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.
484
datasets available to search
ShareScore release 0.9.0
Dataset results
484 results for “environmental effect”
Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly
Open the record for dataset details and reuse information.
Environmental conditions modulate warming effects on plant litter decomposition globally
Open the record for dataset details and reuse information.
Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity
Open the record for dataset details and reuse information.
Data from: Effects of home range size and burrow fidelity on survival and reproduction in eastern chipmunks (Tamias striatus) across different environmental contexts
Open the record for dataset details and reuse information.
Data from: Genetic and environmental effects on morphological traits of social phenotypes in wasps
Open the record for dataset details and reuse information.
Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish
Open the record for dataset details and reuse information.
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
Open the record for dataset details and reuse information.
Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities
Open the record for dataset details and reuse information.
Data from: Environmental enrichment induces intergenerational behavioural and epigenetic effects on fish
Parental effects influence offspring phenotypes through pre- and post-natal routes but little is known about their molecular basis, and therefore their adaptive significance. Epigenetic modifications, which control gene expression without changes in the DNA sequence and are influenced by the environment, may contribute to parental effects. We investigated the effects of environmental enrichment on the behaviour, metabolic rate and brain DNA methylation patterns of parents and offspring of the highly inbreed mangrove killifish (Kryptolebias marmoratus). Parental fish reared in enriched environments had lower cortisol levels, lower metabolic rates and were more active and neophobic than those reared in barren environments. They also differed in 1,854 methylated cytosines (DMCs). Offspring activity and neophobia were determined by the parental environment. Among the DMCs of the parents, 98 followed the same methylation patterns in the offspring, three of which were significantly influenced by parental environments irrespective of their own rearing environment. Our results suggest that parental environment influences the behaviour and, to some extent, the brain DNA methylation patterns of the offspring.
Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection
<p>Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as well as exposure to a natural environment, increased microbiota diversity and altered community composition. Community composition in mice exposed to high temperatures and humidity diverged as much from the microbiota of mice housed outdoors as from the microbiota of control mice. Additionally, infection with the nematode <i>Trichuris muris</i> modulated how the microbiota responded to environmental transitions: The dynamics of several families were buffered by the nematodes, while invasion rates of two taxa acquired outdoors were magnified. These findings suggest that gut bacterial communities respond dynamically and simultaneously to changes within the host's body (e.g., the presence of nematodes) and to changes in the wider environment of the host.</p>
Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs
<p>Environmental DNA (eDNA) analysis has seen rapid development in the last decade, as a novel biodiversity monitoring method. Previous studies have evaluated optimal strategies, at several experimental steps of eDNA metabarcoding, for the simultaneous detection of fish species. However, optimal sampling strategies, especially the season and the location of water sampling, have not been evaluated thoroughly. To identify optimal sampling seasons and locations, we performed sampling monthly or at two-monthly intervals throughout the year in three dam reservoirs. Water samples were collected from 15 and 9 locations in the Miharu and Okawa dam reservoirs in Fukushima Prefecture, respectively, and 5 locations in the Sugo dam reservoir in Hyogo Prefecture, Japan. One liter of water was filtered with glass-fiber filters and eDNA was extracted. By performing MiFish metabarcoding, we successfully detected a total of 21, 24, and 22 fish species in Miharu, Okawa, and Sugo reservoirs, respectively. From these results, the eDNA metabarcoding method had a similar level of performance compared to conventional long-term data. Furthermore, it was found to be effective in evaluating entire fish communities. The number of species detected by eDNA survey peaked in May in Miharu and Okawa reservoirs, and in March and June in Sugo reservoir, which corresponds with the breeding seasons of many of fish species inhabiting the reservoirs. In addition, the number of detected species was significantly higher in shore, compared to offshore samples in the Miharu reservoir, and a similar tendency was found in the other two reservoirs. Based on these results, we can conclude that the efficiency of species detection by eDNA metabarcoding could be maximized by collecting water from shore locations during the breeding seasons of the inhabiting fish. These results will contribute in the determination of sampling seasons and locations for fish fauna survey via eDNA metabarcoding, in the future.</p>
Effects of soil preservation for biodiversity monitoring using environmental DNA
Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guidelines for best practices so far. Here, we assessed the impact of four methods of soil sample preservation commonly used in metabarcoding studies (preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days). For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under optimal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, while the exclusion of rare taxa led to robust results across preservation methods. The differences in community structure among habitats were evident for all treatments, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
Meerkat helpers buffer the detrimental effects of adverse environmental conditions on fecundity, growth and survival
