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671 results for “mediating effect”
Tree seedling abundance mediated by local neighborhood effects and microsite conditions
Tree recruitment across elevational gradients is shaped by myriad factors, including abundance of nearby conspecific adults and abiotic establishment conditions. We measured seedling abundance and overstory basal area for six tree species that dominate northern temperate and montane boreal forests on mountains in the northeastern United States. Data were collected on elevational transects spaced at 100m-intervals of elevation on ten mountains. Associated environmental variables, including vegetation cover, substrate, microclimate, and light environment, were also collected.
Data from: Effects of plastic fragments on plant performance are mediated by soil properties and drought
<p>In recent years, the effects of plastic contamination on soil and plants have received growing attention. Plastic can affect soil water content and thus may interact with the effects of drought on soil and plants. However, the effects of plastic on soil are highly context-dependent, and interactions with drought have been hardly tested. We conducted two greenhouse experiments to test the combined effects of plastic fragments (of varying size and concentration), water availability and soil texture, on soil water content and performance of the plant <em>Arabidopsis thaliana</em>. Plastic fragments had stronger negative effects on soil water content in low water availability, and the shape of this response (linear <em>vs.</em> unimodal) was mediated by soil texture. Conversely, increasing concentration of plastic had positive effects on plant growth. We suggest that plastic fragments introduce fracture points within soil aggregates. This increases number and size of soil pores favoring water loss but also facilitating root growth. Our results suggest complex interactive effects of plastic and drought, that may lead to a decoupling of plant and soil response. These processes should be taken into account in ecological studies and agricultural practices.</p>
Ergolide Mediates Anti-Cancer Effects on Metastatic Uveal Melanoma Cells and Modulates their Cellular and Extracellular Vesicle proteomes
<p>Underlying dataset and extended dataset of the results described in the article "Ergolide Mediates Anti-Cancer Effects on Metastatic Uveal Melanoma Cells and Modulates their Cellular and Extracellular Vesicle proteomes".</p>
Long-term nitrogen enrichment mediates the effects of nitrogen supply and co-inoculation on a viral pathogen
Host nutrient supply can mediate host–pathogen and pathogen–pathogen interactions. In terrestrial systems, plant nutrient supply is mediated by soil microbes, suggesting a potential role of soil microbes in plant diseases beyond soil-borne pathogens and induced plant defenses. Long-term nitrogen (N) enrichment can shift pathogenic and non-pathogenic soil microbial community composition and function, but it is unclear if these shifts affect plant–pathogen and pathogen–pathogen interactions. In a growth chamber experiment, we tested the effect of long-term N enrichment on infection by Barley Yellow Dwarf Virus (BYDV-PAV) and Cereal Yellow Dwarf Virus (CYDV-RPV), aphid-vectored RNA viruses, in a grass host. We inoculated sterilized growing medium with soil collected from a long-term N enrichment experiment (ambient, low, and high N soil treatments) to isolate effects mediated by the soil microbial community. We crossed soil treatments with a nitrogen supply treatment (low, high) and virus inoculation treatment (mock-, singly-, and co-inoculated) to evaluate the effects of long-term N enrichment on plant–pathogen and pathogen–pathogen interactions, as mediated by N availability. BYDV-PAV incidence (0.96) declined with low N soil (to 0.46), high N supply (to 0.61), and co-inoculation (to 0.32). Low N soil mediated the effect of N supply on BYDV-PAV: instead of N supply reducing BYDV-PAV incidence, the incidence increased. In addition, ambient and low N soil ameliorated the negative effect of co-inoculation on BYDV-PAV incidence. BYDV-PAV infection only reduced chlorophyll when plants were grown with low N supply and ambient N soil. Soil inoculant with different levels of long-term N enrichment had different effects on host–pathogen and pathogen–pathogen interactions, suggesting that shifts in the structure and function of soil microbial communities with long-term N enrichment may mediate disease dynamics.
