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530 results for “data availability”
Data from: A test of the seasonal availability of water hypothesis in a C3/C4 mixed grassland
<p>Understanding how cool-season C<sub>3</sub> and warm-season C<sub>4</sub> grasses will respond to climate change is critical for predicting future grassland functioning. With warming, C<sub>4</sub> grasses are expected to increase relative to C<sub>3</sub> grasses. But, alterations in the seasonal availability of water may also influence C<sub>3</sub>/C<sub>4</sub> dynamics because of their distinct seasons of growth. To better understand how shifts in the seasonal availability of water can affect ecosystem function in a northern mixed grass prairie in southeastern Wyoming, we reduced early season rainfall (April – June 2021) using rainout shelters and added the amount of excluded precipitation during the latter half of the growing season (July-September), effectively shifting spring rainfall to summer rainfall. As expected, this shift in precipitation seasonality influenced patterns of soil water availability, leading to increased soil respiration in the summer months and sustained canopy greenness throughout the growing season. Despite these responses, there were no significant differences in C<sub>3</sub> aboveground net primary production (ANPP) between the seasonally shifted treatment (SEAS) and the plots that received ambient (AMB) precipitation. This was likely due to the high levels of spring soil moisture present before rainout shelters were deployed that sustained C<sub>3</sub> grass growth. However, in plots with high C<sub>4</sub> grass cover, C<sub>4</sub> ANPP increased significantly in response to increased summer rainfall. Overall, we provide the first experimental evidence that shifts in the seasonality of precipitation, with no change in temperature, will differentially impact C<sub>3</sub> vs. C<sub>4</sub> species, altering the dynamics of carbon cycling and canopy albedo in this extensive semi-arid grassland.</p>
Data for: Spatial prey availability and pulsed reproductive tactics: encounter risk in a canid-ungulate system
<ol> <li>Predation risk is a function of spatiotemporal overlap between predator and prey, as well as behavioral responses during encounters. Dynamic factors (e.g., group size, prey availability, and animal movement or state) affect risk, but rarely are integrated in risk assessments. Our work targets a system where predation risk is fundamentally linked to temporal patterns in prey abundance and behavior. For neonatal ungulate prey, risk is defined within a short temporal window during which the pulse in parturition, increasing movement capacity with age, and anti-predation tactics have the potential to mediate risk.</li> <li>In our coyote – mule deer (<em>Canis</em> <em>latrans</em> – <em>Odocoileus</em> <em>hemionus</em>) system, leveraging GPS data collected from both predator and prey, we tested expectations of the shared enemy and reproductive risk hypotheses. We asked two questions regarding risk: (A) how do primary and alternative prey habitat, predator and prey activity, and reproductive tactics (e.g., birth synchrony, maternal defense) influence vulnerability of a neonate encountering a predator? (B) How do the same factors affect behavior by predators relative to time before and after an encounter?</li> <li>Despite increased selection for mule deer and intensified search behavior by coyotes during the peak in mule deer parturition, mule deer were afforded protection from predation via predator swamping, experiencing reduced per-capita encounter risk when most neonates were born. Mule deer occupying rabbit habitat (<em>Sylvilagus</em> spp.; coyote's primary prey) experienced the greatest risk of encounter but the availability of rabbit habitat did not affect predator behavior during encounters. Encounter risk increased in areas with greater availability of mule deer habitat, coyotes shifted their behavior relative to deer habitat, and the pulse in mule deer parturition and movement of neonatal deer during encounters elicited increased speed and tortuosity by coyotes.</li> <li>In addition to the spatial distribution of prey, temporal patterns in prey availability, and animal behavioral state were fundamental in defining risk. Our work reveals the nuanced consequences of pulsed availability on predation risk for alternative prey, whereby responses by predators to sudden resource availability, the lasting effects of diversionary prey, and inherent antipredation tactics ultimately dictate risk.</li> </ol>
Data from: In the social amoeba Dictyostelium discoideum, shortened stalks may limit obligate cheater success even when exploitable partners are available
