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4,669 results for “Environment;”
Data from: Melanin in a changing world: brown trout coloration reflects alternative reproductive strategies in variable environments
Melanins are the most widespread pigments in animals but their adaptive significance remains elusive. Recent studies suggest that intraspecific variation in melanin-based coloration reflects individual genetic-based alternative strategies to cope with environment variability, which could be crucial for their responses to climate changes. However, empirical evidence is still scarce. In this study, we tested how skin coloration in natural populations of brown trout Salmo trutta fario would reflect alternative reproductive strategies in different environments. We experimentally manipulated the flow regime (constant vs. variable) in artificial streams and compared the reproductive investment (body mass and plasma triglyceride variations), innate immunity (variations in plasma peroxidase and lysozyme activity) and reproductive success (number of mates and offspring) of differently colored brown trout over 2 reproductive seasons. Results show that darker males had a higher reproductive investment, but similar immune variations during reproduction compared to paler males. In addition, this reproductive investment was higher in variable environments. However, this did not translate into a higher reproductive success in variable environments, as darker males had a similar number of mates and offspring compared to their paler counterparts under a variable water flow. Since climate change will likely lead to an increased flow variability in the next decades, this suggests that darker brown trout could incur a higher energetic cost of reproduction and could be more impacted by climate changes than their paler counterparts. This highlights the need to take into account intraspecific variability to better forecast the response of natural populations to climate changes.
Data from: Independent and interactive effects of plant genotype and environment on plant traits and insect herbivore performance: a meta-analysis with Salicaceae
1. Ecological research has increasingly highlighted the importance of intraspecific variation in shaping the structure and function of communities and ecosystems. Indeed, the effects of intraspecific variation can match or exceed those of interspecific variation. Previous reviews of intraspecific variation in plant traits across heterogeneous environments have focused primarily on mean phenotypic effects. We propose that a richer and fuller understanding of the ecological causes and consequences of intraspecific variation would be provided by partitioning trait variance into its subcomponents (genetic, environment, genotype by environment interaction). 2. We used a meta-analysis of 352 sets of genetic, environment, and genotype by environment (GxE) variation estimates from 72 studies of Salicaceae to compare these sources of variation across plant traits (growth, foliar nitrogen, defense compounds), insect herbivore performance metrics (e.g., survival, growth, fecundity), and environmental conditions (e.g., soil nutrients, water, defoliation). 3. Our findings revealed that variation in levels of defense compounds (both condensed tannins and salicinoids) and insect herbivore performance were primarily genetically determined, while variation in plant growth and foliar nitrogen were more environmentally determined. 4. Plasticity in plant growth, foliar nitrogen levels, and insect herbivore performance varied substantially across different sites (year x location), and nutrient, water, and carbon dioxide environments. Plasticity was lowest for chemical defense traits and all traits in contrasting ozone and defoliation environments. 5. Our quantitative review also revealed several gaps in the literature, including a need for surveying more mature plants (>2 years-old), a wider variety of insect herbivore species (e.g., leaf-modifiers, specialist insects), and underrepresented environmental treatments (e.g., competition, defoliation, disease, light, water). This work will help to assess how the patterns within this meta-analysis may or may not be confined within particular parameters (e.g., plant maturity). 6. Findings from this analysis further highlight the importance of and patterns within intraspecific variation in shaping the evolvability and plasticity of traits and in governing plant-insect interactions.
Data from: Trade-offs in lactation and milk intake by competing siblings in a fluctuating environment
Income breeders which forage without their offspring in attendance should adjust nursing frequency and the quantity and composition of milk to prevailing ecological conditions, and increase the quantity or quality of milk transferred if the frequency of nursing visits declines. When milk delivery to a litter is insufficient, sibling competition should skew milk consumption in favor of dominant litter members. We quantified milk nutritional composition and gross energy density, nursing bout durations, per capita milk transfer (kg), and milk transfer rate (g/min) per nursing bout in singletons and twins in a social carnivore, the spotted hyena. In our study population, the energetic cost of lactation is rank dependent and particularly high because large fluctuations in local prey abundance necessitate long-distance foraging, reducing nursing frequency and intensifying sibling competition, more frequently for low-ranking than high-ranking females. Females increased milk gross energy density, driven by fat content, and increased nursing bout durations as nursing frequency declined. Milk transfer increased as social status declined. Females below median rank also increased milk transfer as nursing frequency declined. Milk transfer was independent of nursing frequency in females above median rank and higher for singletons than cubs in twin litters. Dominant siblings achieved significantly higher amounts and rates of milk transfer than their paired subordinate littermates; this bias increased as sibling competition intensified. Our results show how the interplay between ecological and social constraints determines the quality and quantity of milk transferred, and how socially dominant siblings use aggression to skew milk intake in their favor.
