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9,097 results for “wild”
k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase) Part 3/3
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k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 2/3
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Data from: Demographic, behavioral, and ecological data from a long-term field study of wild baboons in Amboseli, Kenya
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Data for: Social network data in wild great tits during ontogeny
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The heritability of size in a wild annual plant population with hierarchical size structure
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Data from: The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)
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Range-wide study in a sexually polymorphic wild strawberry reveals climatic and soil associations of sex ratio, sexual dimorphism, and sex chromosomes
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Data from: Stress responsiveness in a wild primate predicts survival across an extreme El Niño drought
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Dyadic distances in African savannah elephants as they transition from Semi-captivity to the wild in Okavango Delta, Botswana, 2021 to 2023
Data package contains a dataset of distances(m) of 15 dyads generated from GPS collar data of 6 female savannah elephants as they were being released from semi-captivity to the wild in Okavango Delta, Botswana from November 1st, 2021-November 29th,2023. The dataset is provided as part the manuscript `Dyadic distance in African savannah elephants (Loxotonda africana) increases during release from semi-captivity to the wild`.
Dataset accompanying Riesch et al. 2020. Grazing by wild red deer maintains characteristic vegetation of semi-natural open habitats: Evidence from a 3-year exclusion experiment. Applied Vegetation Science
<p>This repository contains vegetation community data used by Riesch et al. 2020 in an article accepted in Applied Vegetation Science.</p> <p>Metadata are provided in the first excel worksheet. For further details please see the original article.</p>
Data from: Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii
<p>Different host species often differ considerably in susceptibility to a given pathogen, but the causes of such differences are rarely known. The natural hosts of the tick-transmitted bacterium <i>Borrelia afzelii</i>, which is one of causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Previous studies have shown that <i>B. afzelii-</i>infected bank voles (<i>Myodes glareolus</i>) have about ten times higher bacterial load than infected yellow-necked mice (<i>Apodemus flavicollis</i>), indicating that these two species differ in resistance. In this study, we compared the immune response to <i>B. afzelii </i>infection in these host species by using RNA-sequencing to quantify gene expression in spleen. Gene set enrichment analysis (GSEA) showed that several immune pathways were down-regulated in infected animals in both bank voles and yellow-necked mice. Moreover, IFNα response was up-regulated in <i>B. afzelii</i>-infected yellow-necked mice, while IL6 signaling and the complement pathway were down-regulated in infected bank voles; differences in regulation of these three pathways between bank voles and yellow-necked mice could thus contribute to the difference in resistance to <i>B. afzelii</i> between the species. This study provides knowledge of gene expression induced by a zoonotic pathogen in its natural host, and possible species-specific regulation of immune responses associated with resistance.</p>
Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population
Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common garden experiments. The models failed because: 1) size at maturity and fitness both decreased with increases in population density, 2) offspring experienced higher population densities than their parents, and 3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.
Cognitive map-based navigation in wild bats revealed by a new high-throughput tracking system
<p>Seven decades of research on the "cognitive map", the allocentric representation of space, have yielded key neurobiological insights, yet we still lack field evidence from free-ranging wild animals. Using a system capable of tracking dozens of animals simultaneously at high accuracy and resolution, we assembled a large dataset of 172 foraging Egyptian fruit bats comprising >18M localizations collected over 3,449 bat-nights across 4 years. Detailed track analysis, combined with translocation experiments, revealed that wild bats seldom exhibit random search but instead repeatedly forage in goal-directed, long and straight flights that include frequent shortcuts. Alternative non-map-based strategies were ruled out by simulations, time-lag embedding and other trajectory analyses. Our results are consistent with expectations from cognitive map-like navigation and support previous neurobiological evidence from captive bats. </p>
Experimental infection of bumble bees with honey bee associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts
<p>Pathogen spill-over represents an important cause of biodiversity decline. For wild bee species such as bumble bees, many of which are in decline, correlational data point toward viral spill-over from naged honey bees as a potential cause. Yet impacts of honey bee viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well characterised viral inocula, we show that three viral types isolated from honey bees (<i>Deformed wing virus</i> genotype A, <i>Deformed wing virus</i> genotype B and <i>Black queen cell virus</i>) readily replicate within hosts of the bumble bee <i>Bombus terrestris</i>. Impacts of these honey bee-derived viruses – either injected or fed – on the mortality of <i>B. terrestris </i>workers were, however, negligible and likely dependent on host condition. Our results highlight the potential threat of viral spill-over from honey bees to novel wild bee species, though they also underscore the importance of additional studies on this and other non- bee species under field-realistic conditions to evaluate whether pathogen spill-over has a negative impact on wild bee individuals and population fitness.</p>
Data from: Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations?