<p>Cooperation is widespread across life, but its existence can be threatened by exploitation. The rise of obligate social cheaters that are incapable of contributing to a necessary cooperative function can lead to the loss of that function. In the social amoeba <em>Dictyostelium discoideum</em>, obligate social cheaters cannot form dead stalk cells and in chimeras instead form living spore cells. This gives them a competitive advantage within chimeras. However, obligate cheaters of this kind have thusfar not been found in nature, probably because they are often enough in clonal populations that they need to retain the ability to produce stalks. In this study we discovered an additional cost to obligate cheaters. Even when there are wild-type cells to parasitize, the chimeric fruiting bodies that result have shorter stalks and these are disadvantaged in spore dispersal. The inability of obligate cheaters to form fruiting bodies when they are on their own combined with the lower functionality of fruiting bodies when they are not represent limits on obligate social cheating as a strategy<em>.</em></p>
Data from: Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability
<p>Prophages, viral sequences integrated into bacterial genomes, can confer fitness benefits and costs. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding about the selective forces that maintain prophages in bacterial populations is scarce. Combining experimental evolution with stochastic modelling we found that prophage maintenance and loss are primarily determined by environmental conditions that amplify the net fitness effect of the prophage. Whole genome sequencing revealed that prophage loss occurs through environment-specific sequences of selective sweeps, leading to rapid prophage loss when prophages are costly. However, conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can prolong prophage maintenance. The extent of prolonged maintenance depends on the sociality of this accessory gene. Selection for non-cooperative genes is more effective for prophage maintenance as cooperative genes allow for protection of phage-free 'cheaters' that may emerge if prophage costs outweigh their benefits. Our mathematical model suggests that environmental variation plays a larger role than mutation rates in determining prophage maintenance. This challenges our understanding of the role of random chance events relative to environmental factors in shaping the evolutionary trajectory of bacterial populations.</p>
Data supporting "Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence"
<p>Data supporting </p> <p><strong>Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence </strong></p> <p>E. M. Windels, L. Cool, E. Persy, J. Swinnen, P. Matthay, B. Van den Bergh, T. Wenseleers, J. Michiels</p> <p>Version April 16th, 2024</p>
Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259
<p>File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database).</p> <p>File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots).</p> <p>File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.</p> <p> </p> <p> </p>
Data for: Brown juice assisted ensiling of straw and press cake for enhanced biogas production and nutrient availability in digestates
<p>Data for: <span>Brown juice assisted ensiling of straw and press cake for enhanced biogas production and nutrient availability in digestates (https://doi.org/10.1016/j.eti.2023.103248)</span></p>
Data from: Effects of resource availability and interspecific interactions on Arctic and red foxes' winter use of ungulate carrion in the Fennoscandian low-Arctic tundra
<p>In the Arctic tundra, predators face recurrent periods of food scarcity and often turn to ungulate carcasses as an alternative food source. As important and localized resource patches, carrion promotes co-occurrence of different individuals, and its use by predators is likely to be affected by interspecific competition. We studied how interspecific competition and resource availability impact winter use of carrion by Arctic and red foxes in low Arctic Fennoscandia. We predicted that presence of red foxes limits Arctic foxes' use of carrion, and that competition depends on the availability of other resources. We monitored Arctic and red fox presence at supplied carrion using camera traps. From 2006 to 2021, between 16 and 20 cameras were active for two months in late winter (288 camera-winters). Using a multi-species dynamic occupancy model at a week-to-week scale, we evaluated use of carrion by foxes while accounting for the presence of competitors, rodent availability and supplemental feeding provided to Arctic foxes. Competition affected carrion use by increasing both species' probability to leave occupied carcasses sites between consecutive weeks. This increase was similar for the two species, suggesting symmetrical avoidance. Increased rodent abundance was associated with a higher probability of colonizing carrion sites for both species. For Arctic foxes, however, this increase was only observed at carcasses unoccupied by red foxes, showing greater avoidance when alternative preys are available. Supplementary feeding increased Arctic foxes' carrion use, regardless of red fox presence. Contrary to expectations, we did not find strong signs of asymmetric competition for carrion in winter, which suggests that interactions for resources at a short time scale are not necessarily aligned with interactions at the scale of the population. In addition, we found that competition for carcasses depends on the availability of other resources, suggesting that interactions between predators depend on the ecological context.</p>