Data from: Visual environment, attention allocation, and learning in young children: when too much of a good thing may be bad
A large body of evidence supports the importance of focused attention for encoding and task performance. Yet young children with immature regulation of focused attention are often placed in elementary-school classrooms containing many displays that are not relevant to ongoing instruction. We investigated whether such displays can affect children's ability to maintain focused attention during instruction and to learn the lesson content. We placed kindergarten children in a laboratory classroom for six introductory science lessons, and we experimentally manipulated the visual environment in the classroom. Children were more distracted by the visual environment, spent more time off task, and demonstrated smaller learning gains when the walls were highly decorated than when the decorations were removed.
Data from: Larval environment alters amphibian immune defenses differentially across life stages and populations
Recent global declines, extirpations and extinctions of wildlife caused by newly emergent diseases highlight the need to improve our knowledge of common environmental factors that affect the strength of immune defense traits. To achieve this goal, we examined the influence of acidification and shading of the larval environment on amphibian skin-associated innate immune defense traits, pre and post-metamorphosis, across two populations of American Bullfrogs (Rana catesbeiana), a species known for its wide-ranging environmental tolerance and introduced global distribution. We assessed treatment effects on 1) skin-associated microbial communities and 2) post-metamorphic antimicrobial peptide (AMP) production and 3) AMP bioactivity against the fungal pathogen Batrachochytrium dendrobatidis (Bd). While habitat acidification did not affect survival, time to metamorphosis or juvenile mass, we found that a change in average pH from 7 to 6 caused a significant shift in the larval skin microbial community, an effect which disappeared after metamorphosis. Additionally, we found shifts in skin-associated microbial communities across life stages suggesting they are affected by the physiological or ecological changes associated with amphibian metamorphosis. Moreover, we found that post-metamorphic AMP production and bioactivity were significantly affected by the interactions between pH and shade treatments and interactive effects differed across populations. In contrast, there were no significant interactions between treatments on post-metamorphic microbial community structure suggesting that variation in AMPs did not affect microbial community structure within our study. Our findings indicate that commonly encountered variation in the larval environment (i.e. pond pH and degree of shading) can have both immediate and long-term effects on the amphibian innate immune defense traits. Our work suggests that the susceptibility of amphibians to emerging diseases could be related to variability in the larval environment and calls for research into the relative influence of potentially less benign anthropogenic environmental changes on innate immune defense traits.
Data from: Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment
The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila–associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.
Data from: Divergence of gastropod life history in contrasting thermal environments in a geothermal lake
Experiments using natural populations have provided mixed support for thermal adaptation models, probably because the conditions are often confounded with additional environmental factors like seasonality. The contrasting geothermal environments within Lake Mývatn, northern Iceland, provide a unique opportunity to evaluate thermal adaptation models using closely located natural populations. We conducted laboratory common garden and field reciprocal transplant experiments to investigate how thermal origin influences the life history of Radix balthica snails originating from stable cold (6 °C), stable warm (23 °C) thermal environments or from areas with seasonal temperature variation. Supporting thermal optimality models, warm origin snails survived poorly at 6 °C in the common garden experiment and better than cold origin and seasonal snails in the warm habitat in the reciprocal transplant experiment. Contrary to thermal adaptation models, growth rate in both experiments was highest in the warm populations irrespective of temperature, indicating cogradient variation. The optimal temperatures for growth and reproduction were similar irrespective of origin, but cold origin snails always had the lowest performance, and seasonal origin snails often performed at an intermediate level compared to snails originating in either stable environment. Our results indicate that central life-history traits can differ in their mode of evolution, with survival following the predictions of thermal optimality models, whereas ecological constraints have shaped the evolution of growth rates in local populations.
Data from: Survival estimates strongly depend on capture-recapture designs in a disturbed environment inducing dispersal
Capture‐Recapture (CR) approaches are extensively used to estimate demographic parameters. Their robustness relies on the selection of suitable statistical models, but also on the sampling design and effort deployed in the field. In colonial or territorial species showing breeding site fidelity, recurrent local perturbations, such as predation‐induced breeding failure, may lead individuals to disperse locally or regionally. This might induce heterogeneity in individual CR histories and biases in demographic parameter estimates. Here, we assessed the effect of buffer areas and multi‐site designs on annual survival estimate accuracy and precision. First, using simulated data with and without a multi‐site design, we compared survival estimates for different scenarios involving contrasted local and regional dispersal. Then, using data from a local multi‐site long‐term monitoring survey carried out in a colony of black‐legged kittiwakes, we tested the homogeneity of individual CR histories and compared survival estimates from three datasets including one or several breeding cliffs with or without buffer areas. Results from simulations highlighted that a single‐site design consistently led to underestimated or less precise survival values compared to a multi‐site design. Similarly, a multi‐site design allowed detecting significant temporal trends while a single‐site one did not. In the field‐based study, adding buffer areas reduced individual heterogeneity, but all three datasets suffered from strong trap‐dependence possibly due to individual breeding success affecting nest‐site fidelity. Implementing a multi‐site design significantly improved the accuracy and precision of annual survival estimates, regardless of CR models applied. Adapting the spatial scale of sampling design to the local environment and species behaviour is essential to provide robust parameters of key relevance for population monitoring and management. We show that implementing buffer areas and/or multi‐site designs may be especially beneficial for long‐lived species facing regular local perturbation events leading to local dispersal.