Contrasting effects of landscape composition on crop yield mediated by specialist herbivores
<p>Landscape composition not only affects a variety of arthropod-mediated ecosystem services, but also disservices, such as herbivory by insect pests that may have negative effects on crop yield. Yet, little is known about how different habitats influence the dynamics of multiple herbivore species, and ultimately their collective impact on crop production. Using cabbage as a model system, we examined how landscape composition influenced the incidence of three specialist cruciferous pests (aphids, flea beetles, and leaf-feeding Lepidoptera), lepidopteran parasitoids, and crop yield across a gradient of landscape composition in New York, USA. We expected that landscapes with a higher proportion of cropland and lower habitat diversity would lead to an increase in pest pressure of the specialist herbivores and a reduction in crop yield. However, results indicated that neither greater cropland area nor lower landscape diversity influenced pest pressure or yield. Rather, pest pressure and yield were best explained by the presence of non-crop habitats (i.e. meadows) in the landscape. Specifically, cabbage was infested with fewer Lepidoptera in landscapes with a higher proportion of meadows likely resulting from increased parasitism. Conversely, cabbage was infested with more flea beetles and aphids as the proportion of meadows in the landscape increased, suggesting that these pests benefit from non-crop habitats. Furthermore, path analysis confirmed that these landscape-mediated effects on pest populations can have either positive or negative cascading effects on crop yield. Our findings illustrate how different pest species within the same cropping system show contrasting responses to landscape composition with respect to both the direction and spatial scale of the relationship. Such tradeoffs resulting from the complex interaction between multiple-pests, natural enemies, and landscape composition must be considered, if we are to manage landscapes for pest suppression benefits.</p>
Processed data for the study on "Chromatin 3D interactions mediate genetic effects on gene expression"
<p>This repository contains the processed data that was generated as part of the following study:</p> <p>Delaneau et al. (2019) <strong>Chromatin 3D interactions mediate genetic effects on gene expression.</strong></p> <p><em>Abstract:</em> Studying the genetic basis of gene expression and chromatin organization is key to characterize the effect of genetic variability on the function and structure of the human genome. Here, we unravel how genetic variation perturbs gene regulation using a dataset combining activity of regulatory elements, gene expression and genetic variants across 317 individuals and two cell types. We show that variability in regulatory activity is structured at the intra- and inter-chromosomal levels within 12,583 Cis Regulatory Domains and 30 Trans Regulatory Hubs that highly reflect the local (i.e. Topologically Associating Domains) and global (i.e. open/close chromatin compartments) nuclear chromatin organization. These structures delimit cell type specific regulatory networks that control gene expression/co-expression and mediate the genetic effects of <em>cis</em>- and <em>trans</em>-acting regulatory variants on genes.</p> <p> </p> <p>This repository contains:</p> <ol> <li>Chromatin QTLs for H3K27ac, H3K4me1 and H3K4me3 discovered in 317 Lymphoblastoids Cell Lines (LCLs) and 78 Fibroblasts.</li> <li>Molecular QTLs affecting the activity and structure of Cis Regulatory Domains (CRDs) in LCLs.</li> <li>Basic information about the full set of genetic variants being analyzed in the study.</li> <li>The peak coordinates, their hierarchy based on inter-individual correlation and the CRD calls for both LCLs and Fibroblasts.</li> <li>The functional links discovered in LCLs between CRDs and genes.</li> <li>eQTLs for LCLs.</li> <li>A README file containing the description of the file format for each file.</li> </ol>
Data from: Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk
<p>This dataset comprises crowdsourced data using digitized herbarium specimen images from two comprehensively digitized regional floras; the Consortium of Northeastern Herbaria (CNH; <a href="http://portal.neherbaria.org/portal/">http://portal.neherbaria.org/portal/</a>) and Southeast Regional Network of Expertise and Collections (SERNEC; <a href="http://sernecportal.org/portal/index.php">http://sernecportal.org/portal/index.php</a>) for 200 plant species in the eastern United States, and four reproductive phenophases (i.e., flowering, peak flowering, fruiting, and peak fruiting) extracted from the herbarium specimens with associated climate data from PRISM and human population density from US Census Bureau.</p>
Contrasting effects of landscape composition on crop yield mediated by specialist herbivores
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Relyea, R. A., and K. L. Yurewicz. 2002. Predicting community outcomes from pairwise interactions: Integrating density- and trait-mediated effects. Oecologia 131:569-579.