Data for: Habitat diversity, resource availability, and island age in the species-area relationship
<p><strong>Aim: </strong>The island species-area relationship (ISAR) and its theoretical justifications assume the area of islands to be homogeneous across an archipelago, which is generally not the case. We compare the performance of models that adjust or substitute for island area with measures of habitat diversity, island age, and resource availability to account for the violation of this assumption. We further compare the performance of models for two taxonomic groups.</p> <p><strong>Location: </strong>Five hotspot archipelagos (Azores, Galapagos, Hawaii, Cape Verde, Canary Islands).</p> <p><strong>Taxa:</strong> Vascular plants and birds.</p> <p><strong>Methods: </strong>We used the mathematical framework of the power law to compare relevant models, treating the one containing only area as a null model against which others were compared. Data was collated from the GIFT database and from the literature. Models were compared using linear regression within archipelagos and via mixed effect models with archipelago as a random effect.</p> <p><strong>Results:</strong> Weighting of island area by habitat diversity and resource availability systematically improved statistical significance and model fits versus the area only power law. Models including island age did not show the same systematic improvement in model fits. For vascular plants, weighting islands by resource availability (energy and water) performed better than weighting by habitat diversity, although for birds these weightings performed equally well.</p> <p><strong>Main Conclusions:</strong> Given that islands within archipelagos are fairly uniform in climate, topography, and geology, it is worth accounting for this in ISARs. Our results suggest that, for islands in volcanic hotspot archipelagos this is best done by using direct measures of habitat diversity and resource availability rather than using island age as a proxy. Because weighting area by habitat diversity and resource availability produced better predictors of species diversity, the proposed approach may be particularly valuable in conservation science.</p>
Data from: Influences of summer warming and nutrient availability on Salix glauca L. growth in Greenland along an ice to sea gradient
<p>The combined effects of climate change and nutrient availability on Arctic vegetation growth are poorly understood. Archaeological sites in the Arctic could represent unique nutrient hotspots for studying the long-term effect of nutrient enrichment. In this study, we analysed a time-series of ring widths of <em>Salix glauca</em> L. collected at nine archaeological sites and in their natural surroundings along a climate gradient in the Nuuk fjord region, Southwest Greenland, stretching from the edge of the Greenlandic Ice Sheet in the east to the open sea in the west. We assessed the temperature-growth relationship for the last four decades distinguishing between soils with past anthropogenic nutrient enrichment (PANE) and without (controls). Along the East–West gradient, the inner fjord sites showed a stronger temperature signal compared to the outermost ones. Individuals growing in PANE soils had wider ring widths than individuals growing in the control soils and a stronger climate-growth relation, especially in the inner fjord sites. Thereby, the individuals growing on the archaeological sites seem to have benefited more from the climate warming in recent decades. Our results suggest that higher nutrient availability due to past human activities plays a role in Arctic vegetation growth and should be considered when assessing both the future impact of plants on archaeological sites and the general greening in landscapes with contrasting nutrient availability.</p>
Data Availability - DRAFT - 'Process-based similarity' revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements
<p>Datasets and R code related to confidential manuscript submission entitled "‘Process-based similarity’ revealed by discharge-dependent relative submergence dynamics of thousands of large bed elements". Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency. Restrictions apply to the availability of the 2014 DTM and 2D model results, which were used under contractual agreement from the project sponsor. These are available from the senior author with the permission of Yuba Water Agency.</p>
Data from: Estimating maize harvest index and nitrogen concentrations in grain and residue using globally available data
