasonal environment: consequences for experimental evolution
Batch cultures are frequently used in experimental evolution. Even though they are generally considered to simply drive a growth rate increase, traits evolution can be more complex. Indeed, recurrent batches form a seasonal environment as different phases repeat periodically and different traits can be under selection in the different seasons. Moreover, during culture the impact of organisms on the environment is important since the system is closed. Thus, the study of adaptation should take into account the environment and eco-evolutionary feedbacks. Using the data of an experimental evolution on yeast Saccharomyces cerevisiae, we develop a mathematical model to understand which traits are under selection, and what is the role of the environment for selection in a batch culture. We show that two kinds of traits are under selection in seasonal environments: life-history traits, related to growth and mortality, and transition traits, related to the ability to maintain high growth rate when the environment changes. The impact of environmental conditions can be summarized by the length of the different seasons which weight the importance of selection on each trait: the longer a season is, the higher is selection on the associated traits. Since phenotypes drive the length of each season, eco-evolutionary feedbacks emerge. Such feedbacks are known to promote coexistence between different species or strains. Our results show that the design of the batch in an experimental evolution can affect which traits are most selected because of these feedbacks.
Data from: Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation.
Organisms can protect themselves against future environmental change. An example is cross-protection, where physiological adaptation against a present environmental stressor can protect an organism against a future stressor. Another is anticipation, where an organism uses information about its present environment to trigger gene expression and other physiological changes adaptive in future environments. "Predictive" abilities like this exist in organisms that have been exposed to periodic changes in environments. It is unknown how readily they can evolve. To answer this question, we carried out laboratory evolution experiments in the yeast Saccharomyces cerevisiae. Specifically, we exposed three replicate populations of yeast to environments that varied cyclically between two stressors, salt stress and oxidative stress, every 10 generations, for a total of 300 generations. We evolved six replicate control populations in only one of these stressors for the same amount of time. We analyzed fitness changes and genome-scale expression changes in all these evolved populations. Our populations evolved asymmetric cross protection, where oxidative stress protects against salt stress but not vice versa. Gene expression data also suggest the evolution of anticipation and basal gene expression changes that occur uniquely in cyclic environments. Our study shows that highly complex physiological states that are adaptive in future environments can evolve on very short evolutionary time scales.
Data from: Independent effects of host and environment on the diversity of wood-inhabiting fungi
1. Dead wood is a habitat for numerous fungal species, many of which are important agents of decomposition. Previous studies suggested that wood-inhabiting fungal communities are affected by climate, availability of dead wood in the surrounding landscape and characteristics of the colonized dead-wood object (e.g. host tree species). These findings indicate that different filters structure fungal communities at different scales, but how these factors individually drive fungal fruiting diversity on dead-wood objects is unknown. 2. We conducted an orthogonal experiment comprising 180 plots (0.1 ha) in a random block design and measured fungal fruit body richness and community composition on 720 dead-wood objects over the first four years of succession. The experiment allowed us to disentangle the effects of the host (beech and fir; logs and branches) and the environment (microclimate: sunny and shady plots; local dead wood: amount and heterogeneity of dead wood added to plot). 3. Variance partitioning revealed that the host was more important than the environment for the diversity of wood-inhabiting fungi. A more detailed model revealed that host tree species had the highest independent effect on richness and community composition of fruiting species of fungi. Host size had significant but low independent effects on richness and community composition of fruiting species. Canopy openness significantly affected the community composition of fruiting species. By contrast, neither local amount nor heterogeneity of dead wood significantly affected the fungal diversity measures. 4. Synthesis: Our study identified host tree species as a more important driver of the diversity of wood-inhabiting fungi than the environment, which suggests a host-centred filter of this diversity in the early phase of the decomposition process. For the conservation of wood-inhabiting fungi, a high variety of host species in various microclimates is more important than the availability of dead wood at the stand level.
Data from: Carrying capacity in a heterogeneous environment with habitat connectivity
A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.
Data from: Early and adult social environments shape sex-specific actuarial senescence patterns in a cooperative breeder
Sociality modulates life history traits through changes in resource allocation to fitness-related traits. However, how social factors at different stages of the life cycle modulate senescence remains poorly understood. To address this question, we assessed the influence of social environment in both early life and adulthood on actuarial senescence in the Alpine marmot, a cooperative breeder. The influence of helpers on actuarial senescence strongly differed depending on when help was provided, and on the sex of the dominant. Being helped when adult slowed down senescence in both sexes. However, the effect of the presence of helpers the year of birth of a dominant was sex-specific. Among dominants helped during adulthood, females born in the presence of helpers senesced slower, whereas males senesced faster. Among dominants without helpers during adulthood, females with helpers at birth senesced faster. Social environment modulates senescence, but acts differently between sexes and life stages.