<p>1. Recent comparative studies show that cooperative breeding is positively correlated with harsh and unpredictable environments and it is suggested that this association occurs because helpers buffer the negative effects of adverse ecological conditions on fitness.</p> <p>2. In the Kalahari, rainfall varies widely between- and within years, affecting primary production and the availability of the principal prey of cooperatively breeding Kalahari meerkats, Suricata suricatta. Our study aimed to establish whether the presence and number of helpers buffer the negative effects of variation in rainfall on the fecundity and body mass of breeding females, and the survival and growth of pups.</p> <p>3. We investigate the relationship between group size and variation in rainfall on dominant female fecundity, body mass, and offspring survival and growth using an additive modeling approach on twenty-one years of individual-based records of the life histories of individual meerkats.</p> <p>4. We show that breeding female fecundity is reduced during periods of low rainfall but that the effects of low rainfall are mitigated by increases in group size and body mass because heavier females and those in larger groups have increased fecundity and reduced interbirth intervals. Pup growth and survival are also reduced during periods of low rainfall, but more so in smaller groups.</p> <p>5. Our results support the suggestion that cooperative breeding mitigates the detrimental effects of adverse environmental conditions and may enhance the capacity of species to occupy environments where food availability is low and unpredictable.</p>
Legacy effects of fish but not elevation influence lake ecosystem response to environmental change
<p>How communities reorganize during climate change depends on the distribution of diversity within ecosystems and across landscapes. Understanding how environmental and evolutionary history constrain community resilience is critical to predicting shifts in future ecosystem function. </p> <p>The goal of our study was to understand how communities with different histories respond to environmental change with regard to shifts in elevation (temperature, nutrients) and introduced predators. We hypothesized that community responses to the environment would differ in ways consistent with local adaptation and initial trait structure. </p> <p>We transplanted plankton communities from lakes at different elevations with and without fish in the Sierra Nevada Mountains in California to mesocosms at different elevations with and without fish. We examined the relative importance of the historical and experimental environment on functional (size structure, effects on lower trophic levels), community (zooplankton composition, abundance, and biomass), and population (individual species abundance and biomass) responses.</p> <p>Communities originating from different elevations produced similar biomass at each elevation despite differences in species composition; that is, the experimental elevation, but not the elevation of origin, had a strong effect on biomass. Conversely, we detected a legacy effect of predators on plankton in the fishless environment. <em>Daphnia pulicaria</em> that historically coexisted with fish reached greater biomass under fishless conditions than those from fishless lakes, resulting in greater zooplankton community biomass and larger average size. </p> <p>Therefore, trait variation among lake populations determined the top-down effects of fish predators. In contrast, phenotypic plasticity and local diversity were sufficient to maintain food web structure in response to changing environmental conditions associated with elevation. </p>
Data from: Environmental gradients determine the potential for ecosystem engineering effects
Understanding processes that determine biodiversity is a fundamental challenge in ecology. At the landscape scale, physical alteration of ecosystems by organisms, called ecosystem engineering, enhances biodiversity worldwide by increasing heterogeneity in resource conditions and enhancing species coexistence across engineered and non-engineered habitats. Engineering-diversity relationships can vary along environmental gradients due to changes in the amount of physical structuring created by ecosystem engineering, but it is unclear how this variation is influenced by the responsiveness of non-structural abiotic properties to engineering. Here we show that environmental gradients determine the capacity for engineering to alter resource availability and species diversity, independent of the magnitude of structural change produced by engineering. We created an experimental rainfall gradient in an arid grassland where rodents restructure soils by constructing large, long-lasting burrows. We found that greater rainfall increased water availability and productivity in both burrow and inter-burrow habitats, causing a decline in local (alpha) plant diversity within both of these habitats. However, increased rainfall also resulted in greater differences in soil resources between burrow and inter-burrow habitats, which increased species turnover (beta diversity) across habitats and stabilized landscape-level (gamma) diversity. These responses occurred regardless of rodent presence and without changes in the extent of physical alteration of soils by rodents. Our results suggest that environmental gradients can influence the effects of ecosystem engineering in maintaining biodiversity via resource heterogeneity and species turnover. In an era of rapid environmental change, accounting for this interaction may be critical to conservation and management.
Data from: Effects of native bryophytes on exotic grass invasion across an environmental gradient
Understanding the role that native biodiversity plays in controlling exotic species invasion is a critical goal in ecology. In terrestrial plant communities, most research has focused on the effects of native vascular plants on invasion by exotic vascular plants. However, in many ecosystems, native bryophytes and other non-vascular plants are common and can affect the establishment, survival and growth of vascular plants. A more complete picture of how native biodiversity affects exotic plant invasion, demands that more studies measure the effects of native bryophytes on exotic vascular plants. Moreover, there is growing realization that the effects of native species on invaders can range from negative to positive and that a complete picture of interactions between native and exotic plants requires measuring interactions in multiple environments. We used both observational and experimental studies to quantify the effects of native moss on two exotic annual grass species along a 200-m environmental gradient in a coastal dune in northern California. We found the effects of bryophytes to be species-specific and to vary with environmental context. Bryophytes facilitated the survival of one exotic grass species at both ends of the environmental gradient. For the other exotic grass species, bryophytes reduced survival at one end of the environmental gradient and had no effect at the other end. Our findings provide an important test of the effects of native bryophytes on exotic vascular plant invasion, and importantly show that these effects can vary dramatically even across local environmental gradients.