Data from: Pseudomonas putida and Pseudomonas fluorescens species group recovery from human homes varies seasonally and by environment
By shedding light on variation in time as well as in space, long-term biogeographic studies can help us define organisms' distribution patterns and understand their underlying drivers. Here we examine distributions of Pseudomonas in and around 15 human homes, focusing on the P. putida and P. fluorescens species groups. We describe recovery from 10,941 samples collected during up to 8 visits per home, occurring on average 2.6 times per year. We collected a mean of 141 samples per visit, from sites in most rooms of the house, from the surrounding yards, and from human and pet occupants. We recovered Pseudomonas in 9.7% of samples, with the majority of isolates being from the P. putida and P. fluorescens species groups (approximately 62% and 23% of Pseudomonas samples recovered respectively). Although representatives of both groups were recovered from every season, every house, and every type of environment sampled, recovery was highly variable across houses and samplings. Whereas recovery of P. putida group was higher in summer and fall than in winter and spring, P. fluorescens group isolates were most often recovered in spring. P. putida group recovery from soils was substantially higher than its recovery from all other environment types, while higher P. fluorescens group recovery from soils than from other sites was much less pronounced. Both species groups were recovered from skin and upper respiratory tract samples from healthy humans and pets, although this occurred infrequently. This study indicates that even species that are able to survive under a broad range of conditions can be rare and variable in their distributions in space and in time. For such groups, determining patterns and causes of stochastic and seasonal variability may be more important for understanding the processes driving their biogeography than the identity of the types of environments in which they can be found.
Data from: Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment
We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.
Data from: Is sex advantageous in adverse environments? A test of the abandon-ship hypothesis
Understanding the evolution and maintenance of sexual reproduction remains a long-standing challenge in evolutionary biology. Stress often induces sexual reproduction in facultatively sexual species (those species capable of both sexual and asexual reproduction). The abandon-ship hypothesis predicts higher allocation to sex under stress to allow low-fitness individuals to recombine their genotype, potentially increasing offspring fitness. However, effective tests of the abandon-ship hypothesis, particularly in multicellular organisms, are lacking. Here we test the abandon-ship hypothesis, using cyanogenic and acyanogenic defense phenotypes of the short-lived perennial herb Trifolium repens. Cyanogenesis provides an effective defense against herbivores and is under relatively simple genetic control (plants dominant for cyanogenesis at two alleles express the defended phenotype). Thus, maladapted individuals can acquire adaptive defense alleles for their offspring in a single episode of sexual reproduction. Plants were grown under high- and low-herbivory treatments (plants were exposed to herbivorous snails) and a control treatment (no herbivory). Herbivores reduced growth and fitness in all treated plants, but herbivory induced higher sexual allocation only in maladapted (acyanogenic) individuals. Overall, our results support the abandon-ship hypothesis.
Data from: Investigating the production of sexual resting structures in a plant pathogen reveals unexpected self-fertility and genotype-by-environment effects
The sexual stage of pathogens governs recombination patterns and often also provides means of surviving the off-season. Despite its importance for evolutionary potential and between-season epidemiology, sexual systems have not been carefully investigated for many important pathogens, and what generates variation in successful sexual reproduction of pathogens remains unexplored. We surveyed the sexually produced resting structures (chasmothecia) across 86 natural populations of fungal pathogen Podosphaera plantaginis (Ascomycota) naturally infecting Plantago lanceolata in the Åland archipelago, southwest of Finland. For this pathosystem, these resting structures are a key life-history stage, as more than half of the local pathogen populations go extinct every winter. We uncovered substantial variation in the level of chasmothecia produced among populations, ranging from complete absence to presence on all infected leaves. We found that chasmothecia developed within clonal isolates (single strain cultures). Additionally, these clonal isolates all contained both MAT1-1-1 and MAT1-2-1 genes that characterize mating-types in Ascomycetes. Hence, contrary to expectations, we conclude that this species is capable of haploid selfing. In controlled inoculations we discovered that pathogen genotypes varied in their tendency to produce chasmothecia. Production of chasmothecia was also affected by ambient temperature (E), and by the interaction between temperature and pathogen genotype (G × E). These G, E and G × E effects found both at a European scale, as well as within Åland, may partly explain the high variability observed among populations in chasmothecia levels. Consequently, they may be key drivers of the evolutionary potential and epidemiology of this highly dynamic pathosystem.