Data from: Is saltmarsh restoration success constrained by matching natural environments or altered succession? a test using niche models
1.Restored habitats, such as saltmarsh created through managed realignment, sometimes fail to meet targets for biological equivalence with natural reference sites. Understanding why this happens is important in order to improve restoration outcomes. 2.Elevation in the tidal frame and sediment redox potential are major controls on the distribution of saltmarsh plants. We use niche models to characterize ten species' responses to these, and test whether differences in species occurrence between restored and natural saltmarshes in the UK result from failure to recreate adequate environmental conditions. 3.Six species occurred less frequently in recently restored marshes than natural marshes. Failure of restored marshes to achieve the elevation and redox conditions of natural marshes partially explained the underrepresentation of five of these species, but did not explain patterns of occurrence on older (> 50 years) restored marshes. 4.For all species, an effect of marsh age remained after controlling for differences in environmental conditions. This could be due to differences in successional mechanism between restored and natural marshes. In recently restored marshes, high-marsh species occurred lower in the tidal frame and low-marsh species occurred at higher elevations than in natural marshes. This supports the hypothesis that competition is initially weaker in restored marshes, because of the availability of bare sediment across the whole tidal frame. Species that establish outside their normal realized niche, such as Atriplex portulacoides, may inhibit subsequent colonization of other species that occurred less frequently than expected on older restored marshes. 5.Synthesis and applications. Niche models can be used to test whether abiotic differences between restored sites and their natural counterparts are responsible for discrepancies in species occurrence. In saltmarshes, simply replicating environmental conditions will not result in equivalent species occurrence.
Data from: Escherichia coli populations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity
There is considerable understanding about how laboratory populations respond to predictable (constant or deteriorating environment) selection for single environmental variables such as temperature or pH. However, such insights may not apply when selection environments comprise multiple variables that fluctuate unpredictably, as is common in nature. To address this issue, we grew replicate laboratory populations of Escherichia coli in nutrient broth whose pH and concentrations of salt (NaCl) and hydrogen peroxide (H2O2) were randomly changed daily. After ~170 generations, the fitness of the selected populations had not increased in any of the three selection environments. However, these selected populations had significantly greater fitness in four novel environments which have no known fitness-correlation with tolerance to pH, NaCl or H2O2. Interestingly, contrary to expectations, hypermutators did not evolve. Instead, the selected populations evolved an increased ability for energy-dependent efflux activity that might enable them to throw out toxins, including antibiotics, from the cell at a faster rate. This provides an alternate mechanism for how evolvability can evolve in bacteria and potentially lead to broad-spectrum antibiotic resistance, even in the absence of prior antibiotic exposure. Given that environmental variability is increasing in nature, this might have serious consequences for public health.
Data from: Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana
Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.
Data from: Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa
Antibiotic resistance is a growing concern to public health. New treatment strategies may alleviate the situation by slowing down the evolution of resistance. Here, we evaluated sequential treatment protocols using two fully independent laboratory-controlled evolution experiments with the human pathogen Pseudomonas aeruginosa PA14 and two pairs of clinically relevant antibiotics (doripenem/ciprofloxacin and cefsulodin/gentamicin). Our results consistently show that the sequential application of two antibiotics decelerates resistance evolution relative to monotherapy. Sequential treatment enhanced population extinction although we applied antibiotics at sub-lethal dosage. In both experiments, we identified an order-effect of the antibiotics used in the sequential protocol, leading to significant variation in the long-term efficacy of the tested protocols. These variations appear to be caused by asymmetric evolutionary constraints, whereby adaptation to one drug slowed down adaptation to the other drug, but not vice versa. An understanding of such asymmetric constraints may help future development of evolutionary robust treatments against infectious disease.
Data from: On the evolution of migration in heterogeneous environments
Populations often experience variable conditions, both in time and space. Here we develop a novel theoretical framework to study the evolution of migration under the influence of spatially and temporally variable selection and genetic drift. First we examine when polymorphism is maintained at a locus under heterogeneous selection, as a function of the pattern of spatial heterogeneity and the migration rate. In a second step, we study how levels of migration evolve under the joint action of kin competition and local adaptation at a polymorphic locus. This analysis reveals the existence of evolutionary bistability where a low or a high migration rate may evolve depending on the initial conditions. Last, we relax several assumptions regarding selection heterogeneity commonly made in previous studies and explore the consequences of more complex spatial and temporal patterns of variability in selection on the evolution of migration. We found that small modifications in the pattern of environmental heterogeneity may have dramatic effects on the evolution of migration. This work highlights the importance of considering more general scenarios of environmental heterogeneity when studying the evolution of life history traits in ecologically complex settings.