Data from: Parameterizing the robust design in the BUGS language: lifetime carry‐over effects of environmental conditions during growth on a long‐lived bird
1. Since the initial development of the robust design, this capture‐recapture model structure has been modified to estimate temporary emigration, and expanded to include auxiliary information such as band recovery and live resight data using maximum likelihood approaches. These developments have allowed investigators to separately assess individual and group effects on true survival, site fidelity, and temporary emigration. Additionally, recent advances in the BUGS language have allowed researchers to develop increasingly complex, user‐specified models in Bayesian frameworks. 2. The robust design has rarely been implemented in the BUGS language, and previous attempts to parameterize the robust design in BUGS exhibited strong bias in estimates of temporary emigration rates. Given the limitations of current parameterizations of the robust design in Bayesian frameworks, and our research objectives, we have developed a parameterization of the robust design in the BUGS language that produces unbiased estimates of all model parameters. 3. We use this novel model structure to examine lifetime carry‐over effects of environmental conditions during early life on annual breeding probabilities of Pacific black brent (Branta bernicla nigricans) breeding on the Yukon‐Kuskokwim River Delta in western Alaska. We found that individuals that were more structurally developed as goslings bred at increased rates as adults (β = 0.14, f = 0.94), with no effect on adult survival (β = 0.01, f = 0.62). Additionally, we provide evidence for long‐term declines in apparent survival of breeding adult females at the population level (β = ‐0.01, f = 0.90). 4. This novel model structure can be easily expanded (Gibson et al., in review), and has important implications for population modelling at broad scales, where we apply it to a declining population of Pacific black brent. Given long‐term declines in gosling growth on the Yukon‐Kuskokwim Delta, we predict future declines in population trajectories as a result of lifetime carry‐over effects of environmental conditions during growth on adult fecundity, and long‐term declines in adult survival.
Data from: When environmental factors become stressors: interactive effects of vermetid gastropods and sedimentation on corals
Environmental stressors often interact, but most studies of multiple stressors have focused on combinations of abiotic stressors. Here we examined the potential interaction between a biotic stressor, the vermetid snail Ceraesignum maximum, and an abiotic stressor, high sedimentation, on the growth of reef-building corals. In a field experiment, we subjected juvenile massive Porites corals to four treatments: (i) neither stressor, (ii) sedimentation, (iii) vermetids or (iv) both stressors. Unexpectedly, we found no effect of either stressor in isolation, but a significant decrease in coral growth in the presence of both stressors. Additionally, seven times more sediment remained on corals in the presence (versus absence) of vermetids, likely owing to adhesion of sediments to corals via vermetid mucus. Thus, vermetid snails and high sedimentation can interact to drive deleterious effects on reef-building corals. More generally, our study illustrates that environmental factors can combine to have negative interactive effects even when individual effects are not detectable. Such 'ecological surprises' may be easily overlooked, leading to environmental degradation that cannot be anticipated through the study of isolated factors.
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>
Vertical structural complexity of plant communities represents the combined effects of resource acquisition and environmental stress on the Tibetan Plateau
<p><span>Knowledge of vertical structural complexity (VSC) is important, because the resulting spatial partitioning is closely linked to resource utilization and environmental adaptation. However, the spatial pattern of VSC </span><span>on </span><span>large scales and its underlying mechanisms are poorly understood. Here, we systematically investigated 2,013 plant communities through grid sampling on </span><span>the </span><span>Tibetan Plateau (TP). </span><span>VSC was quantified </span><span>as </span><span>the maximum plant height within a plot (Height-max), coefficient of variation of plant height</span><span> (Height-var)</span><span>, and Shannon evenness of plant height (</span><span>Height-even</span><span>)</span><span>. Precipitation dominated the spatial variation in VSC in forests and shrublands, supporting the classic physiological tolerance hypothesis (PTH). In contrast, for alpine meadows, steppes, and desert grasslands in extreme environments, non-resource limiting factors (e.g., wide diurnal temperature ranges and strong winds) dominate VSC variation. Generally, with the shifting of climate from favorable to extreme, the effect of resource availability gradually decreases, but the effect of non-resource limiting factors gradually increase</span><span>s</span><span>, and that the PTH only applicable in "favorable conditions". With </span><span>the help of</span><span> machine learning models, maps of </span><span>VSC</span><span> at 1-km resolution were produced for the TP for the first time</span><span>. Our</span><span> new findings and maps of VSC provide new insights into macroecological studies, especially for adaptation mechanisms and model optimization.</span></p>
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.