Understanding how species interactions shape the structure of ecological communities based on pairwise comparisons has been a difficult undertaking for ecologists because effects in reassembled communities can be different than simple density-mediated interactions would suggest. Part of this complexity occurs because many species change their behavior and morphology with different predators and competitors and, thus, change their per-capita interaction rates (i.e. trait-mediated interactions). Our objective was to use a simple experimental community of two predators (larval dragonflies, Anax longipes, and larval salamanders, Ambystoma tigrinum), two prey (larval green frogs, Rana clamitans, and larval bullfrogs, R. catesbeiana), and a shared prey resource to determine whether we can predict interactions in a reassembled community by combining our knowledge of density- and trait-mediated interactions,. We combined pairwise laboratory experiments on predation rates and predator-induced behaviors with a mesocosm experiment to examine density- and trait-mediated effects. We used a factorial combination of no predators, caged Anax (to induce anti-predator traits without changing prey density), and lethal Anax crossed with no predators, caged Ambystoma, and lethal Ambystoma. The species interactions in the reassembled community were qualitatively predictable based on the pairwise experiments. Lethal Anax preyed upon Ambystoma and green frogs while lethal Ambystoma only preyed upon green frogs. Anax also reduced the activity of the green frogs; this caused a decrease in salamander predation on green frogs, a decrease in green frog acquisition of resources, and an increase in bullfrog acquisition of resources. Ambystoma had no effect on green frog activity, no effect on resource acquisition by green frogs, and no effect on resource acquisition by bullfrogs. These results suggest that we can better understand how species interact in natural communities if we have a more deta
Relyea, R. A. 2000. Trait-mediated indirect effects in larval anurans: Reversing competition with the threat of predation. Ecology 81:2278-2289.
Ecologists recently have been focusing on the role that trait-mediated indirect effects can have on community structure and composition. To date, this work has primarily focused on the effects of predator-induced behavioral plasticity on communities. However, predator-induced morphological plasticity, which has been documented in many taxa, might also lead to trait-mediated indirect effects. Here, I examined how predators altered the behavior and morphology of larval wood frogs (Rana sylvatica) and leopard frogs (R. pipiens) and how these phenotypic changes altered the outcome of competition between the two species. Competition in the absence of caged predators was asymmetric; when reared separately, leopard frogs grew more than wood frogs, but when competing (without predators), wood frogs grew faster than leopard frogs. The presence of caged predators reversed the outcome of competition between the two anuran prey. In the presence of larval dragonflies (Anax spp.) or caged mudminnows (Umbra limi), leopard frogs grew faster than wood frogs while total tadpole biomass production remained unchanged. Thus, there was a predator-mediated indirect effect. Because predators alter both the behavior and morphology of larval anurans and both of these traits are known to affect resource consumption and growth, both are potential mechanisms to explain the change in competitive outcome. Changes in behavior were not related to changes in growth, but changes in morphology (specifically mouth width and tail length) were related to changes in growth. When competitors were added (without predators), wood frogs increased their mouth width by 10% and their tail length by 3%, while leopard frogs increased their mouth width by 5% and did not change their tail length. The greater increase in mouth width for wood frogs should increase their forage intake, since tadpoles feed by scraping periphyton; the importance of a 3% longer tail in competitive ability is unknown. The presence of the p
Data for: Effective population size mediates the impact of pollination services on pollen limitation
<p>Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation ('PL'), like pollinator scarcity and low plant abundance, have been a primary focus of research. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (N<sub>E</sub>) on PL across 13 populations of a common herb. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. N<sub>E</sub> and pollinator visitation interacted to shape PL, but N<sub>E</sub> had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that pollen quantity was an intrinsic population-level attribute that increased with N<sub>E</sub>. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively.<em> </em>Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors.<strong> </strong>Efforts to support pollinators will only enhance plant reproduction in genetically diverse plant populations.</p>
Species richness: a pivotal factor mediating the effects of land use intensification and climate on grassland multifunctionality