Data from: Crowded developmental environment promotes adult sex-specific nutrient consumption in a polyphagous fly
Background: The fitness of holometabolous insects depends largely on resources acquired at the larval stage. Larval density is an important factor modulating larval resource-acquisition, influencing adult survival, reproduction, and population maintenance. To date, however, our understanding of how larval crowding affects adult physiology and behaviour is limited, and little is known about how larval crowding affects adult non-reproductive ecological traits. Here, larval density in the rearing environment of the polyphagous fruit fly Bactrocera tryoni ('Queensland fruit-fly') was manipulated to generate crowded and uncrowded larval treatments. The effects of larval crowding on pupal weight, adult emergence, adult body weight, energetic reserves, fecundity, feeding patterns, flight ability, as well as adult predation risk were investigated. Results: Adults from the crowded larval treatment had lower adult emergence, body weight, energetic reserves, flight ability and fecundity compared to adults from the uncrowded larval treatment. Adults from the crowded larval treatment had greater total food consumption (i.e., consumption of yeast plus sucrose) relative to body weight for both sexes compared to adults from the uncrowded treatment. Furthermore, males from the crowded treatment consumed more yeast relative to their body weight than males from the uncrowded treatment, while females from the crowded treatment consumed more sucrose relative to their body weight than females from the uncrowded treatment. Importantly, an interaction between the relative consumptions of sucrose and yeast and sex revealed that the density of conspecifics in the developmental environment differentially affects feeding of adult males and females. We found no effect of larval treatment on adult predation probability. However, males were significantly more likely to be captured by ants than females. Conclusion: We show that larvae crowding can have important implications to ecological traits in a polyphagous fly, including traits such as adult energetic reserve, flight ability, and adult sex-specific nutrient intake. Our findings contextualise the effects of larval developmental conditions into a broad ecological framework, hence providing a better understanding of their significance to adult behaviour and fitness. Furthermore, the knowledge presented here can help us better understanding downstream density-dependent effects of mass rearing conditions of this species, with potential relevance to Sterile Insect Technique.
Code and resulting candidate gene datasets from Anopheles genome environment association testing
<p>The concept of a fundamental ecological niche is central to questions of geographic distribution, population demography, species conservation, and evolutionary potential. But robust inference of genomic regions associated with evolutionary adaptation to particular environmental conditions remains difficult due to the myriad of potential confounding processes that can generate heterogeneous patterns of variation across the genome. Here, we interrogate the potential role of genome environment association (GEA) testing as an initial step in building an understanding of the genetic basis of ecological niche. We leverage publicly available genomic data from the Anopheles gambiae 1000 Genomes (Ag1000g) Consortium to test the ability of multiple, unique analytical GEA methods to handle confounding genetic variation, control false positive rates, and discern associations with broadly relevant climate variables from randomly correlated allele frequency patterns throughout the genome. We find evidence supporting the ability of commonly implemented GEA methods to account for confounding patterns of spatial and genetic variation, and control false positive rates. But we subsequently fail to find evidence supporting the ability of GEA tests to reject signals of adaptation to randomly simulated environmental variables, indicating that discerning between true signals of genome environment adaptation and genome environment correlations resulting from alternative evolutionary processes remains challenging. Because signals of environmental adaptation are so diffuse and confounded throughout the genome, we argue that genomic adaptation to ecological niche is likely best understood under an omnigenic model wherein highly interconnected, genome-wide gene regulatory networks shape genomic adaptation to key environmental conditions.</p>
Supplementary Information: Learning Protein-Ligand Binding Affinity with Atomic Environment Vectors
<p>Supplementary Information: Learning Protein-Ligand Binding Affinity with Atomic Environment Vectors</p>
Data from: The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion
Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual-based simulations, we model range expansion over a two-dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion. We find that genetic architecture and landscape patchiness both have the ability to change the outcome of adaptation and expansion over the landscape. Adaptation to new environments succeeds via many mutations of small effect or few of large effect, but not via the intermediate between these cases. Higher genetic variance contributes to increased ability to adapt, but an alternative route of successful adaptation can proceed from low genetic variance scenarios with alleles of sufficiently large effect. Steeper environmental gradients can prevent adaptation and range expansion on both linear and patchy landscapes. When the landscape is partitioned into local patches with sharp changes in phenotypic optimum, the local magnitude of change between subsequent patches in the environment determines the success of adaptation to new patches during expansion.
ScienceDex guides
Understand access before you commit
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.