<p class="MsoNormal">Estimates of crop nitrogen (N) uptake and offtake are critical in estimating N balances, N use efficiencies and potential losses to the environment. Calculation of crop N uptake and offtake requires estimates of crop product yield (e.g. grain or beans) and crop residue yield (e.g. straw or stover) and the N concentration of both components. Yields of crop products are often reasonably well known, but those of crop residues are not. While the harvest index (HI) can be used to interpolate the quantity of crop residue from available data on crop product yields, harvest indices are known to vary across locations, as do N concentrations of residues and crop products. The increasing availability of crop data and advanced statistical and machine learning methods present us with an opportunity to move towards more locally relevant estimates of crop harvest index and N concentrations using more readily available data. This dataset includes maize field experiment data. It is a culmination of summary statistic data collected from the literature as well as raw data requested from various researchers and organisations from around the world. These data will enable more locally relevant estimates of crop nutrient offtake, nutrient balances and nutrient use efficiency at national, regional or global levels, as part of strategies towards more sustainable nutrient management.</p>
Fruit-feeding butterfly populations respond to variation in adult food availability: evidence from longitudinal body mass and abundance data
<p>The degree to which variation in adult food availability affects the population dynamics of a species depends on its position on the capital-income breeding continuum. The long-lived butterflies that feed on fruits as adults constitute an example of Lepidoptera with a high degree of income breeding. For three species of fruit-feeding butterflies in Uganda, we assessed the contribution of the income to breeding in the wild, and the consequences of variation in fruit availability for body mass and population dynamics. We interpreted body mass loss within individuals as well as younger individuals having higher body mass than older ones as evidence for the depletion of capital reserves. Despite large sample sizes, we were able to show only modest body mass loss in one species, indicating that large-bodied fruit-feeding butterflies are functionally income breeders in the wild. Butterfly body mass was sensitive to environmental factors, although the responses to fruit availability and weather parameters were dominated by interactive effects. In all three species, periods of higher availability of fruit were followed by periods of higher adult abundance three to five months later, fitting the egg-to-adult time. Our results suggest that adult food is rapidly used for reproduction so that body mass remains stable and population size responds to adult food availability. For these income breeding species, the frequent periods of low adult food availability may select for extended adult longevity for the purpose of postponing reproduction to the onset of more favorable conditions. </p>
Data from: Girth increment changes in response to soil water availability in lowland dipterocarp forest in Borneo: an individualistic time-series analysis
<p><span>Time-series data offer a way of investigating the causes driving ecological processes as phenomena. To test for possible differences in water relations between species of different forest structural guilds at Danum (Sabah, NE Borneo), daily stem girth increments (gthi), of 18 trees across six species were regressed individually on soil moisture potential (SMP) and temperature (TEMP), accounting for temporal autocorrelation (in GLS-arima models), and compared between a wet and a dry period. The best-fitting significant variables were SMP the day before and TEMP the same day. The first resulted in a mix of positive and negative coefficients, the second largely positive ones. An adjustment for dry-period showers was applied. Interactions were stronger in dry than wet period. Negative relationships for overstorey trees can be interpreted in a reversed causal sense: fast transporting stems depleted soil water and lowered SMP. Positive relationships for understorey trees meant they took up most water at high SMP. The unexpected negative relationships for these small trees may have been due to their roots accessing deeper water supplies (if SMP was inversely related to that of the surface layer), and this was influenced by competition with larger neighbour trees. A tree-soil flux dynamics manifold may have been operating. Patterns of mean diurnal girth variation were more consistent among species, and time-series coefficients were negatively related to their maxima. Expected differences in response to SMP in the wet and dry periods did not clearly support a previous hypothesis differentiating drought and non-drought tolerant understorey guilds. Trees within species showed highly individual responses when tree size was standardized. Data on individual root systems and SMP at several depths are needed to get closer to the mechanisms that underlie the tree-soil water phenomena in these tropical forests. Neighborhood stochasticity importantly creates varying local environments experienced by individual trees.</span></p>
Data availability: Random encounter model is a reliable method for estimating population density of multiple species using camera traps
<p>Data of the paper entitled "Random encounter model is a reliable method for estimating population density of multiple species using camera traps" published on Remote Sensing in Ecology and Conservation</p>
Data and code availibility for the paper "Ice-nucleating agents in sea spray aerosol identified and quantified with a holistic multi-modal freezing model" by Alpert et al.