<p>Temperate semi-natural grasslands harbour unique biodiversity, support livestock farming through forage production, and deliver many essential ecosystem services (ESs) to human society; they are highly multifunctional. However, temperate grassland ecosystems are also among the most threatened ecosystems on earth due to land use and climate change. Understanding how biodiversity, climate, and land use intensification impact grassland multifunctionality through complex direct and indirect pathways is critical to better anticipate the future of these fragile ecosystems. </p> <p>Here, we evaluate how local plant species richness (SR) modulates the effect of land use intensification and climate on grassland multifunctionality (using six key ESs: biomass productivity and stability, forage quality, carbon storage, pollination, and local plant rarity) in the French Massif Central, the largest grassland in Western-Europe. We sampled 100 grassland fields with contrasted fertilisation rates, and SR over large elevational and latitudinal gradients related to variation in mean annual temperature (MAT), and drought severity (DS), two key climate change drivers that are predicted to increase in the future.</p> <p>Using a confirmatory path analysis, we found that SR was the main driver of multifunctionality. We also found significant SR × MAT and SR × fertilization interactions suggesting that warm climate and high fertilization rates may alter the biodiversity-ecosystem multifunctionality relationships. Furthermore, increasing temperature and fertilization indirectly influenced multifunctionality by decreasing SR and consequent multifunctionality in warm low-land and highly fertilized grasslands compared to colder montane grasslands or less fertilised ones. DS only impacted some ES individually (e.g. forage quality).</p> <p>Synthesis and applications: we identified SR as a pivotal factor mediating the effects of land use intensification and climate on multifunctionality through both direct and indirect pathways. Failing to account for changes in SR could thus bias any prediction of – or aggravate – the effects of land use intensification and climate change on ESs delivery in temperate grassland ecosystems. Considering that SR, MAT, and fertilization are major proxies of three main global change drivers (biodiversity loss, climate change, and land use intensification) our study may help to better anticipate the effect of multiple interacting global change drivers on grassland ecosystems.</p>
The effect of experimental pollinator decline on pollinator-mediated selection on floral traits
<p>Human-mediated environmental change, by reducing mean fitness, is hypothesized to strengthen selection on traits that mediate interactions among species. For example, human-mediated declines in pollinator populations are hypothesized to reduce mean seed production by increasing the magnitude of pollen limitation and thus strengthen pollinator-mediated selection on floral traits that increase pollinator attraction or pollen transfer efficiency. To test this hypothesis, we measured two female fitness components and six floral traits of <em>Lobelia siphilitica</em> plants exposed to supplemental hand-pollination, ambient open-pollination, or reduced open-pollination treatments. The reduced treatment simulated pollinator decline, while the supplemental treatment was used to estimate pollen limitation and pollinator-mediated selection. We found that plants in the reduced pollination treatment were significantly pollen-limited, resulting in pollinator-mediated selection for taller inflorescences and more vibrant petals, both traits that could increase pollinator attraction. This contrasts with plants in the ambient pollination treatment, where reproduction was not pollen-limited and there was no significant pollinator-mediated selection on any floral trait. Our results support the hypothesis that human-mediated environmental change can strengthen the selection on traits of interacting species and suggest that these traits have the potential to evolve in response to changing environments.</p>
Data and code for: Viviparous mothers impose stronger glucocorticoid‐mediated maternal stress effects on their offspring than oviparous mothers
<p><strong>Data and code accompanying the manuscript "Viviparous mothers impose stronger glucocorticoid‐mediated maternal stress effects on their offspring than oviparous mothers", MacLeod KJ, While GM, Uller, T, Ecology & Evolution 2021.</strong></p> <p>Code is in an R file - can be opened with any txt app.</p> <p>Metadata is in sheet 2 of the main data sheet (xlsx).</p> <p>Queries to kirstyjmacleod@gmail.com</p> <p><strong>Publication abstract</strong>: Maternal stress during gestation has the potential to affect offspring development via changes in maternal physiology, such as increases in circulating levels of glucocorticoid hormones that are typical after exposure to a stressor. While the effects of elevated maternal glucocorticoids on offspring phenotype (i.e., “glucocorticoid‐mediated maternal effects”) have been relatively well established in laboratory studies, it remains poorly understood how strong and consistent such effects are in natural populations. Using a meta‐analysis of studies of wild mammals, birds, and reptiles, we investigate the evidence for effects of elevated maternal glucocorticoids on offspring phenotype and investigate key moderators that might influence the strength and direction of these effects. In particular, we investigate the potential importance of reproductive mode (viviparity vs. oviparity). We show that glucocorticoid‐mediated maternal effects are stronger, and likely more deleterious, in mammals and viviparous squamate reptiles compared with birds, turtles, and oviparous squamates. No other moderators (timing and type of manipulation, age at offspring measurement, or type of trait measured) were significant predictors of the strength or direction of the phenotypic effects on offspring. These results provide evidence that the evolution of a prolonged physiological association between embryo and mother sets the stage for maladaptive, or adaptive, prenatal stress effects in vertebrates driven by glucocorticoid elevation.</p>