<p>Accurately estimating genetic variance components is important for studying evolution in the wild. Empirical work on domesticated and wild outbred populations suggests that dominance genetic variance represents a substantial part of genetic variance, and theoretical work predicts that ignoring dominance can inflate estimates of additive genetic variance. Whether this issue is pervasive in natural systems is unknown, because we lack estimates of dominance variance in wild populations obtained <i>in situ</i>. Here, we estimate dominance and additive genetic variance, maternal variance, and other sources of non-genetic variance in 8 traits measured in over 9000 wild nestlings linked through a genetically resolved pedigree. We find that dominance variance, when estimable, does not statistically differ from zero and represents a modest amount (2-36%) of genetic variance. Simulations show that 1) inferences of all variance components for an average trait are unbiased; 2) the power to detect dominance variance is low; 3) ignoring dominance can mildly inflate additive genetic variance and heritability estimates but such inflation becomes substantial when maternal effects are also ignored. These findings hence suggest that dominance is a small source of phenotypic variance in the wild and highlight the importance of proper model construction for accurately estimating evolutionary potential.</p>
Data from: Fledging mass is color morph specific and affects local recruitment in a wild bird
Early life conditions may have long-lasting effects on life history. In color polymorphic species, morph-specific sensitivity to environmental conditions may lead to differential fitness. In tawny owl (Strix aluco) pheomelanin-based color polymorphism is expected to be maintained because the brown morph has higher adult fitness in warmer environments, while selection favors the grey morph under colder conditions. Here we investigate body mass at fledging and its consequences until adulthood in a population at the species' cold range margin. Using 40 years of data (1979-2017), we show that brown pairs, which mainly produce brown offspring consistent with a one-locus-two-alleles inheritance model, consistently raised heavier offspring than mixed pairs (grey-brown) and grey pairs. Offspring mass declined seasonally, except among offspring raised by brown pairs. Brown offspring could be heavier due to morph-specific parental care and/or offspring growth. Furthermore, mass at fledging is associated with fitness: the probability of local recruitment into the breeding population increased with higher mass at fledging, especially in mild winters and favorable food conditions, although recruitment is not morph-specific. Fledgling mass thus provides a fitness benefit in terms of recruitment probability that is modulated by environmental factors, which appear to level off any direct morph-specific recruitment benefits.