<p>The data and codes used in the paper "Ice-nucleating agents in sea spray aerosol identified and quantified with a holistic multi-modal freezing model" by Alpert et al., published in <em>Science Advances</em> are included in this collection. Detailed descriptions of the files are given in the readme file.</p>
Data from: Responses of invasive and native plants to different forms and availability of phosphorus
<p>Premise<span>—</span>Many studies have assessed the various responses of alien plants to changes in overall nutrient or different nitrogen (N) availabilities. However, in natural soils, nutrients are present as different chemical elements (e.g., N and phosphorus [P]) and forms (e.g., inorganic and organic). Few studies have explored yet whether invasive and native species differ in their responses to varying P availability and forms.</p> <p>Key results<span>—</span>We found that invasive species did not show an overall higher biomass production than that of native species under varied P conditions. However, the biomass response to organic P was, relative to the response to inorganic P, stronger for the invasive species than that for the native species. This coincided with the pattern that invasive species mainly allocated biomass to the root system under organic P conditions.</p> <p>Conclusions<span>—</span>Our study indicates that while invasive species were not more promiscuous than native species were, they took great advantage of the organic-P forms. Therefore, the invasion risk of alien species may increase in habitats with more organic P sources.</p>
Data from: Effects of manipulated food availability and seasonality on innate immune function in a passerine
<p>1. The innate immune system is essential for survival, yet many immune traits are highly variable between and within individuals. In recent years, attention has shifted to the role of environmental factors in modulating this variation. A key environmental factor is food availability, which plays a major role in shaping life-histories, and may affect resource allocation to immune function through its effect on nutritional state.</p> <p>2. We developed a technique to permanently increase foraging costs in seed-eating birds, and leveraged this technique to study the effects of food availability on the innate immune system over a three-year period in 230 zebra finches housed in outdoor aviaries. The immune components we studied were haptoglobin, ovotransferrin, nitric oxide, natural antibodies through agglutination, complement-mediated lysis, and killing capacity of <em>Escherichia</em> <em>coli</em> and <em>Candida</em> <em>albicans</em>, covering a broad spectrum of the innate immune system. We explored effects of food availability in conjunction with other potentially important variables: season, age, sex, and manipulated natal brood size.</p> <p>3. Increased foraging costs affected multiple components of the immune system, albeit in a variable way. Nitric oxide and agglutination levels were lower under harsh foraging conditions, while Escherichia coli killing capacity was increased. Agglutination levels also varied seasonally, but only at low foraging costs. <em>C</em>. <em>albicans</em>' killing capacity was lower in winter, and even more so for animals in harsh foraging conditions that were raised in large broods. Effects of food availability on ovotransferrin were also seasonal, and only apparent in males. Haptoglobin levels were independent of foraging costs and season.</p> <p>4. Males had higher levels of immune function than females for 3 of the measured immune traits. Innate immune function was independent of age and manipulated natal brood size.</p> <p>5. Our finding that food availability affects innate immune function suggests that fitness effects of food availability may at least partially be mediated by effects on the immune system. However, food availability effects on innate immunity varied in direction between traits, illustrating the complexity of the immune system and precluding conclusions on the level of disease resistance.</p>
Raw data: Temperature and water availability drive insect seasonality across a temperate and a tropical region
<p>The more insects there are, the more food there is for insectivores and the higher the likelihood of insect-associated ecosystem services. Yet, we lack insights into the drivers of insect biomass over space and seasons, both for tropical and temperate zones. We used 245 Malaise traps, managed by 191 volunteers and park guards, to characterise year-round flying insect biomass in a temperate (Sweden) and a tropical (Madagascar) country. Surprisingly, we found that local insect biomass was similar across zones. In Sweden, local insect biomass increased with accumulated heat and varied across habitats, while biomass in Madagascar was unrelated to the environmental predictors measured. Drivers behind seasonality partly converged: In both countries, the seasonality of insect biomass differed between warmer and colder sites and wetter and drier sites. In Sweden, short-term deviations from expected season-specific biomass were explained by week-to-week fluctuations in accumulated heat, rainfall, and soil moisture, whereas in Madagascar, weeks with higher soil moisture had higher insect biomass. Overall, our study identifies key drivers of the seasonal distribution of flying insect biomass in a temperate and tropical climate. This knowledge is key to understanding the spatial and seasonal availability of insects — as well as predicting future scenarios of insect biomass change.</p>
Data from: 42 years of no-tillage and cover cropping improved soil oxygen availability and resilience
<p>Healthy soil air-water balance is critical for crop growth. Conservation agricultural practices improve soil physical properties to influence soil oxygen availability. We evaluated the impact of 42 years of hairy vetch (HV) cover cropping (CC) and no-tillage (NT) on soil oxygen dynamics during a cotton growing season experiencing multiple intensive rain events in silt loam soil. HV and NT treatments exhibited higher growing season soil oxygen availability (<em>p </em>< 0.05), and experienced 3 to 4 times fewer hours of oxygen limitation (i.e., oxygen concentration <10%) as compared to no cover (NC) and conventional tillage (CT) treatments. After heavy rainfall, NT-HV treatment exhibited the highest soil oxygen availability, followed by NT-NC, CT-HV, and CT-NC treatments (<em>p </em>< 0.05). While CC and/or NT treatments quickly regained soil oxygen status within 24 hours after saturating rain events, CT-NC suffered from sub-optimal soil aeration until the third day post-rainfall. The combination of CC with NT practices enhanced soil oxygen availability and resilience to extreme precipitation events.</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.