Data from: Seed fate in ant-mediated dispersal: Seed dispersal effectiveness in the Ectatomma ruidum (Formicidae) - Zanthoyxlum ekmanii (Rutaceae) system
<p>Plants are often dispersal limited relying on passive or active agents to find suitable microhabitats for germination. Seeds of pioneer tree species, for example, require light gaps for growth but have short median dispersal distances and often do not provide a food reward to encourage animal dispersal. Zanthoxylum ekmanii seeds are frequently moved by ants but evaluating the effectiveness of ant-mediated seed removal requires knowledge of the species moving the seeds, how far they are moved, and the deposition site. To assess the effectiveness of ants as seed dispersers of Z. ekmanii, we utilized the seed dispersal effectiveness framework. We tracked the movement of seeds from caches on the forest floor, revealing that foragers of Ectatomma ruidum moved 32.8% of seeds an average first distance of 99.8 cm with 68.3% of those seeds taken into a colony. The quality of deposition location was assessed using a seedling emergence study where freshly germinated seeds were buried at different depths. Seedlings were primarily able to emerge from the shallowest depths. Wax castings of E. ruidum colonies demonstrated that seeds brought into the colony were deposited in chambers that had larvae present and experienced more damage than seeds unhandled by ants. Foragers, however, did not have a strong enough bite force to rupture Z. ekmanii seeds likely because their muscle morphology is not structured to maximize force generation. Overall, E. ruidum may help fine tune deposition location, incorporating seeds into the topsoil, though few seeds will likely emerge if soil bioturbation is low.</p>
Large effect loci mediate rapid adaptation of salmon body size after river regulation
<p>Understanding the potential of natural populations to adapt to altered environments is becoming increasingly relevant in evolutionary research. Currently, our understanding of adaptation to human alteration of the environment is hampered by lack of knowledge on the genetic basis of traits, lack of time series, and little or no information on changes in optimal trait values. Here we used time series data spanning nearly a century to investigate how body mass of Atlantic salmon (<em>Salmo salar</em>) adapts to river regulation. We found that the change in body mass followed the change in waterflow, both decreasing to ~1/3 of their original values. Allele frequency changes at two loci in the regions of <em>vgll3</em> and <em>six6 </em>predicted more than 80% of the observed body mass reduction. Modelling the adaptive dynamics revealed that the population mean lagged behind its optimum before catching up ~6 salmon generations after the initial waterflow reduction. Our results demonstrate rapid adaptation mediated by large effect loci and provide insight into the temporal dynamics of evolutionary rescue following human disturbance.</p>
Figure S1. Mediation analysis on the effect of insulin resistance on intraocular pressure. Figure S2. Forest plot showing the OR (95% CI) for EIOP of ALD versus NAFLD and the OR (95% CI) for EIOP of drinkers versus non-drinkers. Abbreviations: OR, odds ratio; CI, confidence interval; ALD, alcoholic liver disease; NAFLD, non-alcoholic fatty liver disease.
<p>Figure S1. Mediation analysis on the effect of insulin resistance on intraocular pressure.</p> <p>Figure S2. Forest plot showing the OR (95% CI) for EIOP of ALD versus NAFLD and the OR (95% CI) for EIOP of drinkers versus non-drinkers. Abbreviations: OR, odds ratio; CI, confidence interval; ALD, alcoholic liver disease; NAFLD, non-alcoholic fatty liver disease.</p>
Fig. 4 in Effects of the interannual variations in the flood pulse mediated by hypoxia tolerance: the case of the fish assemblages in the upper Paraná River floodplain
Fig. 4. Ordination of the samples of the upper Paraná River floodplain, through the detrended correspondence analysis (DCA), in years of short (diamond: 2000 white, 2001 gray) and moderate floods (square: 2002 gray, 2003 black). Numbers 1-6 are codes of the sampling stations (see Fig. 1).
Fig. 5 in Effects of the interannual variations in the flood pulse mediated by hypoxia tolerance: the case of the fish assemblages in the upper Paraná River floodplain
Fig. 5. Fish assemblage attributes in the main habitats of the upper Paraná River floodplain in years of short (2000 and 2001) and moderate (2002 and 2003) floods. The black area of the bars represents the proportion of STH. Numbers 1-6 on the abscissa are codes of the sampling stations (see Fig. 1).
Fig. 2 in Effects of the interannual variations in the flood pulse mediated by hypoxia tolerance: the case of the fish assemblages in the upper Paraná River floodplain
Fig. 2. Monthly (a) and daily level (b, between January and March) of the upper Paraná River recorded in Porto São José municipality. In b (right axis), the number of days between January and March, when the upper Paraná River surpassed the threshold of 350 cm (horizontal braked line). The years 2000 and 2001 were considered as years of short floods and 2002 and 2003 as years of moderate floods. Source: National Department of Waters and Electric Energy.
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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.