Annotation files of 206 MAGs from three different hydrothermal environments
<p>It contains genome annotation files (for 206 genomes). The MAG genomic sequences are deposited to NCBI Genome database under the BioProject ID of PRJNA488180.</p>
Data from: Adaptations and responses of the common dandelion to low atmospheric pressure in high altitude environments
<p>Atmospheric pressure is an important, yet understudied factor that may shape plant ecology and evolution.</p> <p>By growing plants under controlled conditions at different experimental stations in the Swiss alps, we evaluated the impact of ecologically realistic atmospheric pressures between 660 and 950 hPa on the growth and defence of different dandelion populations.</p> <p>Low atmospheric pressure was associated with reduced root growth and defensive sesquiterpene lactone production. Defence suppression only occurred in populations originating from lower altitudes. Populations from higher altitudes constitutively produced less sesquiterpene lactones and did not suffer from suppression under low atmospheric pressure.</p> <p><em>Synthesis</em>. We conclude that atmospheric pressure modulates root growth and defence traits, and that evolutionary history shapes plant phenotypic responses to atmospheric pressure. Our findings have important implications for our understanding of altitudinal gradients and the future use of plants as a source of food and bioactive metabolites in extraterrestrial habitats.</p>
R-scripts for the calculation of HW and Bioclimatic models in: "Small vertebrate and mollusc community response to the Holocene environment and climate changes in the Kraków-Częstochowa Upland (Poland)"
<p>HW_Holocene: Tables and R script used for calculation of HW percentage values.</p> <p>PalBER_Bioclimaticmodel_modified: Tables and R script used for the calculation of the climate values through Bioclimatic model. Modified after Royer et al., 2020.</p>
Characterizing the modern light environment and its influence on circadian rhythms
<p>Humans have largely supplanted natural light cycles with a variety of electric light sources and schedules misaligned with day-night cycles. Circadian disruption has been linked to a number of disease processes, but the extent of circadian disruption among the population is unknown. In this study, we measured light exposure and wrist temperature among residents of an urban area during each of the four seasons, as well as light illuminance in nearby outdoor locations. Daily light exposure was significantly lower for individuals, compared to outdoor light sensors, across all four seasons. There was also little seasonal variation in the realized photoperiod experienced by individuals, with the only significant difference occurring between winter and summer. We tested the hypothesis that differential light exposure impacts circadian phase timing, detected via the wrist temperature rhythm. To determine the influence of light exposure on circadian rhythms, we modeled the impact of morning and nighttime light exposure on the timing of the maximum wrist temperature. We found that morning and nighttime light exposure had significant but opposing impacts on maximum wrist temperature timing. Our results demonstrate that, within the range of exposure seen in everyday life, nighttime light can delay the onset of the maximum wrist temperature, while morning light can lead to earlier onset. Our results demonstrate that humans are minimizing natural seasonal differences in light exposure, and that circadian shifts and disruptions may be a more regular occurrence in the general population than is currently recognized.</p>
Impacts of City Shape on Rainfall in Contrasting Environments
<p>WRF-LES simulation of rainfall over inland and costal environment. Results here are under the quasi-equilibrium state.</p>
FIGURE 4 in The Ciidae (Coleoptera: Tenebrionoidea) of the Maritime Provinces of Canada: new records, distribution, zoogeography, and observations on beetle-fungi relationships in saproxylic environments
FIGURE 4. The Distribution of Octotemnus laevis Casey and Orthocis punctatus (Mellié) in the Maritime Provinces of Canada.
FIGURE 2 in The Ciidae (Coleoptera: Tenebrionoidea) of the Maritime Provinces of Canada: new records, distribution, zoogeography, and observations on beetle-fungi relationships in saproxylic environments
FIGURE 2. The Distribution of Cis creberrimus Mellié, Cis fuscipes Mellié, Cis levettei (Casey), and Cis subtilis Mellié, in the Maritime Provinces of Canada.
FIGURE 1 in The Ciidae (Coleoptera: Tenebrionoidea) of the Maritime Provinces of Canada: new records, distribution, zoogeography, and observations on beetle-fungi relationships in saproxylic environments
FIGURE 1. The Distribution of Ceracis sallei Mellié, Ceracis thoracicornis (Ziegler), Cis americanus Mannerheim, and Cis horridulus Casey in the Maritime Provinces of Canada.
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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.