Data from: Multi-scalar drivers of biodiversity: local management mediates wild bee community response to regional urbanization
It is critical to understand the specific drivers of biodiversity across multiple spatial scales, especially within rapidly urbanizing areas, given the distinct management recommendations that may result at each scale. However, drivers of biodiversity patterns and interactions between drivers are often only measured and modeled at a single scale. In this study, we assessed bee community composition at three time periods in 20 grassland and 20 agriculture sites located across two major metroplexes. We examined how local environmental variables and surrounding landscape composition impact bee abundance, richness, and evenness, including comparisons between groups with different nesting strategies and body sizes. We collected nearly 13,000 specimens and identified 172 species. We found that levels of regional land-use differentially impacted bee abundance and diversity depending on local habitat management. Specifically, within agriculture sites, bee richness was greater with increasing landscape-level semi-natural habitat, while in grassland sites, bee richness was similar across landscapes regardless of semi-natural habitat cover. Bee evenness at both site types declined with increasing landscape-level habitat heterogeneity, due to an increase of rare species at the grassland sites, but not in the agricultural sites; further indicating that diversity is driven by the interaction of local habitat quality and landscape-level habitat composition. We additionally found that agriculture sites supported higher abundances, but not richness, of small-bodied and below-ground nesting bees, while grassland sites supported higher abundances of above-ground nesting bees, and higher richness of large-bodied species. Increased levels of local bare ground were significantly related to multiple metrics of bee diversity, including greater below-ground nesting bee abundance and richness. Local floral richness was also significantly related to increases of overall bee abundance, as well as the abundance and richness of small bees. Overall, we suggest that local land managers can support bee abundance and diversity by conserving areas of bare soil and promoting native floral diversity, the latter especially critical in highly urban agricultural spaces. Our results provide the first documentation of significant interactions between local habitat management and landscape composition impacting insect communities in urban systems, indicating that bee conservation practices depend critically on land-use interactions across multiple spatial scales.
Data from: Telomere attrition with age in a wild amphibian population
<p>Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (<em>Epidalea calamita</em>). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout<br> their ontogeny, and that most attrition occurs during the first 1–2 years.We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.</p>
Data S1. Laboratory behavioral data from: Measuring the fitness advantage conferred by autotomy in the wild
<p>Data S1. Laboratory behavioral data. The composition is summarized in figure S1.</p> <p>Autotomy, the self-amputation of body parts, serves as an anti-predator defense in many taxonomic groups of animals. However, its adaptive value has seldom been quantified. Here, we propose a novel modeling approach for measuring the fitness advantage conferred by the capability for autotomy in the wild. Using a predator-prey system where a land snail autotomizes and regenerates its foot specifically in response to snake bites, we conducted a laboratory behavioral experiment and a 3-year multi-event capture–mark–recapture (CMR) study. Combining these empirical data, we developed a hierarchical model and estimated the basic life history parameters of the snail. Using samples from the posterior distribution, we constructed the snail's life table as well as that of a snail variant incapable of foot autotomy. As a result of our analyses, we estimated the monthly encounter rate with snake predators at 3.3% (95% CI: 1.6–4.9%), the contribution of snake predation to total mortality until maturity at 43.3% (15.0–95.3%), and the fitness advantage conferred by foot autotomy at 6.5% (2.7–11.5%). This study demonstrated the utility of the multi-method hierarchical modeling approach for the quantitative understanding of the ecological and evolutionary processes of anti-predator defenses in the wild.</p>
Data S2. CMR data from: Measuring the fitness advantage conferred by autotomy in the wild
<p>Data S2. CMR data. The composition is summarized in tables S2, S3, and S10.</p> <p>Autotomy, the self-amputation of body parts, serves as an anti-predator defense in many taxonomic groups of animals. However, its adaptive value has seldom been quantified. Here, we propose a novel modeling approach for measuring the fitness advantage conferred by the capability for autotomy in the wild. Using a predator-prey system where a land snail autotomizes and regenerates its foot specifically in response to snake bites, we conducted a laboratory behavioral experiment and a 3-year multi-event capture–mark–recapture (CMR) study. Combining these empirical data, we developed a hierarchical model and estimated the basic life history parameters of the snail. Using samples from the posterior distribution, we constructed the snail's life table as well as that of a snail variant incapable of foot autotomy. As a result of our analyses, we estimated the monthly encounter rate with snake predators at 3.3% (95% CI: 1.6–4.9%), the contribution of snake predation to total mortality until maturity at 43.3% (15.0–95.3%), and the fitness advantage conferred by foot autotomy at 6.5% (2.7–11.5%). This study demonstrated the utility of the multi-method hierarchical modeling approach for the quantitative understanding of the ecological and evolutionary processes of anti-predator defenses in the wild.</p>
ScienceDex guides
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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.